amyloid fibril structure prediction

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phil
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Message 31077 - Posted: 13 Nov 2006, 19:12:37 UTC

This thread will feature discussion of a new type of simulation being introduced in the 5.40 release. We are trying to build high-resolution models of the fibrils formed by medically-relevant amyloids. The first prediction jobs will focus on the Alzheimer\'s beta(1-40) fragment. More details to follow.
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Message 31092 - Posted: 13 Nov 2006, 22:26:55 UTC

Amazing. I\'m proud to help you guys at least trying to discover something. You may count with my pc\'s 100% crunching Rosetta.
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Message 31094 - Posted: 13 Nov 2006, 23:34:37 UTC

I also commend the research going on, Especially now with the Alzheimer\'s research.

G^R
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Message 31106 - Posted: 14 Nov 2006, 4:46:59 UTC
Last modified: 14 Nov 2006, 14:59:49 UTC

Hi guys. Thanks for the posts. I too am excited about harnessing the amazing computational power that you are donating to improve our understanding of the basis of amyloid fibril formation.

Here\'s a bit more background. Rather than one giant post I\'m going to reply to the thread multiple times as I find useful links and other information.

Amyloid disease: a number of diseases (Alzheimer\'s, Parkinson\'s, Type II diabetes, the transmissible spongiform encephalies \"Mad Cow\",...) are associated with the deposition of protein aggregates in the diseased tissues. It\'s been very difficult to determine the molecular structure of these aggregates because they are fibrous and insoluble, resisting crystallization. For this reason they are attractive targets for computational modeling.

We are working on building high-resolution predictions for medically relevant amyloids, starting with the Alzheimer\'s-beta fragment (1-40). We are collaborating with a group at the NIH who use solid-state NMR to probe the structure of Abeta1-40 aggregates. Our goal is to determine by simulation the set of low-energy conformations that are compatible with the current collection of experimental distance constraints that they have given us. By analyzing this set of solutions we will propose new experiments which should be maximally informative in determining the structure. We will then use the results of these new experiments to build models and iterate this procedure to generate high-resolution models.

Why predict amyloid structures? The expectation is that knowledge of the high-resolution structure of amyloid fibrils will aid in the design of small molecules which can inhibit fibril formation and/or break down existing deposits.

The simulation: fibrils are thought to be symmetric assemblies, which means that they are formed by stacking together many identical copies of a protein or peptide. What you see on your screen are 12 copies of the Abeta(10-40) sequence (our collaborators tell us that residues 1-9 are likely to be disordered and outside the core of the fibril). There will be a low-resolution simulation (no sidechains visible, lots of movement), followed by a high-resolution refinement (sidechains visible in the left panel, simulation appears to go much more slowly). Not all low-resolution trajectories will go on to high-res refinement -- we are filtering for conformations which satisfy the experimental constraints.

Wikipedia entry for Amyloid

OK -- post with questions and I will continue to look for info to add. Thanks for your interest and your spare cycles!!

-Phil

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Message 31112 - Posted: 14 Nov 2006, 6:16:34 UTC

Great Phil! Best description of the function, and user experience of a new release yet! ...and BEFORE it\'s downloaded to my machine! Love it! When people raise questions, we\'ll be able to direct them straight here for why their model is slow during refinement, or looks different then they are used to.

Could to help us to understand what \"medically relevant\" really means to you?

And once you feel you\'ve got a good model of this... how will you test to determine if you\'re correct? Or close? given that there is no crystalization experiment to compare to? Will you compare with NMR data? Or test for interactions with other known structures?
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Message 31116 - Posted: 14 Nov 2006, 7:28:11 UTC

This is great news....bringing all our machines back to R@H as well...Cheers, Rog.
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Message 31119 - Posted: 14 Nov 2006, 8:32:15 UTC

Here are some of the target we targetes at Find-a-Drug with the THINK virtual screen program. (related to Alzheimer\'s inhibition which is different to stucture prediction we are doing, but here as a refrence for anyone interested)


-----
With amyloid in the name..

Amyloid beta-Protein precursor (APPI) PDB-1AAP
T R Hynes et al Biochemistry (1990) 29.43 p10018-22

Amyloid beat-Peptide- Binding Alchohol Dehydrogenase (ABAD) PDB-1U7T
C R Kissinger et al J Mol Biol (2004) 342.3 p943-52



other targets aimed at...
Beta-secretase (memapsin2) PDB-1M4H, 1TQF, 1FKN, 1M4H, 1XS7
K W Underwood et al Structure (2003) 11 p627, L Hong et al Science (2000) 290 p150

Trypsin IV PDB-1H4W
G Katona et al J Mol Biol (2002) 315.5 p1209-18

N-Methyl-D-Aspartate (NMDA) receptor, PDB-1PB7,1PB8,1PBQ
H Furukawa and E Gouaux EMBO J (2003) 22.12 p2873-85

c-Jun N-terminal kinases (JNKs) PDB-1PMN,1PMQ
L Resnick & M Fennell DDT (2004) 9.21 p932-939

Estrogen-beta receptor PDB-1QKM
L Zhao and R D Brinton, J Med Chem (2005) 48.10 3463-6

Metalloproteinase-12 (Mmp-12) PDB-1UTT
R Morales et al J Mol Biol (2004) 341 p1063

P53 PDB-1YCS
X Zhu et al J Med Chem (2002) 45 p5090-7
-----

There could be more we did but would probably take somebody who knows what they are looking for ;-)

Team mauisun.org
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Message 31131 - Posted: 14 Nov 2006, 15:11:12 UTC - in response to Message 31112.  


Could to help us to understand what \"medically relevant\" really means to you?

And once you feel you\'ve got a good model of this... how will you test to determine if you\'re correct? Or close? given that there is no crystalization experiment to compare to? Will you compare with NMR data? Or test for interactions with other known structures?


Good questions. How will we validate our model? Mainly by comparison with experimental data. We can propose new solid-state NMR experiments that would support or contradict the model, eg, if we say that the sidechains of residues 19 and 34 are within X Angstroms then they can do an experiment with peptide labeled at those positions and see if they get a signal. In addition, there are a variety of experiments whose results one could predict from a structural model. For example, even though the fibrils don\'t form ordered 3-dimensional crystals suitable for X-ray crystallography, they do have enough 1-dimensional order to yield characteristic diffraction patterns when you shoot X-rays through them. If we have a three-dimensional model then we can predict what this pattern should look like and compare with the pattern that is actually observed. THere are several other experiments of this type which can\'t be used to determine the structure but which can support or refute an existing model.

As for \"medically relevant\" -- I confess I have very little clinical background or experience. My naive definition is to be associated with one or more human diseases.

Thanks for the interest and please do post with more questions which I may or may not be able to answer!

Take care,
Phil
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Message 31135 - Posted: 14 Nov 2006, 17:14:16 UTC - in response to Message 31106.  

...
The simulation: fibrils are thought to be symmetric assemblies, which means that they are formed by stacking together many identical copies of a protein or peptide.


What interests me is the question of water in the structure

I know the general Rosetta sim is based on a single protein surrounded by water, and if I understand correctly the model caters for the different enrgy regime where water is present (outside the structure) and where it is absent (inside folds which are tight enough to exclude water), so that the modelled protein follows the real one in folding up the hydrophobics on the inside away from the water.

My speculation is that there may be pockets of water trapped between the identical copies of the protein/peptide, for example sandwiched between two hydrophilic amino acids. In contrast to the normal Rosetta case, where the positions of the water molecules are not constrained outside the protein, but only by the protein itself, the water molecule may even be fixed at both ends.

First does this make sense in biochem terms?

Second, if so, how does your model approach all the extra degrees of freedom that follow from having the position of the relatively tiny water molecules becoming significant?

River~~
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Message 31140 - Posted: 14 Nov 2006, 19:04:31 UTC

...If we have a three-dimensional model then we can predict what this [x-ray diffraction] pattern should look like and compare with the pattern that is actually observed.


...and presumably we (mankind) can learn to do the opposite? Use what is known from the diffraction pattern to bias the computational modelling? (thus allowing the computational model to benefit from the x-ray studies, and arrive at the correct answer with less computing power expended) ...or is this already done to some extent.
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Message 31143 - Posted: 14 Nov 2006, 20:01:37 UTC

So you start with Abeta(10-40) which means 30 structures. When do you think you will have established those 30 structures and what\'s the plan afterwards? Do you have a definite set of amyloids you want to study or does it all depend on the progress you make?

How accurate do you want to predict the structure? I understand high-resolutions means pretty accurate but is you goal a prediction as accurate as X-ray crystallography (<1.5 Angstrom)?
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Message 31218 - Posted: 16 Nov 2006, 5:27:19 UTC - in response to Message 31135.  
Last modified: 16 Nov 2006, 14:34:47 UTC


What interests me is the question of water in the structure

I know the general Rosetta sim is based on a single protein surrounded by water, and if I understand correctly the model caters for the different enrgy regime where water is present (outside the structure) and where it is absent (inside folds which are tight enough to exclude water), so that the modelled protein follows the real one in folding up the hydrophobics on the inside away from the water.

My speculation is that there may be pockets of water trapped between the identical copies of the protein/peptide, for example sandwiched between two hydrophilic amino acids. In contrast to the normal Rosetta case, where the positions of the water molecules are not constrained outside the protein, but only by the protein itself, the water molecule may even be fixed at both ends.

First does this make sense in biochem terms?

Second, if so, how does your model approach all the extra degrees of freedom that follow from having the position of the relatively tiny water molecules becoming significant?

River~~


This is a very important question. In fact I\'ve read a number of papers which argue the same thing, that there may be columns of water inside the fibril. For most applications we use an implicit solvation model, which tries to assess the degree to which each atom is accessible to water by summing contributions from all nearby atoms. Polar atoms prefer to remain solvent accessible while hydrophobic ones will prefer to be buried. This does not distinguish between the inside and the outside of the fibril per se -- if there is a void in the center of a model the solvation term will reward polar atoms that neighbor the void on the assumption that water could be there. Unfortunately this doesn\'t take into account the fact that water has a discrete size and some voids may not be large enough. We do also have explicit water models but I am not using these for the fibril modeling because they are too computationally expensive.

In summary you may be right that internal molecules are present and it may be necessary to model them explicitly, which would indeed increase the number of degrees of freedom... I am excited to analyze the models that we are getting to look for internal cavities.







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Message 31219 - Posted: 16 Nov 2006, 5:30:37 UTC - in response to Message 31140.  

...If we have a three-dimensional model then we can predict what this [x-ray diffraction] pattern should look like and compare with the pattern that is actually observed.


...and presumably we (mankind) can learn to do the opposite? Use what is known from the diffraction pattern to bias the computational modelling? (thus allowing the computational model to benefit from the x-ray studies, and arrive at the correct answer with less computing power expended) ...or is this already done to some extent.


This is done in the case of x-ray diffraction patterns taken from crystals. It\'s more challenging to derive detailed structures from fiber diffraction data but perhaps this could be done. But you can see features in the data that correspond to structural repeats -- eg the 4.8A repeat that corresponds to stacked beta-strands.
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Message 31220 - Posted: 16 Nov 2006, 5:33:36 UTC - in response to Message 31143.  

So you start with Abeta(10-40) which means 30 structures. When do you think you will have established those 30 structures and what\'s the plan afterwards? Do you have a definite set of amyloids you want to study or does it all depend on the progress you make?

How accurate do you want to predict the structure? I understand high-resolutions means pretty accurate but is you goal a prediction as accurate as X-ray crystallography (<1.5 Angstrom)?


I didn\'t do a good job of explaining my terminology: when I say Abeta(x-y), x and y are positions in the protein sequence. eg 10-40 means residues 10-40 of the abeta peptide, or 31 amino acids.

The plan is hopefully to propose further experiments and iterate between experiment and simulation to converge on a \"high-resolution\" structure, at least for the core regions. I think 1.5 Angstroms would be fantastic -- in reality some parts of the structure may be disordered and these we just have to ignore.

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Message 31253 - Posted: 16 Nov 2006, 15:15:23 UTC - in response to Message 31219.  
Last modified: 16 Nov 2006, 15:17:16 UTC

It\'s more challenging to derive detailed structures from fiber diffraction data but perhaps this could be done. But you can see features in the data that correspond to structural repeats -- eg the 4.8A repeat that corresponds to stacked beta-strands.


Hi phil,

a good example is the famous \"photograph 51\" from which Watson and Crick derived the double helix structure of the DNA:

Photograph 51

This diffuse pattern of a non-crystalline specimen was enough to tell that the DNA is a helix by the equidistant blackening and the angles involved. If you look close, you see that there should be 5 such patterns from the inside out.

There are three [the center does not count, it is referred to as zero\'th order] clearly visible and the fifth, most outward one, is very faint. But the total lack of the fourth told Watson and Crick that they had to deal with a double helix, one of which is displaced by 3/8th of a turn against the other.

That seems to be little information, but if you know a sequence and thus how the thing is composed in general, that can give you a lot of insight into possible structural motifs. For Watson and Crick it was enough for a breakthrough.
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Message 31838 - Posted: 29 Nov 2006, 23:01:03 UTC - in response to Message 31253.  

a good example is the famous \"photograph 51\" from which Watson and Crick derived the double helix structure of the DNA:

Photograph 51

[snip] For Watson and Crick it was enough for a breakthrough.


Yet nobody ever seems to find it necessary to give credit to the photographer. Least of all, the Nobel Prize committee. Rosalind Franklin took Photo 51.

http://www.pbs.org/wgbh/nova/photo51/

Simone
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Message 31852 - Posted: 30 Nov 2006, 10:59:23 UTC
Last modified: 30 Nov 2006, 11:00:46 UTC

Yes,

that is correct, and she probably contributed much more to the succes of Watson and Crick than most sources tell. She did all the experimental work that made the determination of the DNA structure possible, from preparation of DNA samples in their A and B form to taking the best x-ray images ever achieved until then. And she was a very good interpreter of features that have to underly x-ray data too.

Watson and Crick were, apart from getting access to the famous photograph 51, lucky to find an unpublished article which gave them clues Franklin and her colleagues had overlooked - and pretty quickly solved the problem. It would just have taken some time to have that done by somebody else, maybe Franklin could have done it, as she already was certain it had to be a double, triple or quadruple helix.

And she found out that the bases had to be inside with a sugar and phosphate framework outside. Watson and Crick had that from the article and as they were sure it was a double helix solved the problem rather straightforward by accounting for the bonding of the bases to one another based on hydrogen bonding. It was like a knot that had gotten unravelled and everything fitted.

Watson and Crick though insisted for a long time they did not know those unpublished data. The reason was that the King\'s College published their own article to at least get the credit for the experimental work, if not the discovery itself. By denying to having known the facts stated there they made it look like it was all their own conception.

Watson later confessed he did know the data in his book \"The Double Helix\" in 1968 and even Crick admitted that that was true after the publication. Regarding the Nobel Prize, Rosalind Franklin died in 1958 and Watson and Crick got the prize four years later, six years before the book. Had Waston and Crick told the truth about that article while Franklin was alive, she might have gotten larger credit. But her part in the story was underestimated by withholding the truth, to state it diplomatically.
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Message 31906 - Posted: 1 Dec 2006, 17:53:38 UTC - in response to Message 31838.  

a good example is the famous \"photograph 51\" from which Watson and Crick derived the double helix structure of the DNA:

Photograph 51

[snip] For Watson and Crick it was enough for a breakthrough.


Yet nobody ever seems to find it necessary to give credit to the photographer. Least of all, the Nobel Prize committee. Rosalind Franklin took Photo 51.

http://www.pbs.org/wgbh/nova/photo51/

Simone


Undoubtedly Rosalind Franklin deserves equal credit with W & C for her part in the double helix discovery.

It is not true that nobody ever seems to find it necessary to give that credit to her - Watson & Crick were among those who did give her the credit, including if I remember rightly in comments made by them at the time of receiving the prize.

It is particularly unfair to criticise the Nobel prize committee if they had any choice in the matter, despite many people feeling that they are fair game for criticism either indirectly in the form of passing comments like yours or more directly, I have seen accusations elsewhere that this was an intentionally sexist decision by the committee.

In fact, the committee are constrained by the will of Alfed Nobel, who made it quite clear that the prize was to be awarded to living scientists. Sadly Franklin died in 1958, and the importance of the double helix work was not entirely recognised at that time. The Nobel prize was awarded in 1962, by which time is was legally four years too late for Franklin to be awarded the prize.

Presumably Nobel drafted his will in this way in the hope that the money would be spent by scientists who had already benefitted humankind and on more of the same prize-winning areas of study. He did not know that the prizes were to become more important for the recognition they conferred than for the value of the cash. But whatever his reasons were, the Nobel prizes are a private trust formed by his will, and the trustees did not (still do not) have the power to change the rules.

River~~
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Message 32746 - Posted: 16 Dec 2006, 11:40:21 UTC

Hello to all, I am italian student of chemistry interested to the argument. I wanted to know if the study on the prediction structure of the amyloid fibrils (in Alzheimer research) were finished and if it were possible to consult turns out obtained to you. Thanks to the next time.
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Message 32758 - Posted: 16 Dec 2006, 16:43:17 UTC
Last modified: 16 Dec 2006, 16:47:38 UTC

Tommy, Welcome to Rosetta!

I haven\'t seen any of these amyloid tasks for some time. I would assume they are working on refinements to the program, as they really are just getting started on this research method.

Dr. Baker said in his journal today that he and the team will be writing some papers on the work they did over the Summer with CASP. And, in general, you can count of the project team writing papers about all of their work, when they feel they\'ve got something to write about.

I was searching the web one day for related papers, to see if I could find any that I could understand! I found a website that may be of interest to you (many of you). It\'s called http://www.sciencemag.org. It requires a subscription to read more then the abstracts, but I think you will find by review of your search results and how they link in to related papers, that it is well worth the roughly $60 euros it costs for a student subscription.

Here\'s a link directly to my search for amyloid fibrils
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