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Design of protein-protein interfaces

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Sarel Profile

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Message 56754 - Posted 7 Nov 2008 7:08:03 UTC

Hello,

My name is Sarel Fleishman and I've been a postdoc in the Baker lab for the past two years. My project deals with structure prediction and design of protein-protein interfaces and you may have read a few messages from me on CAPRI and structure prediction. Now, I'm very excited to tell you that with minirosetta v1.40 we can do design work using the massive computational power of Rosetta @ Home.

A few words on protein-interface design. The primary challenge in this field is to be able to take a protein target and to design another protein that would bind to it in a specific way. Nature provides us with hundreds of thousands of examples of such protein-binding events. Such events are used for the amplification of signals within and between our cells in processes related to growth and development as well as for recognition, e.g., in the immune system. When such signals go awry, protein interactions become the center of events for uncontrolled cell growth, or cancer. Many pathogenic bacteria and viruses hijack molecular recognition processes to promote their growth and proliferation causing sickness and endangering lives.

These processes being so central to both health and disease it is hardly surprising that being able to manipulate them computationally is a major ongoing goal of molecular biology. Being able to target a protein and bind to it would open the way to novel therapies for a large number of diseases.

We have selected a small number of protein targets for which we want to design protein binders. As an example, one such target that I have been working on is cholera toxin. This protein is a crucial component of the process by which the cholera bacterium causes cells in the gut to excrete large amounts of water, which causes death from dehydration (see the following wiki page for more details: http://en.wikipedia.org/wiki/Cholera). We have developed a computational strategy that allows us to design proteins to bind to the cholera toxin and disable it.

We are now in the process of testing this and similar design methodologies on a number of other targets. But expanding the number of targets we quickly realized that we need a lot more computational resources to adequately address this problem. This is why we have turned to Rosetta @ Home and to you for your help in this exciting project.

The simulations that you will see in protein interface design will be quite different from one another. In each case we tailor the design strategy to the particular protein target, stressing, for instance, the formation of interactions with a specific key region on the protein surface. In general, though, the simulations will involve docking steps, where the protein binder moves with respect to the target and design, where amino acid residues on the surface of the protein binder change in order to better attach to the target. Promising protein designs are synthesized in our lab and tested for binding to the target protein.

I am working on this project with my colleagues Eva and Jacob, and for each target that we test using Rosetta @ Home we will provide background material on the target and why we selected it on this thread.

These design simulations tend to use more memory than many prediction runs (typically at most 800Mb). We will test different ways of reducing this memory load so that our simulations could run on all participating computers in the Rosetta @ Home project, but initially we will only run these simulations on computers that can handle this memory restriction. Please report any problems that you might have with this simulation.

Thank you very much for participating in this project! I'm looking forward to getting feedback and results from you.
____________

jcorn

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Message 56763 - Posted 7 Nov 2008 18:05:54 UTC

My name is Jacob Corn, and I'm a postdoc in the Baker Lab, working with Eva and Sarel on the design of protein-protein interfaces. As Sarel mentioned, this is an incredibly important problem, both for basic science and molecular medicine. But it is also an incredibly difficult problem. Without your support, we would never have enough computing power to work on these kinds of projects.

One target that I am attempting to design towards is interleukin 23 (aka IL23). Your body normally uses this protein to trigger the inflammatory response, which is a normal part of your body's immune system. However, if IL23 messages start to run out of control, they can cause serious autoimmune disorders, such as Chron's Disease. You can find more information on IL23 here
http://en.wikipedia.org/wiki/Interleukin_23
and Chron's Disease here
http://en.wikipedia.org/wiki/Chron%27s_disease.

This week you may receive jobs with titles like "IL23p40_p40BrubYhbond_design_jecorn". These design simulations first dock two proteins against each other (one of which is IL23), then try to iteratively optimize the surface of one protein to better match the surface of IL23. Using the results of your calculations, I will the designed proteins and test them for binding to IL23, hopefully producing a new inhibitor to combat runaway diseases caused by runaway IL23 signals.

I'm very excited about this project, and look forward to your feedback.
____________

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Message 56778 - Posted 8 Nov 2008 22:17:33 UTC - in response to Message ID 56763.

I'm very excited about this project, and look forward to your feedback.


It's been great getting some new 'science' news from your and the rest of the project team. This sort of stuff is *really* motivating to a lot of us - please keep the news coming, and good luck with your project.
____________
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Michael G.R.

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Message 56795 - Posted 9 Nov 2008 22:14:08 UTC - in response to Message ID 56778.

It's been great getting some new 'science' news from your and the rest of the project team. This sort of stuff is *really* motivating to a lot of us - please keep the news coming, and good luck with your project.


I second that.
____________

Naesbye

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Message 56803 - Posted 10 Nov 2008 13:24:41 UTC

Me too. Having a fundamental idea of what we're helping out with, and knowing that it serves a beneficial purpose is very inspiring.

dcdc Profile

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Message 56805 - Posted 10 Nov 2008 16:28:47 UTC

fourthed - this info gets posted around various team forums - i'll post it on the XPC forum at some point as a lot of them don't read these forums but do read their team forums. Keeps everyone interested and often gets people to ramp up productivity.
____________

robertmiles Profile

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Message 56855 - Posted 11 Nov 2008 21:31:12 UTC - in response to Message ID 56754.

Hello,

My name is Sarel Fleishman and I've been a postdoc in the Baker lab for the past two years. My project deals with structure prediction and design of protein-protein interfaces and you may have read a few messages from me on CAPRI and structure prediction. Now, I'm very excited to tell you that with minirosetta v1.40 we can do design work using the massive computational power of Rosetta @ Home.

These design simulations tend to use more memory than many prediction runs (typically at most 800Mb). We will test different ways of reducing this memory load so that our simulations could run on all participating computers in the Rosetta @ Home project, but initially we will only run these simulations on computers that can handle this memory restriction. Please report any problems that you might have with this simulation.

Thank you very much for participating in this project! I'm looking forward to getting feedback and results from you.


Sounds like a good idea, but we need better estimates of how long these workunits will run and how much memory they will take. I've had as much memory as my motherboard can handle (2 GB for a CPU with 2 cores) for some time, but am now getting into the same slowdown of regular tasks that persuaded me to buy that much memory. Also, some of the minirosetta w1.40 workunits, typically those with 4704 in their names, are running much longer than my preferred 6 hours, without giving any workunits from other BOINC projects a chance to run, and then giving a poor credits to CPU time required ratio.

Could they be set up to make more frequent checkpoints?

Also, do you know where to find a program that can measure both the parts of workunits in progress in physical memory and in virtual memory, for Vista SP1?

dcdc Profile

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Message 56856 - Posted 11 Nov 2008 21:50:30 UTC - in response to Message ID 56855.

Could they be set up to make more frequent checkpoints?
unfortunately not - it's been discussed a number of times with the same conclusion - there are only certain points that are suitable for checkpointing.


Also, do you know where to find a program that can measure both the parts of workunits in progress in physical memory and in virtual memory, for Vista SP1?
I think process explorer works on Vista(?)

____________

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Message 56888 - Posted 13 Nov 2008 0:05:13 UTC

R@H Web designer should post this on the homepage and make it look neat and professional so people who come to the website for the first time can say "wow, this is for real" and join and not LEAVE.

Just an opinion.
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jcorn

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Message 56916 - Posted 13 Nov 2008 20:01:31 UTC

Hi everyone,
A quick update on computational design in general, and IL23 in particular.

As many people noticed, these design jobs are taking longer and using more memory than most R@H work units. This is because we are working with proteins that are much larger than what you normally fold during an abinitio run. For reference, imagine that abinitio runs are folding a steel chain with 1-inch links, and that the position of each link changes during the course of the workunit. Abinitio workunits then origami-fold about 8 feet of constant chain into a nice, pretty structure.

By contrast, our design workunits are dealing with two chains, each of which is twenty five to fifty feet long. Not only can the whole folded chain move, the positions of each link can shift slightly, *and* we're constantly swapping out links as the simulation progresses! We have twenty different links to play with, and each position on each chain could be any one of the twenty. Our challenge is to figure out how the two chains should lay on top of one another and what link should be at what position to make the the chains best fit together. As you can imagine, all of that takes a great deal of computing power, and about half a gigabyte of memory. We've put a temporary hold on future design workunits until we do a more benchmarking and fix the issues that you've brought up. For example, we are considering restricting design runs to machines with no less than 1GB of RAM.

Now the good news: Thanks to all of your work, the IL23 design project is moving at an incredible pace. Over the last 5 days, you generated half a million potential therapeutics for IL23! That's completely unprecedented for this kind of project, and would have taken me forever to do on our lab computers. So even though it was a somewhat rocky start, you have all made a very significant contribution towards creating an IL23 anti-inflammatory drug. I'm very much looking forward to sifting through all of the potential therapeutics you've designed, and I feel that R@H really holds the key to making this project work.
____________

robertmiles Profile

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Message 56986 - Posted 16 Nov 2008 8:05:26 UTC - in response to Message ID 56856.
Last modified: 16 Nov 2008 8:06:59 UTC



Also, do you know where to find a program that can measure both the parts of workunits in progress in physical memory and in virtual memory, for Vista SP1?
I think process explorer works on Vista(?)


dcdc,

How do I even find process explorer? When I did a help file search for process explorer, it gave me at least 60 help file pages to check for more information, but none of the first 30 say anything about whether Vista even includes a program by that name, much less how to start it.

robertmiles Profile

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Message 56987 - Posted 16 Nov 2008 8:28:06 UTC - in response to Message ID 56916.

Hi everyone,
A quick update on computational design in general, and IL23 in particular.

By contrast, our design workunits are dealing with two chains, each of which is twenty five to fifty feet long. Not only can the whole folded chain move, the positions of each link can shift slightly, *and* we're constantly swapping out links as the simulation progresses! We have twenty different links to play with, and each position on each chain could be any one of the twenty. Our challenge is to figure out how the two chains should lay on top of one another and what link should be at what position to make the the chains best fit together. As you can imagine, all of that takes a great deal of computing power, and about half a gigabyte of memory. We've put a temporary hold on future design workunits until we do a more benchmarking and fix the issues that you've brought up. For example, we are considering restricting design runs to machines with no less than 1GB of RAM.



Do machines with more than one CPU core, but no more memory than 1 GB times the number of CPU cores, qualify? Mine, for instance. If so, is there something to prevent all the CPU cores from trying to run such workunits at the same time? I don't mind the extra time required, so long as there are enough checkpoints to restart after Vista updates and similar causes for a reboot
without losing too much CPU time. I would, however, expect accurate enough estimates of the time and memory required to give me a reasonable amount of credits and to help decide when my machine can start such a workunit without slowing it down too much.

dcdc Profile

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Message 56989 - Posted 16 Nov 2008 11:11:46 UTC - in response to Message ID 56986.
Last modified: 16 Nov 2008 11:14:38 UTC



Also, do you know where to find a program that can measure both the parts of workunits in progress in physical memory and in virtual memory, for Vista SP1?
I think process explorer works on Vista(?)


dcdc,

How do I even find process explorer? When I did a help file search for process explorer, it gave me at least 60 help file pages to check for more information, but none of the first 30 say anything about whether Vista even includes a program by that name, much less how to start it.

http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx
____________

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Message 56993 - Posted 16 Nov 2008 13:46:43 UTC

I found a number of web sites refering to IL23.

IL-23: a master regulator in Crohn disease
http://www.nature.com/nm/journal/v13/n1/full/nm0107-26.html

Major Genetic Link to Crohn's and Colitis Found
http://www.ccfa.org/about/press/il23

Production of IL12p70 and IL23 by monocyte-derived dendritic cells in children with...
http://gut.bmj.com/cgi/content/full/57/10/1480?rss=1

IL-23 drives a pathogenic T cell population that induces autoimmune inflammation
http://jem.rupress.org/cgi/content/abstract/201/2/233

IL23 (Cytokines & Cells Online Pathfinder Encyclopaedia)
http://www.copewithcytokines.de/cope.cgi?key=IL23

Interleukin-23 promotes a distinct CD4 T cell activation state characterized by the production of interleukin-17
http://www.ncbi.nlm.nih.gov/pubmed/12417590

Interleukin 23 - Wikipedia
http://en.wikipedia.org/wiki/Interleukin_23

Looks like it is imvolved in at least some of the autoimmune diseases.

Sarel Profile

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Message 57144 - Posted 21 Nov 2008 19:58:55 UTC
Last modified: 21 Nov 2008 21:10:49 UTC

There has been a lot of interest in this thread, so I thought that I would write a little more about our design strategy and the importance of Rosetta @ Home's computational resources for the project's success. First, our approach in designing a new protein inhibitor to a natural target revolves around the idea that nature provides us with many thousands of diverse examples of protein interactions from which to learn. Studying these interactions in detail, we find that there are many unifying principles, such as the importance of energetic considerations (for more information, see http://en.wikipedia.org/wiki/Van_der_Waals_force). But, beyond these unifying principles it is striking to see just how diverse a phenomenon protein-protein interactions is! A great resource to learn more about the beauty and the implications of protein structures and interactions is the RCSB's molecule of the month feature, and here's one such feature on one of my targets, cholera toxin:
http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb69_1.html
As these illustrations and many other examples show, many protein interactions are uniquely optimized to take advantage of the physical interactions between chemical groups on the proteins' surfaces. Additionally, the surfaces of the proteins usually show very high shape complementarity as in the spectacular example provided by the protein that constitutes the majority of our connective tissue, collagen:
http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb4_1.html

Building on the idea that Rosetta captures correctly the unifying energetic principles, as evidenced by its successes in structure prediction and many different protein design tasks, we are still faced with the daunting challenge of how to best capture the great diversity encompassed by the protein-interaction phenomenon. In other words, how can we, for instance, find a protein, the surface of which would ideally fit with the surface of our target of choice as in the collagen example above? This is exactly the point where we need all that sampling power that you make available through the Rosetta @ Home project. Given a target protein, such as cholera toxin, we would like to massively test different amino-acid sequences. We would then like to make sure that each such sequence makes good physical sense, shows high shape complementarity, and would provide sufficient affinity. Since each target implies its own set of unique challenges (e.g., its molecular shape is unique), we specifically tailor a different protocol (or sequence of design steps) to each target and we want to test several such protocols for each given target in a trial-and-error way. Multiply all these computationally intensive tasks by the many millions of conformations that we would like to test for our potential binders with respect to the target and you see how it is that only through Rosetta @ Home we can begin to imagine finding a comprehensive solution to this great challenge!
____________

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Message 57154 - Posted 22 Nov 2008 0:55:53 UTC

More on Chron's disease and IL23:

http://cat.inist.fr/?aModele=afficheN&cpsidt=17443120

http://www.medicalnewstoday.com/articles/55268.php

http://www.ncbi.nlm.nih.gov/pubmed/18512248?dopt=AbstractPlus

http://www.journals.elsevierhealth.com/periodicals/crosup/article/PIIS1873995408702192/abstract?rss=yes

http://www3.interscience.wiley.com/journal/119553484/abstract?CRETRY=1&SRETRY=0

http://www.ncbi.nlm.nih.gov/pubmed/18512248

http://www.ccfa.org/about/press/il23

http://query.nytimes.com/gst/fullpage.html?res=9E05E5DA113FF934A35752C1A9609C8B63

http://gut.bmj.com/cgi/content/abstract/gut.2007.135053v1

http://www.eurekalert.org/pub_releases/2006-10/uom-sfg102606.php

robertmiles Profile

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Message 57155 - Posted 22 Nov 2008 1:20:41 UTC

Diabetes and IL23:

http://www3.interscience.wiley.com/journal/120175976/abstract

http://cat.inist.fr/?aModele=afficheN&cpsidt=17383689

http://www3.interscience.wiley.com/journal/112217095/abstract

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=182190

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6W7H-4HJRRWT-1&_user=4420034&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000063005&_version=1&_urlVersion=0&_userid=4420034&md5=f2e4614bbe3740e47b946b9e032a5ae3

http://jvi.asm.org/cgi/content/full/78/17/9093

http://www.jimmunol.org/cgi/reprint/170/11/5438.pdf

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Message 59423 - Posted 7 Feb 2009 17:16:37 UTC - in response to Message ID 56856.

Also, do you know where to find a program that can measure both the parts of workunits in progress in physical memory and in virtual memory, for Vista SP1?
I think process explorer works on Vista(?)
[/quote]

It does, but it took a few months to find where it went when I installed it.

It appears to be showing me that BOINC is still using both cores of my CPU at 100%, even though I first tried to lower this to 98% and then 90% in order to help test for certain problems over on RALPH@home.

Sarel Profile

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Message 64838 - Posted 7 Jan 2010 0:35:29 UTC

Hello,

Since I last wrote (a long time ago) we've made substantial progress in the design of protein interactions. We have developed a new methodology and tested it extensively in recapitulating known protein interactions as well as in the design of new interactions. In all of our tests the results have been very favourable, and most importantly, we now have a handful of designs that show specific binding towards their targets in experiments!

We're obviously very excited about the potential applications of this methodology for the design of inhibitors and binders of drug targets and other biomedically interesting proteins. The target that has most excited us is hemagglutinin from pandemic influenza strains, including of the swine and Spanish flu. This protein is a prime drug candidate and its structure with an antibody that neutralizes these strains of influenza has been solved. We are using our new methodology in order to compute binders of hemagglutinin that may be easier to mass produce than is the antibody. As might be expected, the complexity of designing a binder towards hemagglutinin surpasses that of other protein targets that we had previously attempted and therefore requires substantially more computational resources. We are hoping that with your contributions to ROSETTA@HOME we may obtain many putative inhibitors for experimental testing.

We have other targets in our pipeline that we are very excited about. The design simulations that we will send out will contain a description of the target protein, so for instance, the simulations pertaining to hemagglutinin will be labeled "design of an inhibitor of influenza hemagglutinin". We'll also update this thread with descriptions of other targets and the results of the simulations and experimental characterization. We're excited to see how many new solutions to this problem you will come up with!
____________

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Message 64839 - Posted 7 Jan 2010 1:28:42 UTC

Thank you for the update, Sarel. Sounds like promising developments.
____________

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Message 64846 - Posted 7 Jan 2010 11:39:19 UTC

Great News and please, keep us updating! :) It should help to encourage us, the readers, and further our teammates, friends etc. to bigger involvement in R@H.

Sarel Profile

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Message 65045 - Posted 19 Jan 2010 19:37:42 UTC

Hello,

I wanted to give you a brief update that I've received many excellent models of hemagglutinin binders from your computer! From the very large collection of designs that your computers produced I've selected 15 that we will start testing over the next few weeks. 15 is a very large number, but we want many many more so expect more such simulations in the near future.

Many thanks! Sarel.
____________

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Message 65125 - Posted 27 Jan 2010 0:57:20 UTC

Hi all,

my name is Tim Whitehead and I've been a postdoc in the Baker lab for about a year. My projects deal with the prediction and design of protein-protein interfaces. In this thread, Sarel has explained the design problem for protein-protein interfaces. Progress in this area can drive the next generation of treatments against pathogens like Mycobacterium tuberculosis or Influenza.

I have been working with Sarel on the design and experimental characterization of designs that target disparate proteins on both pathogens. We have a couple of successes thus far, which we are extremely excited about, but need to have better and better designs to show the validity of our design approach.

In this thread, Sarel has explained why and how we are targeting Influenza by designing a protein inhibitor of a protein that is displayed on the surface of the virus.

For Tuberculosis, our task is slightly more difficult. TB is caused by a bacterium called Mycobacterium tuberculosis. The bacteria is encased in a waxy coating of mycolic acid, which hurts our body's ability to expell the bacterium (for more information, see http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis).
Instead of designing an enzyme that could degrade the coating, we are targeting a protein that is involved in the `synthesis` of mycolic acid. You may have already seen BOINC descriptions that say "docking of designs against 2CGQ" - 2CGQ is the protein that we are trying to inhibit. I am hoping that your contribution from ROSETTA@HOME will give us the increased quality of our designs that we need. Thanks for the help!

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Message 65126 - Posted 27 Jan 2010 6:34:38 UTC

My name is Eva-Maria Strauch and I am one of the post-docs in the Baker lab working on the design of protein-protein interactions. I am very excited about having the possibility to run on R@H, thanks to your generous contributions! Protein design requires a lot of sampling since there are so many many different possibilities to be considered carefully. This will work out now faster with your help!

I am currently designing proteins to bind to a model system which we use to calibrate our computational protocols. This particular target is the back end of a human immune-system antibody (Fc fragment, which is what you will see under the work unit descriptions http://en.wikipedia.org/wiki/Fc_region). The cool thing about Fc is that nature provides us with several proteins that bind to it, hence it taught us very important lessons on how to design possible binding proteins to it. We now want to see whether we've figured this one out and can mimic nature's ability to come up with binders towards this target. Success will further contribute to the optimization of our protocols to generate several protein-based inhibitors to attack cancer and infectious diseases. Questions we want to answere with this design project are: How well do we perform in comparison with nature? and if we understood all the information we got out of those native interactions, are we able to produce several de novo binding proteins that mimic the atomic interactions seen with native interaction Fc has with different proteins? This project will contribute to our understanding of how proteins recognize one another. Promising designs will be experimentally verified and also further characterized to see how well we performed, and what was possibly missing that we should include into our computational design protocol.
Thanks again for your contribution!

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Message 65129 - Posted 27 Jan 2010 16:11:29 UTC

Thanks for the update, very interesting stuff. Keep up the good work!
____________

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Message 65130 - Posted 27 Jan 2010 16:31:08 UTC

Thanks for you contribution to the thread/forum. It is much appreciated.
____________

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Message 65206 - Posted 4 Feb 2010 19:05:22 UTC

Hi boincers,
Since I last wrote, Tim Whitehead (username taw) and I have spent a lot of time testing the anti-IL23 designs that you made. So far we have a promising hit, but in science as in life, the results are somewhat ambiguous. I'll keep everyone updated when things are more concrete, but there's hope that your number-crunching has made a bona-fide binder for IL23!

I've also started designing against a new target, called Insulin-like Growth Factor 1 (IGF1). IGF is a central regulator of the speed of cell division: many tumors have been linked to having too much IGF around. Interestingly, the when an organism's cells are globally told to divide more slowly, by inhibiting IGF, the animal actually lives longer! As they say, the candle that burns twice as bright, burns half as long. In fact, since IGF is closely related to insulin and energy metabolism, some people have theorized that the increases in life span from caloric restriction are actually a side-effect of crosstalk with IGF signaling. So anti-IGF therapies hold promise as both anti-cancer agents and as anti-aging therapies.

I'm very excited to see what designs you can come up with, and everything is in place to test them in the lab. Look for workunits that start with "igf", eg - "igfhum" or "igffn3". Thanks for your help!
____________

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Message 65207 - Posted 4 Feb 2010 19:06:49 UTC

For those who'd like more information on IGF-1, check out the wikipedia page

http://en.wikipedia.org/wiki/Insulin-like_growth_factor_1
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Michael G.R.

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Message 65216 - Posted 5 Feb 2010 20:07:42 UTC

Very exciting news, Jcorn. Thanks for the update. Am particularly excited about IGF research because I've read a bit about it lately. Seems very important in a lot of things that go right and wrong with metabolism.
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Message 65330 - Posted 15 Feb 2010 18:15:03 UTC
Last modified: 15 Feb 2010 18:20:22 UTC

Hello,

my name is Rickard and I'm a visiting biotech student from Uppsala University (Sweden). I'm involved in a project aiming at creating proteins that bind to lysozyme. I'm being supervised mainly by Sarel, but I'm also getting help from the other postdocs in the lab. This work is the final part of my education, so it is great to be working in such an amazing group of people on this extremely interesting project.

While most of the others in the group are trying to design binders to therapeutically relevant targets, I am not. The protein I am working on, lysozyme, has for a long time been a favorite model protein among scientists. The reason is that it is very easy to work with, so there is loads of experimental data available. Of particular interest to us is the relatively large number of solved structures of lysozyme complexed with other proteins. This is extremely useful since we can learn a lot from looking at them. Nature has solved the binding problem in many different ways. It will be interesting to see if we can do something similar. By choosing an easy-to-work-with protein we make the biochemistry part of the project a little bit easier, and we are able to focus on testing and improving our design methodology. I would like to say that lysozyme, despite not being a pharmaceutical target, is an interesting protein to make a binder for. One reason is that lysozyme, just like many therapeutically relevant proteins, is an enzyme so if we can get a binder that inhibits its activity then it is likely that we can design inhibitors for other enzymes as well. At this point in time it is also the only enzyme that we are targeting in the lab.

Designing lysozyme binders with the humongous computational power that you are providing is very exciting! The results that Sarel, Jacob and the others have got from you have been very promising so I'm very much looking forward trying it out.

Thank you for helping out!

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Message 65551 - Posted 14 Mar 2010 14:54:47 UTC
Last modified: 14 Mar 2010 14:56:07 UTC

I got a strange WU which generates 10000 decoys (yes, ten thousand).
And does not show any graphics, except the 1st original(starting) model.
Link: fcDE-W3b_1dAl_1zzo_ProteinInterfaceDesign_11Mar2010_18648_49_0

This is a new type of protein-protein interfaces algorithm, which allows to discard "unpromising" model even more early than it was before?
Or is it a just fault in the program?

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Message 65556 - Posted 15 Mar 2010 5:56:27 UTC - in response to Message ID 65551.

I got a strange WU which generates 10000 decoys (yes, ten thousand).
And does not show any graphics, except the 1st original(starting) model.
Link: fcDE-W3b_1dAl_1zzo_ProteinInterfaceDesign_11Mar2010_18648_49_0

This is a new type of protein-protein interfaces algorithm, which allows to discard "unpromising" model even more early than it was before?
Or is it a just fault in the program?


thanks for pointing this out! That does sound weird. We are looking into what is going on. The WU did produce some valuable decoys though! but we are taking those WU off till we figure out what could be the cause of this.

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Message 65569 - Posted 17 Mar 2010 2:12:48 UTC

Hello.

A Question for Administrator`s /scientist`s:

Sorry but i am realy not sure how to ask :p Anyway...

What is the chanse that rosetta@home can investigate/"do a research" on
SMN1 and SMN2 protein?

http://en.wikipedia.org/wiki/SMN1 and http://en.wikipedia.org/wiki/SMN2

If not.. Who do you recommend i can contact in distributed computing "family" to get some numbers crunched on SMN1 and SMN2.

Sorry my realy bad English.

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Message 66178 - Posted 17 May 2010 19:22:09 UTC
Last modified: 17 May 2010 19:25:37 UTC

Hello,

As you've seen on David's thread a design from your Rosetta @ Home contributions is a tight binder of influenza's hemagglutinin protein making it a candidate to serve as an inhibitor and hopefully a therapeutic. This is exceptionally good news. Many thanks to all of the participants!

This news is making us all very excited of course and we are starting to think about the next steps. One promising avenue for future research is to use this computational technology to design specific inhibitors of proteins that are important regulators of cellular activity but where experimental research has been stymied by the lack of specific, non-toxic effectors. Let's take a few steps back and try to see the broader picture. Our understanding of molecular biology progresses through the identification of key players and systems in the cell and then by modulating these effectors and observing the results on cell viability and function. This process parallels the concept of reverse engineering of mechanical and electronic systems.

A major tool in this process involves the use of genetic knockouts. These are mutations to genes that disable a protein's function. Using this technique myriad gene functions have been described, including genes that are important tumor-suppressors or promoters, metabolite importers and regulators of cell size, form, and fate. But, gene knockouts are not very subtle tools and they often have far-reaching consequences on cell viability, making it difficult to interpret the results of the knockout experiment. For a beautiful and accessible description of the parallels between reverse engineering and molecular biology and where the difficulties lie, see "Can a Biologist Fix a Radio?" (Biochemistry (Moscow), Vol. 69, No. 12, 2004, pp. 1403-1406; protein.bio.msu.su/biokhimiya/contents/v69/pdf/bcm_1403.pdf).

One way to deal with these difficulties is by using specific inhibitors that are invoked at specific times to block a certain protein function rather than pulling the brakes on a protein from the cell's inception. The ideal inhibitor would selectively modulate one interaction without affecting other interactions, thus allowing a subtle study of the significance of interactions in the cell. Thus specific inhibitors, where they have been discovered and deployed, have yielded very important lessons on the function of proteins that are crucial in many cellular signaling pathways, to give but one example. But, these inhibitors are rare and very difficult to identify. We think that similar to the influenza binder, we should be able to use computational protein design to generate novel and highly specific protein inhibitors of important cellular players and help in elucidating their functions.

Over the next few weeks we will launch new jobs on Rosetta @ Home that target proteins where an inhibitor could help make progress in our understanding of cell biology. As we prepare each of these targets for Rosetta @ Home we will describe the rationale for pursuing them in this thread.

One of these targets is RhoA. This protein belongs to the family of oncogenic Ras proteins which are involved in cell division and regulation. RhoA is known to be a major player in cancer. As mentioned above, knocking out RhoA causes many different problems for cell viability. It is easy to understand why if you merely look at the number and variety of its interaction partners (see, http://en.wikipedia.org/wiki/RHOA)! By generating a specific inhibitor of RhoA we hope to enable probing the effects of its modulation at specific points in the living cycle of the cell and under different conditions -- studies that are nearly impossible to perform today.

Finally, I'd like to thank all of the participants in Rosetta @ Home for the immense boost in computational throughput over the past few weeks! Without the 40% increase in computational power it would have been impossible for us to work on these targets in parallel to the needs of the group who are working on CASP! Please keep these contribution levels!
____________

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Message 66323 - Posted 25 May 2010 18:14:16 UTC

I just wanted to update you on another project I have been working on and I am running on rosetta@home.

Enterohaemorrhagic and enteropathogenic E. coli strains (like O157:H7, http://en.wikipedia.org/wiki/E._coli_O157) are some of the most important food-borne pathogens in North America, Europe and Japan, and contribute worldwide to pediatric morbidity and mortality. You might have heart about the outbreaks in the States that involved green spinach, iceberg lettuce or ground beef.

In order to cause diarrhea, these bacteria attach to the intestines before they get into your body. For that they have developed a special anchor-hook system to stick to the cells of our guts just like Velcro. I am targeting this molecular mechanism to produce protein-based inhibitors that prevent bacterial attachment and thereby reduce or prevent their colonization of our guts.

Thus far, traditional approaches to neutralize this particular interaction have not been very successful. Neither antibodies nor small peptides have been efficiently produced that target the interface of this molecular
machinery. We think that our new methodology could facilitate the development of a new therapeutic against these bacteria. You will see several jobs that are called "design against intimin" or such.

Thanks for supporting us with your computer time! It is a great help!

Eva

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Message 66469 - Posted 5 Jun 2010 4:28:43 UTC

We've started to design proteins against another exciting target called MDMX. MDMX is known to interact with one of the key tumor-suppressor genes, p53. p53 has such a central role in physiology that it has been called "guardian of the genome". MDMX inhibits p53 and causes its degradation through a complex mechanism. But, the specific role of MDMX in p53 inhibition is something of a mystery because a close homolog of MDMX called MDM2 is involved in very similar interactions with p53. The difficulty in deciphering the specific roles of MDMX lie in the fact that to date a specific inhibitor of MDMX has not been identified. That is, inhibitors of MDMX inhibit MDM2 to the same extent so that perturbing MDMX alone (and vice versa) is very difficult.

Our goal in this project is to design an inhibitor of MDMX that would not interact with MDM2. We plan to take advantage of subtle differences between the two proteins in order to design a protein that will be highly specific to MDMX. Hopefully with this protein in hand, research into the role of MDMX will gain a new and important tool.

Over the next few weeks I will submit jobs with the word MDMX in their title to Rosetta @ Home. I'm very excited to see what comes out!

In the meantime, here's some further reading for those who are interested in the intricacies of this important system:
http://en.wikipedia.org/wiki/Mdm2
http://en.wikipedia.org/wiki/P53
http://en.wikipedia.org/wiki/MDM4 (MDMX is also known as MDM4)
____________

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Message 66481 - Posted 6 Jun 2010 0:34:55 UTC

Hi Sarel.

That didn't take long, i've gotten one of your new tasks this morning.

MDMX_3jzp_1o6d_ProteinInterfaceDesign_4Jun2010_21359_52

____________


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Message 66514 - Posted 8 Jun 2010 1:44:14 UTC

Only I went to ask about a new type of tasks, which drew my attention... And here is a ready description posted already. Excellent speed.
But the question still is: it is simple (short) protein? (But in wiki i found info about 490-amino acids, it is not short i think) Or improve of algorithm? This type of job (MDMX_ *) generates much more decoys for the same time, compared with other protein-protein tasks i saw before. From a few hundreds to 1200 decoys in only 2 hours (7200 sec) tasks at mid-level processor. I already had a lot of these tasks, that's only 3 for example:

http://boinc.bakerlab.org/rosetta/result.php?resultid=343957927
http://boinc.bakerlab.org/rosetta/result.php?resultid=344057490
http://boinc.bakerlab.org/rosetta/result.php?resultid=343943380

And judging by the normal ratio between Claimed and Granted credit is not a feature of my computer, but it happens at all.

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Message 66515 - Posted 8 Jun 2010 3:31:10 UTC
Last modified: 8 Jun 2010 3:31:57 UTC

Some of the newly developed protocols have phases which produce models rapidly, even for larger proteins. So entire lines of tasks are created which can scour the landscape and locate the major features of the terrain. Then this information can be used to create additional lines of tasks which focus on the points of highest interest.

You are correct, these tasks run "fast" on everyone's machine, as compared to other typical tasks anyway. So the credit per hour of CPU time should be in line with other tasks. Since the models are relatively easier (then models for other tasks) for a machine to produce, each is granted less credit.

I believe those were the main questions you had. If I missed it, let me know.
____________
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Message 66522 - Posted 8 Jun 2010 17:09:33 UTC - in response to Message ID 66514.

Thanks for your feedback! Mod.Sense's replies on the conformational sampling is very accurate. With regard to the size of the protein, you are right that MDMX is a much larger protein than what we are modeling in these design trajectories. What we are interested in is the interaction surface of MDMX with p53. That is (thankfully) a very small domain allowing us to do things more quickly and efficiently.

Only I went to ask about a new type of tasks, which drew my attention... And here is a ready description posted already. Excellent speed.
But the question still is: it is simple (short) protein? (But in wiki i found info about 490-amino acids, it is not short i think) Or improve of algorithm? This type of job (MDMX_ *) generates much more decoys for the same time, compared with other protein-protein tasks i saw before. From a few hundreds to 1200 decoys in only 2 hours (7200 sec) tasks at mid-level processor. I already had a lot of these tasks, that's only 3 for example:

http://boinc.bakerlab.org/rosetta/result.php?resultid=343957927
http://boinc.bakerlab.org/rosetta/result.php?resultid=344057490
http://boinc.bakerlab.org/rosetta/result.php?resultid=343943380

And judging by the normal ratio between Claimed and Granted credit is not a feature of my computer, but it happens at all.


____________

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Message 66528 - Posted 9 Jun 2010 12:50:37 UTC

Thank you. Now it is clear from this acceleration comes. Due to the possibility of modeling is not all the protein completely, but only the most important (for the current study), part of it.

2 Sarel
And yet another question. I am not a scientist, so this may seem silly, but as a result of observing the process of calculations I had the idea.
It concerns the limit of 500 steps in modeling protein-protein including the last MDMX. It is clear that the shorter limit is introduced to speed up processing. And in most cases it seems to be enough - a graph of energy usually manages to "find minimum" for these 500 steps and more just jumping around him.

But periodically I see a model in which the energy almost continuously go down, but the simulation of the same breaks at the limit of 500 steps. (Obviously not a straight line, but with variations here and there, but the overall trend is absolutely clear - down) Though if given the additional steps would be found a configuration with a much lower energy. And since this model does not differ from the total mass, because its calculation was stopped before she could reach its minimum. Simply increasing the number of steps are not very effective way, because it increase the use of computing resources in times (or reduce the number of models with fixed resources), for 5% of models (about as much on my observations do not manage to reach the "saturation") is not effective. (Though perhaps this is the most valuable model, so that theoretically could be more valuable than the other 95%)

But what if instead of a fixed hard limit on the number of steps to use a dynamic limit is based on "delta energy" criteria? Ie compare the minimum energy found suppose the last 100 steps (for example, concrete value must be chosen experimentally), with previous values. If there is some improvement, then give the model additional steps, and so until the reduction of energy does not stop. The fixed limits (in particular number of steps) are also needed, but only as a acceptable framework - minimum (say cover those 500) and maximum (it should be big enough, but within reasonable limits. To finish on time "bad model", without waiting for the activation of watchdog).

Perhaps this idea has already been tried before? Then it would be interesting to know the results and why abandoned.

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Message 66530 - Posted 9 Jun 2010 16:40:37 UTC - in response to Message ID 66528.

That's a very good question! With respect to the ProteinInterfaceDesign simulations, on Rosetta @ Home our goal is to scan the vast conformational-sequence space in order to get good leads. Sampling for those is then intensified on our own machines where we can run high-memory trajectories for longer. So, in a sense we are implementing a primitive version of your suggestion. During energy minimization, by the way, we have exactly this delta energy criterion that you mention as a stopping condition.

What you are suggesting is actually being attempted now in a more sophisticated form than what I mentioned above by some of the people on the Rosetta team for structure prediction of very large proteins, where very many trajectories are run, clustered and the best few are then intensified. From what I've seen this is an extremely promising direction of research so let's keep our fingers crossed for it!

Thank you. Now it is clear from this acceleration comes. Due to the possibility of modeling is not all the protein completely, but only the most important (for the current study), part of it.

2 Sarel
And yet another question. I am not a scientist, so this may seem silly, but as a result of observing the process of calculations I had the idea.
It concerns the limit of 500 steps in modeling protein-protein including the last MDMX. It is clear that the shorter limit is introduced to speed up processing. And in most cases it seems to be enough - a graph of energy usually manages to "find minimum" for these 500 steps and more just jumping around him.

But periodically I see a model in which the energy almost continuously go down, but the simulation of the same breaks at the limit of 500 steps. (Obviously not a straight line, but with variations here and there, but the overall trend is absolutely clear - down) Though if given the additional steps would be found a configuration with a much lower energy. And since this model does not differ from the total mass, because its calculation was stopped before she could reach its minimum. Simply increasing the number of steps are not very effective way, because it increase the use of computing resources in times (or reduce the number of models with fixed resources), for 5% of models (about as much on my observations do not manage to reach the "saturation") is not effective. (Though perhaps this is the most valuable model, so that theoretically could be more valuable than the other 95%)

But what if instead of a fixed hard limit on the number of steps to use a dynamic limit is based on "delta energy" criteria? Ie compare the minimum energy found suppose the last 100 steps (for example, concrete value must be chosen experimentally), with previous values. If there is some improvement, then give the model additional steps, and so until the reduction of energy does not stop. The fixed limits (in particular number of steps) are also needed, but only as a acceptable framework - minimum (say cover those 500) and maximum (it should be big enough, but within reasonable limits. To finish on time "bad model", without waiting for the activation of watchdog).

Perhaps this idea has already been tried before? Then it would be interesting to know the results and why abandoned.


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Message 66532 - Posted 9 Jun 2010 22:40:08 UTC - in response to Message ID 66530.

That's a very good question! With respect to the ProteinInterfaceDesign simulations, on Rosetta @ Home our goal is to scan the vast conformational-sequence space in order to get good leads. Sampling for those is then intensified on our own machines where we can run high-memory trajectories for longer.


Out of curiosity, how much memory do the more intense studies that are in-house require and is that a limiting factor to the lab's throughput? I assume all the computational limitations (in-house and R@H) are limiting in some way...

____________

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Message 66541 - Posted 10 Jun 2010 17:43:30 UTC - in response to Message ID 66532.

It varies, but I think that 750Mb would be a good guesstimate. Though that's not too bad, another thing that makes these trajectories a poor fit for Rosetta @ Home is that they might take several hours to produce output. Since we only do these runs for a few tens of the best of what we found on Rosetta @ Home, we can do it efficiently on our own machines.

That's a very good question! With respect to the ProteinInterfaceDesign simulations, on Rosetta @ Home our goal is to scan the vast conformational-sequence space in order to get good leads. Sampling for those is then intensified on our own machines where we can run high-memory trajectories for longer.


Out of curiosity, how much memory do the more intense studies that are in-house require and is that a limiting factor to the lab's throughput? I assume all the computational limitations (in-house and R@H) are limiting in some way...


____________

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Message 66634 - Posted 22 Jun 2010 3:28:09 UTC

I see lot of new p-p tasks with names started like "simIF_" and dated 18Jul2010
Its new protein target?

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Message 66639 - Posted 22 Jun 2010 17:34:35 UTC

hi, thanks for asking. The simIF jobs are for the design of protein-based neutralizers for intimin, the bacterial Velcro system that allows Ecoli to stay in your intestines (see post http://boinc.bakerlab.org/rosetta/forum_thread.php?id=4477&nowrap=true#66323).

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Message 66689 - Posted 24 Jun 2010 21:16:00 UTC

Hello,

My name is James Moody and I am a new graduate student in the Baker lab. I am working on protein-protein interface design and am excited to have the help of all of the participants of Rosetta@home!

Right now I am working on designing a protein to bind to a regulatory molecule called EED. EED works with other proteins in our cells to control which parts of our DNA will be used to control the cell and which parts will be silenced (turned off). EED is thought to work by bringing other proteins together and is part of a larger protein machine called the Polycomb Repressive Complex 2 (PRC2). PRC2 helps to ensure, for example, that we have the right number of arms and legs and that they are in the right place on our bodies (by controlling our Hox genes).

Scientists are working to better understand how EED works to control the activity of our DNA and its link to things like stem cells, development, and cancer. To do this, we need a way to interrupt the normal function of EED. This is especially difficult since there are currently no drugs that block EED function. An engineered protein would be able to prevent EED from sticking to one of its binding partners (histone tails) and could be turned on and off at will by the researcher. It is hoped that such a protein would allow researchers to carry out new experiments on EED that were impossible before.

Engineering this novel interaction with EED into another protein requires computationally screening through as many as possible of a billion possibilities, evaluating each protein for how tightly it sticks to EED, and then redesigning the new protein to stick even better. Such a task would be impossible without the help of Rosetta@home participants!

Thank you so much for lending yourselves to participate in this project. Things that I send to rosetta@home are tested first on our machines and then on a subset of Rosetta@home participants to ensure that they don't cause any problems for you. Please don't hesitate to ask if you have questions, feedback, or see errors.

If you would like to learn more about EED or related topics, the following webpages might be helpful!

http://en.wikipedia.org/wiki/Polycomb-group_proteins
http://en.wikipedia.org/wiki/EED
http://en.wikipedia.org/wiki/Histones
http://en.wikipedia.org/wiki/Nucleosome
http://en.wikipedia.org/wiki/Hox_genes

--James

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Message 66752 - Posted 3 Jul 2010 20:57:20 UTC

Hi everyone,
I am working on another cool project that aims to generate a new molecular tool to dissect bacterial cell division. In order to propagate, cells need to divide. Separation of two daughter cells from a single cell is quite a complicated event that involves a fine-tuned and concerted molecular machinery. It requires figuring out where to actually draw the line, the assemble of several different proteins into one “divisosome” that will eventually perform the physical separation, and of course on top of all this, the cell needs to keep track of the DNA so that each cell gets its own copy. So it is imaginable that this is a fairly complicated happening.

Bacterial and mammalian cells are very similar in some parts of this event, but also very divergent in others. Of course, it is important to understand both. In mammals, uninhibited cell division results in cancer, but inhibited cell division can effect your body’s ability to regenerate. By knowing the difference between the mammalian and bacterial systems, one might be able to target bacterial cells specifically for new therapeutics without hurting mammalian cell division. The goal of this project is to produce molecular tools that help to analyze the complexity of the bacterial divisosome.

To picture cell division, you could imagine, one would take a string around a cell, pull and thereby separate the cell. Now you just have to imagine that the cells are actually making the string inside of themselves. They make a huge polymer (sort of like PVC). To get this molecular string, they polymerize several units of a protein that is similar between bacterial and mammalian cells, but one of the differences is the machinery it uses to coordinate this polymerization. Hence, one of my first targets of the cell division apparatus is a protein that is important for the localization of the polymer (aka string).

Thanks for your support! This wouldn’t be possible without your help.

/Eva

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Message 67031 - Posted 28 Jul 2010 18:49:10 UTC

One of the most important ways in which molecular biologists learn about the functions of protein systems in the cell is by introducing mutations to the protein and seeing what the effects on cellular functions are. This method is extremely powerful but carries the risks that damage will be indiscriminate and the functional readout would be convoluted by many different effects. A more refined way of perturbing cellular functions would be to inhibit a specific interaction within the cell, keeping all other interactions, including of the target protein, intact. Such specific inhibition is more subtle and reduces unwanted effects, and indeed specific inhibitors of cellular pathways accelerate advances in our understanding of cell physiology.

The design of protein inhibitors promises to take this approach and make it widely available to systems that have been recalcitrant to the development of specific inhibitors to date. Since protein interactions have very large surface areas we can design inhibitors that would be exquisitely specific to the target protein as we've done for influenza hemagglutinin. In a posting above, I mentioned that we're designing proteins that would inhibit MDMX but not MDM2, despite very close homology between the two proteins.

A new protein target that we're interested in is called ERGIC-53. A complex between ERGIC-53 and another protein called MCFD2 has been shown to be an important cargo receptor that shuttles proteins between various compartments in mammalian cells. Even though the complex has been extensively studied major questions about its function remain unanswered, among which are how the complex interacts with its cargo proteins. A specific inhibitor of the interaction between ERGIC-53 and MCFD2 will provide a way to control the formation and dissociation of the cargo receptor in a time-controlled manner, decreasing unwanted effects, and hopefully increasing our understanding of this important system.

I should mention that mutations in either ERGIC-53 and MCFD2 have been identified in human populations and cause an inherited bleeding disorder. For more information on this link between the cargo receptor and disease, please see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1895703/

Over the next few weeks I will submit workunits with different strategies for designing anti-ERGIC proteins. Thank you very much for your contributions to this project!
____________

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Message 67671 - Posted 9 Sep 2010 23:43:11 UTC

One of the most thrilling directions of research for protein-interface design is generating binding proteins for use as diagnostics in developing countries. The aim here is to develop materials for an early-detection kit, where the materials are cheap and robust enough to last for months or years without refrigeration. Diagnostics kits are typically comprised of antibodies, which are often expensive to mass produce and sometimes deteriorate over long periods of time. We believe that redesigning small stable proteins as binders would provide proteins of the necessary qualities to significantly improve the usefulness of diagnostics.

Our first target with a possible diagnostic application is the envelope protein of dengue virus. Dengue is a mosquito-borne virus that is widespread in the tropics and causes debilitating fever and death. Early-detection kits are extremely important because dengue-infected individuals should be protected from mosquito bites to cut off the spread of disease in their community.

Over the next few weeks I will submit design trajectories to Rosetta @ Home which will be labeled "Dengue binder design". I'm looking forward to seeing the binders that your computers will crunch this time!

To read more about dengue please see:
http://en.wikipedia.org/wiki/Dengue_fever
____________

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Message 68665 - Posted 19 Nov 2010 1:47:49 UTC

Hello,

As you may have read on David's blog we've had a lot of exciting developments on the influenza hemagglutinin front lately, including a crystal structure confirming one of the designs and biochemical data with respect to another that show that the protein inhibits the action of hemagglutinin. Hopefully this means that the proteins can serve as platforms for the development of therapeutics and diagnostics for many different flu types. More broadly, the thought that protein design could produce proteins that are as useful as antibodies is a sign of the field's maturity. I'm very pleased to mention also that both of these designs, and in fact 80% of the designs we generated in the hemagglutinin project came from your computers on Rosetta @ Home. This project has been so complex that without your amazing resources it would have been impossible to get working binders.

On a related issue, we're designing more putative binders of RhoA, so you will see more design jobs labeled "design of inhibitors of RhoA". I previously introduced RhoA in entry:
http://boinc.bakerlab.org/forum_thread.php?id=4477&nowrap=true#66178

Many thanks! Sarel.
____________

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Message 68753 - Posted 5 Dec 2010 17:48:50 UTC

I remember seeing an article saying that a certain important virus used a cluster of three of a certain protein for entering human cells, and normally had the rest of its envelope arranged to hide this cluster. Also, single instances of this protein appeared elsewhere on its envelope, perhaps to allow the body's natural defenses to bind where they wouldn't harm the virus.

Unfortunately, I've lost the link to where I found it, or I'd insert that link here. I'll keep trying to find it again, so you can consider whether it's practical to design a protein that binds to clusters of three of the virus's protein, but not to single instances.

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Message 68755 - Posted 5 Dec 2010 19:31:13 UTC
Last modified: 5 Dec 2010 19:46:25 UTC

Could be one of these, but the others look related as well:

http://www.rkm.com.au/VIRUS/Influenza/Swine-Flu.html

http://www.biomedcentral.com/1472-6807/9/62/figure/F5

http://vir.sgmjournals.org/cgi/content/full/88/12/3209

http://www.biomedcentral.com/1472-6807/9/62

The hemagglutinin protein, which you've done some work on already.

The influenza virus.

If the hemagglutinin protein is safe enough without the rest of the virus, you could also consider binding clusters of three of them at the right distance, in order to use the clusters as a vaccine.

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Message 68844 - Posted 19 Dec 2010 16:02:39 UTC

In the last few days I see a lot of new WUs from the *ProteinInterfaceDesigh* series starting from 8, 10 and 16 December.
For example ApBp_eed2_eed2_* or rhoA8Dec2010_1lb1_2bf0_* or AEty_1_eed2_eed2_* etc
Some brief updates on the new search targets?

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Message 68859 - Posted 22 Dec 2010 22:26:57 UTC - in response to Message ID 68844.

Right! We introduced the RhoA project in this entry:

http://boinc.bakerlab.org/forum_thread.php?id=4477&nowrap=true#66178

Hopefully more on eed soon...

Thanks for your interest, Sarel.

In the last few days I see a lot of new WUs from the *ProteinInterfaceDesigh* series starting from 8, 10 and 16 December.
For example ApBp_eed2_eed2_* or rhoA8Dec2010_1lb1_2bf0_* or AEty_1_eed2_eed2_* etc
Some brief updates on the new search targets?


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Message 68860 - Posted 22 Dec 2010 22:38:18 UTC

For those you you asking about EED:

See <http://boinc.bakerlab.org/forum_thread.php?id=4477&nowrap=true#66689> for a description of this project. If you have other questions don't hesitate to ask!

Thanks again for all of your help!

--James

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Message 70152 - Posted 28 Apr 2011 8:58:21 UTC
Last modified: 28 Apr 2011 11:05:43 UTC

Hello,

My name is Shawn Yu, and I'm a new graduate student in the Baker lab. I have several really exciting projects in protein-protein interface design that I want to share with everyone involved with Rosetta@home. I'm designing proteins to bind to targets on the measles and Ebola viruses.

De novo protein-protein interface design has been an elusive problem in the field for quite some time. It is an extremely challenging endeavor that will require us to continually refine our algorithms and seek more computional power. Relatively recently--due in large part to the generosity and support of Rosetta@home users--we able to tackle these problems with reasonable expectation of success, as demonstrated with the influenza project, but we would like to continue to expand on this success.

Each viral target represents a different challenge that tests our knowledge of how protein interacts in different ways, so they are really interesting for their scientific merits alone. Furthermore, these methods are mutually reinforcing, so with more successful designs we'll have a better idea of what works and what doesn't work. In the long term, I hope the results from these projects can form the basis of future protein-based therapies, and I know many Rosetta@home users like myself contribute their time because they hope to help find cures to these diseases.

Over the next week, I will be discussing more details about my projects. In the meantime, thank you so much for volunteering your time and your computers to help to our projects. You are making a major contribution to our research!

-- Shawn

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Message 70240 - Posted 4 May 2011 8:38:21 UTC - in response to Message ID 70152.

As I had alluded to earlier, I am working on a protein to bind to the hemagglutinin protein (MV-H) of measles virus. Measles is a significant cause of childhood morbidity and mortality worldwide. Measles virus enters our cells in a two-step process: an attachment protein allows it to bind to a host cell receptor, which allows a second protein to mediate fusion of the virus to the host cell. MV-H is the attachment protein responsible for the first step, and SLAM (or CD150) is the predominant host cell receptor to which MV-H binds.

Recently, researchers were able to solve crystal structures of MV-H in complex with SLAM. As you might imagine, a high-resolution structure of the target (MV-H) is crucial to our design efforts, so we were quite excited about this development!

In several recent design efforts in the Baker lab, such as with influenza, we identified several "hotspot" residues on the target surface; although these hotspots made up only a small portion of the surface, they contributed a very large proportion to the binding interaction. We designed disembodied amino acid residues ("stubs") to interact specifically in these regions and then fit the rest of the designed protein accordingly around these stubs.

Likewise, in our measles project, we have identified hotspots on MV-H where we would like our protein to bind. One interesting challenge unique to measles is that our hotspot approach focuses on charged amino acids such as lysines to bind to oppositely charged regions of MV-H. Most of the previous success we have had involved binding to hydrophobic regions, but we'd like to push the envelope on what we can do!



I think the final designed protein binder will include some subset of the amino acids depicted above. It would bind MV-H where it would have bound to SLAM, thereby preventing its entry into our cells. However, in order to find a possibly successful design, we have to search through an astronomically large number of configurations, and the assistance of Rosetta@home users is of critical importance to this effort. So once again, thank you very much for your contributions to our research! Please let me know if you have any questions or comments!

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Message 70275 - Posted 7 May 2011 20:22:07 UTC

What will your tasks be called so we know when they come to our systems?

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Message 70282 - Posted 8 May 2011 12:40:03 UTC

Hi!
My computer is crunching something like this at the moment:

MVH_2s_K_2q6m_ProteinInterfaceDesign_20110505_26665_45_0

And I think this must be what we're talking about ;)
Am I right?

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Message 70289 - Posted 8 May 2011 20:03:18 UTC - in response to Message ID 70282.

Hi!
My computer is crunching something like this at the moment:

MVH_2s_K_2q6m_ProteinInterfaceDesign_20110505_26665_45_0

And I think this must be what we're talking about ;)
Am I right?


Sounds right to me!
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Message 70296 - Posted 9 May 2011 18:58:15 UTC - in response to Message ID 70275.

What will your tasks be called so we know when they come to our systems?


Hi!
My computer is crunching something like this at the moment:

MVH_2s_K_2q6m_ProteinInterfaceDesign_20110505_26665_45_0

And I think this must be what we're talking about ;)
Am I right?


Hey, this is correct! I'll be submitting a lot of different jobs for these guys with different strategies, but all of them will begin with "MVH_" and will contain "ProteinInterfaceDesign" in the middle!

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Message 70320 - Posted 11 May 2011 17:20:11 UTC
Last modified: 11 May 2011 17:36:00 UTC

I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this. I cannot sit for ages checking on the task properties.

Is it possible to predict when a checkpoint will take place?

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Message 70321 - Posted 11 May 2011 22:50:33 UTC - in response to Message ID 70320.

I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this. I cannot sit for ages checking on the task properties.


Ditto on complaint. Four hours between checkpoints is a bit much!

BTW, I have a program manager that I use solely for watching when tasks checkpoint. I have EF Commander Free permanently pointed at the "...\Application Data\BOINC\slots" folder.

This program updates dynamically whereas the Properties window is a snapshot.

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Message 70330 - Posted 13 May 2011 0:00:56 UTC - in response to Message ID 70321.

I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this. I cannot sit for ages checking on the task properties.


Ditto on complaint. Four hours between checkpoints is a bit much!

BTW, I have a program manager that I use solely for watching when tasks checkpoint. I have EF Commander Free permanently pointed at the "...\Application Data\BOINC\slots" folder.

This program updates dynamically whereas the Properties window is a snapshot.


Thanks for the feedback, we're looking into this!

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Message 70331 - Posted 13 May 2011 3:17:08 UTC - in response to Message ID 70330.

I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this. I cannot sit for ages checking on the task properties.


Ditto on complaint. Four hours between checkpoints is a bit much!

BTW, I have a program manager that I use solely for watching when tasks checkpoint. I have EF Commander Free permanently pointed at the "...\Application Data\BOINC\slots" folder.

This program updates dynamically whereas the Properties window is a snapshot.


Thanks for the feedback, we're looking into this!


Also, have you been having problems with one particular set of jobs, or is it a more general problem with many different Rosetta@home jobs?

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Message 70333 - Posted 13 May 2011 15:46:13 UTC

Hi everybody,

Our paper describing the design of flu inhibitors using Rosetta @ Home has just been published as a Research Article by Science.

To summarize the results, using the resources provided by your computers we were able to identify ~80 designed proteins that might be candidates as flu diagnostics and inhibitors. Two of these proteins bound to Spanish and avian flu hemagglutinin quite tightly and one of them was crystallized in the presence of Spanish flu hemagglutinin to show that the designed interaction is exceptionally accurate.

Beyond the specific application to the flu, your resources have been extremely useful in getting our methods up to scratch to deal with this and other very challenging problems. If you follow some of the previous posts in this thread you can see the sort of problems that we're hoping to address with this new method and your contributions. Hopefully, these will help address some significant outstanding challenges in the development of antivirals and in studying recalcitrant biological questions.
____________

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Message 70334 - Posted 14 May 2011 1:03:22 UTC - in response to Message ID 70331.

[quote]I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this.


Ditto on complaint. Four hours between checkpoints is a bit much!

Thanks for the feedback, we're looking into this!


Also, have you been having problems with one particular set of jobs, or is it a more general problem with many different Rosetta@home jobs?


I'm fairly sure it was one of the Measles Protein interface design tasks - MVH etc. Most tasks update ok.

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Message 70335 - Posted 14 May 2011 11:13:03 UTC
Last modified: 14 May 2011 11:16:06 UTC

@ Sarel. It's good to see the results of our crunching being of benefit.

@ Shawn. I have a preference of 4 hours (i.e. 14400 seconds) of runtime. One of the MVH tasks (this one) ran for 21381 seconds and yielded a paltry 2.65 points credit. It completed only 5 decoys.

Another task (second one) ran for 27798 seconds and completed 12 decoys and I received 59.17 points, also well below the average rate for this machine on Rosetta.

Both of these tasks had watchdog force a shutdown. What occurred to me is that each decoy seems to take quite long to complete causing the last one to run well beyond the preferred work unit run time. It appears that the forced shutdown by watchdog is wasting valuable crunching time.

What to do about this is difficult to answer:
1. Should we increase the preferred runtime so that the proportion of time wasted when watchdog ends the unit is reduced?
2. We are not able to select different types of work units for each profile (as is the case at WCG) in order to minimise time lost. This would help.
3. Does checkpointing occur only at the end of each decoy? Is it possible to change this?
4. Is it possible to reduce the run length of the decoys?

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Message 70337 - Posted 14 May 2011 16:53:32 UTC
Last modified: 14 May 2011 16:58:11 UTC

From observing my own machine, and your comments, it seems that some models are taking dramatically longer (say 5x) then others. This is why the runtime estimates are difficult. When the first 4 models complete in say 3 hours, one would estimate there is easily time to complete one more within your 4hr preference, and so one more begins. But that 5th one happens to run for over 4 hours itself (it takes 4 hours over preferred runtime for the watchdog to be envoked). I should point out that the reason the watchdog waits 4 hours after end of runtime preference is that this is typically enough time to complete that last model and end without the watchdog's intervention.

This is also the reason for sporatic credit granted. If you happen to run without hitting a long-running model, you will get better credit, because credit is granted on a per model average of runtime, across all project hosts, for the specific protein and method being used. Since others are often hitting a long running model in their run, their average time per model swings higher then the machine that got lucky and did not hit any of those.

Changing the runtime preference really doesn't improve you odds, it just depends on whether the last model under review at the end of the runtime preference happens to be long-running.
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Message 70338 - Posted 14 May 2011 17:36:27 UTC - in response to Message ID 70335.
Last modified: 14 May 2011 17:40:32 UTC

@ Sarel. It's good to see the results of our crunching being of benefit.

@ Shawn. I have a preference of 4 hours (i.e. 14400 seconds) of runtime. One of the MVH tasks (this one) ran for 21381 seconds and yielded a paltry 2.65 points credit. It completed only 5 decoys.

Another task (second one) ran for 27798 seconds and completed 12 decoys and I received 59.17 points, also well below the average rate for this machine on Rosetta.

Both of these tasks had watchdog force a shutdown. What occurred to me is that each decoy seems to take quite long to complete causing the last one to run well beyond the preferred work unit run time. It appears that the forced shutdown by watchdog is wasting valuable crunching time.


What makes you think the watchdog forced a shutdown? The line (from the stderr out):
BOINC :: Watchdog shutting down...
appears for all of the workunits including those ending just prior to reaching the preferred runtime. The watchdog will shut down mid-model once the workunit has reached the preferred runtime plus 4 hours. Neither of your examples had run that long. I did once speculate that new conditions in addition to the runtime limit and the number of models limit had been introduced but never received any response. In that case though, workunits were ending far earlier than expected but completing far fewer than 100 models.

I checked my MVH tasks for credit and mine too seem to receive fewer credits than average (but then I don't usually pay attention to credits so this is a pretty wobbly impression). However I did complete far more models than you, 389 and 226 in just under 10 hours for 95.72 and 75.44 credits. Generally speaking, this discrepancy just means that this particular type of workunit runs less efficiently on your(my) machines than on other machines compared to the efficiency with which you(me) run other types of workunits. Given the very large variety of workunits on Rosetta this is bound to happen occasionally. I suppose it's possible that the initial second per model estimate was dramatically wrong(a typo perhaps) and everyone's credit is significantly less than expected. In your case you most likley hit upon an interesting model quite early on and so didn't complete many models in total, thus low total credit. Mod.sense wrote a nice explanation of how this works but I can't put my finger on it at this moment.



Best,
Snags


edited to add: Wow, I really am a slow writer. :/

And to add my appreciation to the scientists for posting here. Though you post too infrequently to satisfy when you do post you do an excellent job of explaining what you are working on. Thank you.

(That said, I still fantasize about a catalog cross-referencing proteins and strategies so one could know what was being worked on by looking up the workunit name.)

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Message 70339 - Posted 14 May 2011 17:44:47 UTC - in response to Message ID 70337.

Thanks for the response, Mod.Sense.

I agree with you:

Changing the runtime preference really doesn't improve you odds, it just depends on whether the last model under review at the end of the runtime preference happens to be long-running.


However, what I mean is that the proportion of my total run time which did useful crunching will be higher if a longer target CPU run time were selected. If I had a 16 hour run time preference, I would waste a much smaller proportion of my crunching time if 4 hours were wasted on every work unit than would be the case if I merely used the default of 3 hours per work unit and then wasted 4 hours at the end of each one.

Should the administrators not be suggesting that we increase this run time preference if the machine is always on? In particular since it seems that there is no way of determining (or selecting) which work unit type we will receive. In my limited experience, the MV-H tasks seem to be prone to this long checkpoint issue.

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Message 70345 - Posted 15 May 2011 6:15:25 UTC

Warped, actually, since even the long-running models generally will complete before the watchdog steps in, it is not a major benefit. But I see your point. If any effort is being wasted, then having fewer chances for it to occur (i.e. fewer WU completions per day) would further minimize any impacts.

Snags, yes the watchdog shutting down message is normal. It indicates that the watchdog, and other processes are ending normally... not that the watchdog has taken any action.
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Message 70346 - Posted 15 May 2011 6:17:05 UTC

Let's get back on-topic in this protein-protein interfaces thread. We take the rest of the discussion back to other threads.
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Message 70348 - Posted 15 May 2011 12:22:11 UTC

Mod - maybe you can move the other discussion to whatever place it belongs to get this thread back in shape (you can delete my post after you move the non topic discussion)

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Message 70361 - Posted 17 May 2011 1:52:55 UTC

Hey guys, thanks for the feedback on the MVH jobs. I'll see what I can do to keep the tasks more manageable.

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Message 70367 - Posted 17 May 2011 22:49:30 UTC

I wanted to address some of the issues posted recently by Rosetta@home users in this thread, as they pertained specifically to protein interface design.

As you might be aware, these types of jobs (including my MVH ones) tend to be a bit "jumpy" in terms of how long the trajectories take. Sometimes, one hour of CPU time might yield a lot of structures (and 100 credits). Other times, a trajectory on one model might take a long time, and nearly 6 hours of CPU time might yield less than 3 credits, as unfortunately happened to Warped. The amount of credit granted is normalized for each job type, so hopefully next time you are assigned one of these jobs, you'll be lucky enough to get more credits.

If you are assigned one of the longer tasks (and we have no way of knowing beforehand which tasks are longer), you unfortunately won't get as many credits. But on the other hand, these longer trajectories tend to result in better design models--if you're naturally optimistic, you might be happy that you've stumbled into one of the tasks that are more likely yield an MVH inhibitor! =)

In the meantime, I will be submitting new MVH jobs but managing the workunits so that don't take as long to compute and are less "jumpy" in terms of overall length. Sarel has also developed new options for our protocols that would also help in this regard, and David K and other members of the lab are working hard to get those features integrated into Rosetta@home.

Thanks again for your contributions!

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Message 70386 - Posted 23 May 2011 5:29:39 UTC

I promised an update on my Ebola project, and I've recently focused more of my time on this target, so I thought I'd give you guys another update!

As you might know, Ebola virus causes terrible hemorrhagic fever, which usually results in death in the patient 6-9 days after the onset of symptoms. Unfortunately, there are currently no therapeutics available for human use, but hopefully, we can do something to change that.

Recently, researchers at the Scripps Institute were able to determine the crystal structure of the Ebola virus surface glycoprotein (GP) in conjunction with a neutralizing antibody (KZ52) from a human survivor of a 1995 outbreak in the former Zaire. KZ52 interacts with both the GP1 and GP2 subunits of the GP complex, but more so with GP2.

We're trying to use the hotspot method (which I mentioned during my discussion of the measles project) to design our protein, which would bind GP in roughly the same place that KZ52 also binds. A very preliminary picture of some of stubs we're considering looks as follows:



Of course, computational design of protein binders is tricky, and each specific project also has its own particular challenges. In this case, there isn't much surface area for KZ52 to interact with GP, but we're hoping to design a binder that can make more use of the surface that is available.

Thanks once again for being involved with Rosetta@home! I'm really excited about this project, and I would love to share it with everyone, so once again, please let me know if you have any questions or comments!

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Message 71811 - Posted 16 Dec 2011 16:43:19 UTC

Hello,

as I have described in the LigDes thread originated by Mr. Moretti, I am pretty interested in the scientific progress of Rosetta@home, including projects mentioned in this thread like Ebola virus surface glycoprotein research.

As it would be nice to keep up everyone with your science, please do not hesitate to post us some updates! :) They are always very welcome. :)

Best Regards from Warsaw,
a.m.
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Message 72155 - Posted 17 Jan 2012 1:08:52 UTC

In response to recent requests for an update on what we are doing with your donated computer time, here goes:

The communication networks inside every one of our cells depend in many cases on proteins interacting with one another. When these communication networks go awry, cancer often results. I'm using Rosetta to design proteins that will interfere with three protein-protein interactions often involved in cancer. I'll tell you about the first project below, and the others shortly.

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:

<http://en.wikipedia.org/wiki/MDM4>
<http://en.wikipedia.org/wiki/Mdm2>
<http://en.wikipedia.org/wiki/P53>

Thanks for lending us your spare computer time. Projects like this one require so much computational time that they would be impossible without you. I'll post more about the other two projects at a later date.

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Message 72157 - Posted 17 Jan 2012 10:29:54 UTC

How do I know I am running your WU's?

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Message 72161 - Posted 17 Jan 2012 18:53:21 UTC

Good call. Work units involving the design of proteins to bind to Mdm4 will contain the word "Mdm4" in their name.
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Message 72162 - Posted 17 Jan 2012 19:29:33 UTC

As promised, here is the continuation of the story begun in message 72155:

Project 2:
The second of these interactions involve a protein called EED and another called Ezh2. If you think about DNA as a ladder, then each of our cells has about six billion rungs worth of ladder. In order to keep all of that DNA from getting hopelessly tangled, our cells keep it on little spools, called histones, when not in use. Think of this like a massive film archive. It turns out that there is a lot of DNA that never gets used, so the cells put special flags on those spools (histones) that say something like "never use this section of DNA". EED is a large protein that attaches to those flags and brings along Ezh2, a "flagging machine" for the ride. EED makes sure that Ezh2 adds flags to histones that are supposed to get them, and not to histones carrying DNA the cell actually wants to use. Some cancer cells reduce the amounts of EED or Ezh2 to prevent flagging of DNA regions that they want to use to take over our bodies. Other cancer cells expand the amounts of EED or Ezh2 to flag DNA regions that are getting in the way. Scientists are working hard to better understand how EED, Ezh2, and friends work in normal cells and what goes wrong in cancer cells. Some are trying to develop drugs that prevent Ezh2 from attaching to EED. This means that the drugs have to stick to EED more tightly than Ezh2. Although Ezh2 attaches relatively loosely to a large patch on the surface of EED, their aren't any drugs yet available that do what we want.

I'm trying to make proteins that will do the same job. I used Rosetta@home to design a set of proteins that mimic Ezh2 in order to block it from attaching to EED. Just to give you a sense of how much computing I need for a project like this, I submitted just under two million work units to Rosetta@home, and donor's computers ran my protocol just under a billion times to give me about 54 designs to look at, from which fourteen were suitable for testing. This took about a month to run on Rosetta@home. From initial experiments, it looks like eight of the designs stick to EED, and one in particular sticks three times better than the Ezh2 found in our cells. Now I'm working to improve the best design at the lab bench and hope to send it to co-workers for testing in living cells. There's still a lot of work to be done to make sure that everything is working right with this design, but I want to give a big thank-you to all of you who donated your computer time to make this possible! For more information about EED, Ezh2, and related proteins, please visit:

<http://en.wikipedia.org/wiki/EED>
<http://en.wikipedia.org/wiki/SUZ12>
<http://en.wikipedia.org/wiki/EZH2>
<http://en.wikipedia.org/wiki/PRC2>
<http://en.wikipedia.org/wiki/Polycomb-group_proteins>

Work units for this project carried the word "EED" in their name. I'll post more about the third project shortly.
____________

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Message 72163 - Posted 17 Jan 2012 19:54:40 UTC - in response to Message ID 72162.
Last modified: 17 Jan 2012 19:54:58 UTC

Great to hear from you!

When only I get some free time, I'll make some translations & news basing on your posts. I am pretty sure MadMax and others will be happy as well.

Kind regards from BOINC@Poland,
a.m.

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Message 72164 - Posted 17 Jan 2012 20:24:59 UTC

And here is the third of the projects I mentioned in posts 72162 and 72155:

Project 3:
The third of these interactions involve a protein called RhoA and another protein called Dbs. Most of the cells in our bodies have the ability to crawl around on command. This is really important when we develop as embryos. Cells are crawling everywhere to get into the right spot and morph us from something that looks like an alien into something that looks like a baby. As adults, must of our cells have stopped crawling around and settled down to do their respective jobs. If you have ever cut yourself and noticed that the cut got smaller and smaller as it healed, that's because the skin cells on the edges of the cut crawled into the gap to seal it up. Cells have rigid skeletons to give them shape and keep their insides organized, so in order the crawl around, they have to constantly rearrange their skeletons as they go. Just imagine the information processing and communication that has to happen inside the cell for this to happen in an organized manner. Imagine a circus tent with a thousand people inside it and they all decide to move the tent a mile away without taking it down or anyone leaving the tent. There are lots of protein-protein interactions required for this to work right in our cells. One of these is a protein switch called RhoA. RhoA can be either in the "on" position or the "off" position. When a cell wants to crawl around, it uses Dbs to switch RhoA to the "on" position so that the cell's skeleton will be rearranged faster. When cells don't want to move around, they use proteins called RhoGAPs to turn RhoA "off" so that the cell's skeleton is rearranged more slowly. Since cancer cells grow like crazy, eventually things become crowded where they live and so some of the cancer cells decide to strike out on their own, colonizing new parts of our bodies. Doctors call this "metastasis" and it's bad news for cancer patients. In order to start crawling to a new home, a cancer cell speeds up rearrangement of the it's skeleton, either by expanding the amounts of RhoA or Dbs in the cell or by reducing the amounts of RhoGAPs so that they aren't around to turn off RhoA. RhoA is a very flexible protein and no one has been able to develop a drug that will keep RhoA turned "off" by preventing Dbs from attaching and switching it "on".

I'm trying to make proteins that will attach to RhoA and prevent Dbs from switching it "on". This is a tricky venture, since RhoA is very, very flexible and attaches only loosely to Dbs. I used Rosetta@home to design a set of 16 proteins to do the job, but none of these stuck to RhoA when tested. In the coming months I'll use Rosetta@home to try a different design strategy that I think will work. If successful, these proteins would be the first RhoA inhibitors available and should provide scientists a new tool to better study how RhoA works and how cancer cells take control of it. Work units for this project will contain the word "RhoA" in their name.

Thanks again for all of your donated computer time. You're help makes these projects possible!

____________

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Message 72168 - Posted 17 Jan 2012 23:48:14 UTC - in response to Message ID 72164.

Moody:

You said "Thanks again for all of your donated computer time. You're help makes these projects possible!"

I want to say "Thank you for all your work. You're a reason why this project is worthwhile!"

Mark

____________

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Message 72171 - Posted 18 Jan 2012 9:52:07 UTC

Very interesting! If only I knew this sooner :D

I do have a question, are these projects the ones that dr Baker mentions in his journal?

I also want to describe a new research direction we are now embarking on aimed at future cancer therapies. There are a small set of proteins which are frequently found at much higher levels than normal on the surface of cancer cells. We are starting to design small proteins which bind tightly to these tumor cell markers. If we are successful, we have collaborators who will be testing these proteins for their ability to target cancer cell killing agents to the tumors.


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Message 72184 - Posted 20 Jan 2012 6:59:25 UTC

The projects that James is working on that he has described below all involve targeting proteins that are on the inside of the cell. the projects we are just beginning target proteins on the outside of cancer cells. since the rosetta@home methods allow in principle the design of tighly binding proteins to any target, we have a lot to do!
____________

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Message 72208 - Posted 23 Jan 2012 21:50:58 UTC

moody
Many thanks for the information and update on current work and goals of the project!

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Message 72713 - Posted 9 Apr 2012 21:36:30 UTC

Those of you who followed this thread from the beginning might be aware of efforts of Sarel and Tim, as well as others in the lab, to design binders to influenza virus hemagglutinin. That project has been very successful, as Rosetta@home contributors helped identify two proteins (HB36 and HB80) that bound to group 1 influenza A subtypes (such as H1 and H5) with very high affinity. For the more technically inclined, you can read about this development here: http://www.sciencemag.org/content/332/6031/816.full

Given the success of this project, more scientists in the lab are now working on designing new binders to bind other influenza subtypes, such as H3. In the long term, we would like to develop a variety of antibodies that bind to different combinations of influenza subtypes with different specificities, which could offer potentially interesting therapeutic and diagnostic applications. You will be seeing (and may have already seen) jobs with descriptions such as "H3 Influenza Binder".

Hopefully, that helps clarify what you are volunteering your computational resources towards! Thank you so much for your time, not only with your computers, but also providing us valuable feedback on these forums!

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Message 73691 - Posted 24 Aug 2012 18:41:10 UTC

Computationally-designed Wnt Surrogate Protein

Wnt protein is widely recognized as a crucial component of vertebrate development. For more than three decades, scientists have sought to understand the structure of this important molecule. Unfortunately, obtaining a detailed understanding of Wnt's structure has proven to be quite difficult. After much work, a research group led by Dr. K. Christopher Garcia at Stanford University published the structure of Wnt bound to its target protein in June 2012. This binding event is partially facilitated by a fatty acid, an addendum to Wnt that is known to complicate molecular structure determination.
Wnt protein is secreted into the space around growing cells. It then binds to its target (Frizzled protein) on the surface of some of these cells. The attachment of Wnt to Frizzled leads to the transmission of a signal into the cell, which alters the development and physiological behavior of that cell by changing the way that the cell accesses the information in its DNA. This signaling event is modified by a number of supplementary proteins in the same pathway.
Our current project aims to replace naturally occurring Wnt with a surrogate protein through protein engineering methods. We first look at the structure of Wnt's target protein and use computer models that rely on the Baker Lab's Rosetta computational design technology to determine chemically favorable binding locations. We then look at how we might combine the mixture of possible binding sites into an optimal binding pattern. Finally, we use the distributed computing abilities of the BOINC network to attempt to find a previously-studied protein that can be seeded with our binding pattern. In a successfully engineered project, the newly created protein will show its ability to bind to the target (Frizzled in this case) during validation tests.
In parallel with our standard techniques, which already rely heavily on the CPU time of our Rosetta@home participants, we have submitted the structure of the target and a potential binder to FoldIt players. FoldIt will allow people to interact directly with the Rosetta scoring algorithms, allowing the binding region to be custom-designed with the help of real-time feedback.
The creation of a successful Wnt-surrogate binder will signify an important advance in our ability to quickly employ emerging scientific data to facilitate the clinically-focused goals of our team of molecular engineers. Binding to Frizzled should allow us to interrupt the Wnt signaling pathway in a way that will be immediately useful as a tool for the many laboratories that are focused on human development. Looking farther into the future, control of the Wnt signaling pathway may allow us to limit the growth of Wnt-mediated tumors and may even prove useful in tissue engineering. Through the efforts of the scientists in the Baker Lab, our partners who dedicate their computing time to Rosetta@home, and FoldIt players, we will begin testing the preliminary designs for a Wnt surrogate at our principal laboratory in Seattle, Washington in late August 2012.

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Message 73692 - Posted 24 Aug 2012 19:54:06 UTC

Thanks for the update!
____________

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Message 73694 - Posted 24 Aug 2012 23:51:39 UTC

Thanks for the new information. Always interested to hear what my workunits might be contributing to.

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Message 73707 - Posted 27 Aug 2012 17:31:16 UTC

Thanks for new information from Science part!

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Message 73844 - Posted 16 Sep 2012 10:54:17 UTC

Hi.
Last days i see in queue lof of WUs from protein-protein interfaces series with names like
Ebolanator3_..._ProteinInterfaceDesign_2Sep2012...
It new research target?
Probably connected to Ebola virus? Or it just similar name?

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Message 73845 - Posted 16 Sep 2012 18:10:14 UTC - in response to Message ID 73844.

Yes! we are now trying to design drugs that prevent Ebola from killing people-with your help hopefully we will succeed!

Hi.
Last days i see in queue lof of WUs from protein-protein interfaces series with names like
Ebolanator3_..._ProteinInterfaceDesign_2Sep2012...
It new research target?
Probably connected to Ebola virus? Or it just similar name?


____________

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Message 74822 - Posted 2 Jan 2013 9:50:36 UTC - in response to Message ID 72155.

In response to recent requests for an update on what we are doing with your donated computer time, here goes:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. Thanks for lending us your spare computer time. Projects like this one require so much computational time that they would be impossible without you. I'll post more about the other two projects at a later date.


Any news about this project??

____________

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Message 75635 - Posted 20 May 2013 17:07:14 UTC

To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:

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Message 75648 - Posted 21 May 2013 9:21:00 UTC - in response to Message ID 75635.

To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4.


Thats' great!!!!
____________

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Message 75683 - Posted 30 May 2013 1:40:57 UTC - in response to Message ID 75635.
Last modified: 30 May 2013 1:42:34 UTC

Moody:

Thanks VERY much for the update. Rosetta is the only BOINC project for which I look at the "Science" message board before turning to the "Number Crunching" board. I do so because of posts such as your post. It is truly fascinating to read about the science being explored and created!

Thanks again.
____________

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Message 75686 - Posted 30 May 2013 12:49:19 UTC

2 moody
Thanks for science update!

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Message 75771 - Posted 18 Jun 2013 18:30:21 UTC

To our awesome Rosetta@Home contributors:

At the beginning of 2012 we told you that it looked like eight designed proteins stuck to EED as desired. Further experiments showed us that of our eight initial hits, only two were real, and those two proteins were too weak to be improved with laboratory techniques. We've gone back to the drawing board, using more aggressive modeling techniques to design better binding proteins to mimic Ezh2. It turns out that no known protein structure is similar enough to the Ezh2 binding helix to allow us to simply transplant key amino acids from Ezh2 to a new host protein, as we tried before. What were doing now is making new proteins from scratch that have the exact shape that we need to mimic Ezh2. The "EED" runs you'll now see on Rosetta@Home are structure prediction of designs to see if they have the desired curvature when Rosetta folds them up. Thanks again for all of your donated computer time!

For those new to this thread/message board, here is what I wrote previously about the EED project:

The second of these interactions involve a protein called EED and another called Ezh2. If you think about DNA as a ladder, then each of our cells has about six billion rungs worth of ladder. In order to keep all of that DNA from getting hopelessly tangled, our cells keep it on little spools, called histones, when not in use. Think of this like a massive film archive. It turns out that there is a lot of DNA that never gets used, so the cells put special flags on those spools (histones) that say something like "never use this section of DNA". EED is a large protein that attaches to those flags and brings along Ezh2, a "flagging machine" for the ride. EED makes sure that Ezh2 adds flags to histones that are supposed to get them, and not to histones carrying DNA the cell actually wants to use. Some cancer cells reduce the amounts of EED or Ezh2 to prevent flagging of DNA regions that they want to use to take over our bodies. Other cancer cells expand the amounts of EED or Ezh2 to flag DNA regions that are getting in the way. Scientists are working hard to better understand how EED, Ezh2, and friends work in normal cells and what goes wrong in cancer cells. Some are trying to develop drugs that prevent Ezh2 from attaching to EED. This means that the drugs have to stick to EED more tightly than Ezh2. Although Ezh2 attaches relatively loosely to a large patch on the surface of EED, their aren't any drugs yet available that do what we want.

I'm trying to make proteins that will do the same job. I used Rosetta@home to design a set of proteins that mimic Ezh2 in order to block it from attaching to EED. Just to give you a sense of how much computing I need for a project like this, I submitted just under two million work units to Rosetta@home, and donor's computers ran my protocol just under a billion times to give me about 54 designs to look at, from which fourteen were suitable for testing. This took about a month to run on Rosetta@home. From initial experiments, it looks like eight of the designs stick to EED, and one in particular sticks three times better than the Ezh2 found in our cells. Now I'm working to improve the best design at the lab bench and hope to send it to co-workers for testing in living cells. There's still a lot of work to be done to make sure that everything is working right with this design, but I want to give a big thank-you to all of you who donated your computer time to make this possible! For more information about EED, Ezh2, and related proteins, please visit:

<http://en.wikipedia.org/wiki/EED>
<http://en.wikipedia.org/wiki/SUZ12>
<http://en.wikipedia.org/wiki/EZH2>
<http://en.wikipedia.org/wiki/PRC2>
<http://en.wikipedia.org/wiki/Polycomb-group_proteins>

Work units for this project carried the word "EED" in their name.

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Message 75773 - Posted 19 Jun 2013 4:23:42 UTC

Exciting news, thanks for the update!
____________

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Message 75781 - Posted 20 Jun 2013 10:31:35 UTC

Thanks for this totally inspiring update (I'm a recent returnee to R@H after a spell on another project).

While reading your update, my over-riding thought is how amazing it is that we (i.e. you, the scientists, or the human race in general) now know all this incredibly complex stuff, that wasn't known a few years ago. Whenever I read these updates about the mechanisms of proteins, bindings, targets, interactions, etc, I'm in awe of the scientific process - and every little new thing that is learned can never be taken away from us; it's a step on the road that will never be undone. I really believe that complete cures will be found one day, and it'll be because of work like this.

Told you I found it inspiring. Thanks again for the update.
____________
Alver Valley Software Ltd - Contributing ALL our spare computing power to BOINC, 24x365.

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Message 75987 - Posted 28 Aug 2013 19:45:17 UTC - in response to Message ID 75635.

To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:


They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise.


Any news if the MB17 worked on the cancer cells?

____________

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Message 75988 - Posted 28 Aug 2013 20:59:32 UTC - in response to Message ID 56754.
Last modified: 28 Aug 2013 21:11:55 UTC

Hello,

My name is Sarel Fleishman and I've been a postdoc in the Baker lab for the past two years. My project deals with structure prediction and design of protein-protein interfaces and you may have read a few messages from me on CAPRI and structure prediction. Now, I'm very excited to tell you that with minirosetta v1.40 we can do design work using the massive computational power of Rosetta @ Home.

A few words on protein-interface design. The primary challenge in this field is to be able to take a protein target and to design another protein that would bind to it in a specific way. Nature provides us with hundreds of thousands of examples of such protein-binding events. Such events are used for the amplification of signals within and between our cells in processes related to growth and development as well as for recognition, e.g., in the immune system. When such signals go awry, protein interactions become the center of events for uncontrolled cell growth, or cancer. Many pathogenic bacteria and viruses hijack molecular recognition processes to promote their growth and proliferation causing sickness and endangering lives.

These processes being so central to both health and disease it is hardly surprising that being able to manipulate them computationally is a major ongoing goal of molecular biology. Being able to target a protein and bind to it would open the way to novel therapies for a large number of diseases.

We have selected a small number of protein targets for which we want to design protein binders. As an example, one such target that I have been working on is cholera toxin. This protein is a crucial component of the process by which the cholera bacterium causes cells in the gut to excrete large amounts of water, which causes death from dehydration (see the following wiki page for more details: http://en.wikipedia.org/wiki/Cholera). We have developed a computational strategy that allows us to design proteins to bind to the cholera toxin and disable it.

We are now in the process of testing this and similar design methodologies on a number of other targets. But expanding the number of targets we quickly realized that we need a lot more computational resources to adequately address this problem. This is why we have turned to Rosetta @ Home and to you for your help in this exciting project.

The simulations that you will see in protein interface design will be quite different from one another. In each case we tailor the design strategy to the particular protein target, stressing, for instance, the formation of interactions with a specific key region on the protein surface. In general, though, the simulations will involve docking steps, where the protein binder moves with respect to the target and design, where amino acid residues on the surface of the protein binder change in order to better attach to the target. Promising protein designs are synthesized in our lab and tested for binding to the target protein.

I am working on this project with my colleagues Eva and Jacob, and for each target that we test using Rosetta @ Home we will provide background material on the target and why we selected it on this thread.

These design simulations tend to use more memory than many prediction runs (typically at most 800Mb). We will test different ways of reducing this memory load so that our simulations could run on all participating computers in the Rosetta @ Home project, but initially we will only run these simulations on computers that can handle this memory restriction. Please report any problems that you might have with this simulation.

Thank you very much for participating in this project! I'm looking forward to getting feedback and results from you.

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Message 76458 - Posted 19 Feb 2014 23:32:24 UTC

Hi all - as the IPD/Baker lab technical writer, I will be regularly updating R@home message boards with research updates. I've created a new thread for this (R@h Research Updates) but will also be trying to update project-specific threads such as this one!

Computational Design of an Enzyme-Based Protein Inhibitor

Computational design of protein-protein interactions to generate new binding proteins for any specified site or surface of interest on a target protein can lead to a number of novel therapeutic and biochemical tools. As an example, in recent work by Sarel and collaborators, novel proteins have been designed to bind to a conserved epitope on influenza hemagglutinin.

Computational design of a protein that binds polar surfaces, however, has not been previously accomplished. In a September 2013 paper published in the Journal of Molecular Biology, Procko et al describe the computational design of a protein-based enzyme inhibitor that binds the polar active site of hen egg lysosome (HEL). A hot spot design approach first identified key, conserved interaction residues that contribute to much of the binding energy to HEL within a large interface. Rosetta software then identified a protein scaffold that supported the hot spots while also optimizing contact with surrounding surfaces to obtain a high affinity protein binder.

Follow this this link to read more about this exciting work: http://depts.washington.edu/bakerpg/drupal/Computational-design-of-a-protein-based-enzyme-inhibitor-pub

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Message 76472 - Posted 20 Feb 2014 22:46:26 UTC - in response to Message ID 76458.

Awesome news :)

Does IPD = Institute for Protein Design?
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Message 76481 - Posted 21 Feb 2014 21:08:02 UTC - in response to Message ID 76472.

Awesome news :)

Does IPD = Institute for Protein Design?


Yes! IPD is the Institute for Protein Design. You can find more research updates in the news section of the IPD's website here:

http://depts.washington.edu/ipd/

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Message 76584 - Posted 3 Apr 2014 17:48:58 UTC - in response to Message ID 75987.

Tom,

I apologize for the long delay in getting back to you. The top MB17 variants bind Mdm4 (Mdmx) or Mdm2 tightly enough to yank them out of human cells and trigger the self-destruction pathway (p53 apoptosis pathway) in colon cancer cells. We're now looking at other types of cancer cells. We're now working on making the MB17 variants bind more tightly to Mdm4 or Mdm2. We're also studying how the p53 pathway works using the MB17 variants. The work is on-going so we don't have the full story yet. MB17 and its variants were intended to aid as cancer research tools and we're cautiously optimistic that they'll work to that end. We're hoping that the things we learn will fuel the development of new kinds of cancer drugs and treatment strategies. You likely have recently seen Rosetta@Home jobs with either Mdm4, Mdm2, or MB17 in the name. These represent ongoing efforts to design improved Mdm4 and Mdm2 binding proteins using new tools in the Rosetta software suite.

Once again I want to give a big thank-you to you and all of our Rosetta@Home contributors!
_______

[quote]To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:


They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise.


Any news if the MB17 worked on the cancer cells?

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Message 76599 - Posted 8 Apr 2014 13:34:26 UTC

Thanks for the update: always good to see our crunching has practical application.
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Message 77641 - Posted 11 Nov 2014 12:05:09 UTC - in response to Message ID 76584.

The top MB17 variants bind Mdm4 (Mdmx) or Mdm2 tightly enough to yank them out of human cells

Hi moody, that sounds very exciting - can you expand a bit on how exactly this occurs?

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Message 80390 - Posted 18 Jul 2016 10:27:03 UTC

Hi all!

Sorry if this is not a right thread to post it, but...

Will this article be useful in rosetta's calculations methods?

http://www.pnas.org/content/early/2016/07/12/1603929113.abstract


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Message 80413 - Posted 22 Jul 2016 12:18:28 UTC - in response to Message ID 80390.

Will this article be useful in rosetta's calculations methods?

It looks like something you might be able to do on a GPU.

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