Accurate design of co-assembling multi-component protein nanomaterials

Scientists at the Institute for Protein Design (IPD), in collaboration with researchers at UCLA and HHMI, can now design and build self-assembling protein nanomaterials made up of multiple components with near atomic-level accuracy.

Background

A previously published 2012 Science paper described a new computational method for the design of protein building blocks that self-assemble to a desired symmetric architecture. The general conceptual approach for this protein nanomaterial design consists of two steps: docking of protein building blocks on defined symmetric axes followed by design of low energy protein-protein interfaces between the building blocks (to drive self-assembly). With this computational method, King et al designed single-component protein nanomaterials that self-assemble into octahedral and tetrahedral symmetric cage-like complexes. The designed protein crystal structures fit the computational predictions within one angstrom, demonstrating the exceptional accuracy of the computational design method.

In a Nature paper published this week entitled 'Accurate design of co-assembling multi-component protein nanomaterials', IPD translational investigator Dr. Neil King, Baker lab graduate student Jacob Bale, Baker lab senior fellow Will Sheffler and collaborators take this work to the next step: design of protein assemblies that are made up of two distinct components.

This time, Rosetta computational design software capabilities were expanded to model multiple different protein building blocks at the same time. Two different sets of building blocks are docked along symmetry axes to identify large interfaces between subunits that have high densities of contacting residues. The sequences at the interfaces are redesigned to stabilize the interaction and to drive co-assembly of the two sets of protein building blocks. Individually expressed protein building blocks can be mixed together to initiate nanoparticle assembly. Once again, x-ray crystal structures demonstrated that the protein structures are in very high agreement with the design models. The computational method is generalizable to produce a number of different symmetrical architectures composed of distinct protein subunits in various arrangements.

Why is this important?

Protein self-assembly plays a critical role in many biological processes (e.g. viruses self-assemble into complexes that encase, protect and deliver viral DNA to a host cell). Efforts to make novel self-assembling materials have seen success with DNA and RNA (see DNA origami), but attempts to design self-assembling protein structures that would have greater functional and structural properties have been challenging to date. Protein nanomaterials, such as the ones described in the two papers mentioned above, have potential applications in vaccine design, targeted drug delivery, imaging agents and new biomaterials. Multi-component self-assembling systems offer a number of advantages including a wider range of modular protein architectures. Furthermore, complexes requiring two or more components to assemble allow for increased control over the timing of cage assembly.

What’s next?

Work is ongoing at the IPD to begin functionalizing these protein nanomaterials for various applications. Furthermore, to expand the scope of the protein nanocages with tunable properties and varying sizes and structures, the next step would be to design self-assembling protein nanomaterials composed of de novo designed building blocks, i.e. ones not based on scaffolds that already exist in nature.

For links to the paper, images, and additional press coverage, please see this story at: https://www.ipd.uw.edu/accurate-design-of-co-assembling-multi-component-protein-nanomaterials/

I hope the idea of a monthly newsletter hasn't fallen by the wayside: I'd certainly enjoy reading it.

I hope the idea of a monthly newsletter hasn't fallen by the wayside: I'd certainly enjoy reading it.

A newsletter is definitely still in the works! Will be sure to update R@h users soon. Will continue to post here in the meantime.

A computationally design inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells

This work is described in a recent issue of Cell: Procko, E. et al. Cell 157, 1644-1656. (2014)

What if scientists could design a completely new protein that is precision-tuned to bind and inhibit cancer-causing proteins in the body? Collaborating scientists at the UW Institute for Protein Design (IPD) and Molecular Engineering and Sciences Institute (MolES) have made this idea a reality with the designed protein BINDI. BINDI (BHRF1-INhibiting Design acting Intracellularly) is a completely novel protein, based on a new protein scaffold not found in nature, and designed to bind BHRF1, a protein encoded by the Epstein-Barr virus (EBV) which is responsible for disregulating cell growth towards a cancerous state.

EBV is implicated in multiple cancers, including Burkitt’s lymphoma and Hodgkin’s lymphoma. BHRF1 is a homologue of the prosurvival human Bcl-2 proteins and interacts with ‘executioner’ proteins to prevent apoptosis (cell death) and maximize virus production. The activity of Bcl-2 proteins is counteracted by a set of proapoptotic proteins that share a 26-residue Bcl-2 homology 3 (BH3) helical motif that binds a hydrophobic groove on the Bcl-2 protein. Senior fellow Dr. Erik Procko of the IPD and Stayton lab graduate student Geoffrey Berguig in the UW Department of Bioengineering, along with collaborators at the Fred Hutchinson Cancer Research Center, sought to design a protein that could bind the BH3 groove of BHRF1 and inhibit its cancer-causing activity in vivo.

BHRF1-binding proteins were created by grafting side chains from the a BH3 peptide onto a larger and more rigid de novo helical scaffold to allow for greater affinity and specificity of interaction with BHRF1, beyond just the BH3 motif. The designs were solubly expressed and tested by yeast surface display for binding to BHRF1. Candidate designs were further optimized via rounds of error-prone PCR mutagenesis and site-specific saturation mutagenesis followed by fluorescence activated cell sorting (FACS) to obtain binders optimized for affinity, stability and specificity; a binder is desired that targets BHRF1 over other closely related Bcl-2 proteins. One design, BINDI, bound BHRF1 with a Kd of 220 pM (very tight binding) and displayed significantly increased E. coli expression and improved specificity.

The crystal structure of BINDI was shown to be in very close agreement with the computationally designed model. When introduced into EBV-infected cancer cell lines, BINDI effectively induced apoptosis. To test BINDI in an EBV-position B cell lymphoma mouse model, a novel antibody-micelle carrier was used to overcome the challenge of in vivo intracellular delivery of proteins. When treated intravenously with BINDI coupled to the micelle carrier, these mice experienced extended lifespans and slowed tumor progression. This data is the first demonstration that a de novo computationally designed protein can reduce tumor growth and prolong survival in a preclinical model.

At question is whether this technology can be applied beyond cancer treatment to other disease areas. To this end, designer proteins, such as BINDI, that selectively kill target cells provide an advantage over the toxic compounds used in currently developed antibody-drug conjugates. The ability to design functional proteins using de novo scaffolds suggests that is possible to design such proteins to bind any target of interest. Work is ongoing at the IPD and in the Stayton lab to optimize dosing, targeting and delivery of BINDI to increase its therapeutic efficacy.

Here are some links to news coverage of this research:

http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells%E2%80%99-death
http://www.moles.washington.edu/news-events/2014/06/moles-research-lab-collaboration-leads-to-next-generation-cancer-fighting-therapy/
http://www.neomatica.com/2014/06/27/designed-protein-overcomes-epstein-barr-virus-strategy-evading-immune-system/

Reddit thread: http://www.reddit.com/r/science/comments/29tpqe/epsteinbarr_virus_infects_human_cells_and_makes/

http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells%E2%80%99-death
http://www.moles.washington.edu/news-events/2014/06/moles-research-lab-collaboration-leads-to-next-generation-cancer-fighting-therapy/
http://www.neomatica.com/2014/06/27/designed-protein-overcomes-epstein-barr-virus-strategy-evading-immune-system/

Reddit thread: http://www.reddit.com/r/science/comments/29tpqe/epsteinbarr_virus_infects_human_cells_and_makes/

:)

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http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells%E2%80%99-death
http://www.moles.washington.edu/news-events/2014/06/moles-research-lab-collaboration-leads-to-next-generation-cancer-fighting-therapy/
http://www.neomatica.com/2014/06/27/designed-protein-overcomes-epstein-barr-virus-strategy-evading-immune-system/

Reddit thread: http://www.reddit.com/r/science/comments/29tpqe/epsteinbarr_virus_infects_human_cells_and_makes/

:)

wow :)

Please take a moment to read this letter from David Baker, Director of the IPD, highlighting the exciting accomplishments and progress made at the UW Institute for Protein Design in the past year!

https://www.ipd.uw.edu/letter-from-the-director-ipd-update/

https://www.ipd.uw.edu/wordpress/wp-content/uploads/2014/08/IPD_Update_WEB_8_14_14.pdf

3 pages

Standing on these successes, we recently integrated streamlined protein design methods for the de novo preparation of hyper-stable mini-protein scaffolds (30-40 amino acids) using high throughput gene synthesis and massively parallel screening methods which enable manufacturing and testing of tens of thousands of new proteins in a matter of weeks. With funding support from the Defense Threat Reduction Agency (DTRA), we recently launched a “War on Ebola” to test these new capabilities by designing medical countermeasures (MCMs) that could address the recurring hemorrhagic fever outbreaks in Africa.

what David Baker ?

"war on Ebola"

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Good to see that we are taking action on this terrible disease. All my computing resources are working on Rosetta. I don't care what the process is called - war, fight, campaign: as long as we work on the elimination of Ebola, it's OK with me. Ebola is not only a threat in Africa, but everywhere as recent events have demonstrated.

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Any new updates on research?

Thx

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

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They botched the link and left a trailing "/" on the path. It is a very common error:

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf/

REALLY here without the trailing "/" character

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

They botched the link and left a trailing "/" on the path. It is a very common error:

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf/

REALLY here without the trailing "/" character

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

Thanks. Now I definitely know it's way over my head...

---

They botched the link and left a trailing "/" on the path. It is a very common error:

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf/

REALLY here without the trailing "/" character

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

Thanks. Now I definitely know it's way over my head...

No, not way over your head. My fingers did not type as clearly as my brain told them.

The name of the file was "misspelled" ... because they left an extra character on the end.

I think he meant that now that he's read the link, he knows more about how much he doesn't know :)

They botched the link and left a trailing "/" on the path. It is a very common error:

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf/

REALLY here without the trailing "/" character

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

Thanks. Now I definitely know it's way over my head...

No, not way over your head. My fingers did not type as clearly as my brain told them.

The name of the file was "misspelled" ... because they left an extra character on the end.

---

Rosetta Moderator: Mod.Sense

Something (a lot) like that... ;)

I think he meant that now that he's read the link, he knows more about how much he doesn't know :)

They botched the link and left a trailing "/" on the path. It is a very common error:

https://www.bakerlab.org/wp-content/uploads/2016/05/680.full_.pdf/

REALLY here without the trailing "/" character

Reviving this thread with the goal of more frequent updates on science coming out of the Rosetta community

Last week, Baker lab postdoc Scott Boyken, grad student Zibo Chen, and collaborators came out with a breakthrough paper in Science titled 'De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity'.

This is an exciting and significant breakthrough for de novo protein design. A particular challenge for current protein design methods has been the accurate design of polar binding sites or polar binding interfaces, both of which require hydrogen bonding interactions. Hydrogen bond networks are governed by complex physics and energetic coupling, that until now, could not be computed within the scope of design. The computational method described in this paper, HBNet, now provides a general method to accurately design in hydrogen bond networks. This new capacity should be useful in the design of new enzymes, proteins that bind small molecules, and polar protein interfaces. Thanks Rosetta@home community for your participation!

The PDF of this article can be found here. An article on this work was also published in Geekwire.

This is way too technical for me to appreciate, but as long as you're saying "This is an exciting and significant breakthrough for de novo protein design" that's good enough for me.

The link to the PDF isn't working for me btw

Thanks. Now I definitely know it's way over my head...

No, not way over your head. My fingers did not type as clearly as my brain told them.

The name of the file was "misspelled" ... because they left an extra character on the end.

---

Sorry for the link issue! Thank you for catching that.

Brand new paper from the Baker lab in Nature! Thank you yet again for your contributions, Rosetta@home volunteers.

"Design of a hyperstable 60-subunit protein icosahedron" describes the design of a 20-sided nano-sized particle that could be used to deliver drugs or to develop powerful new vaccines.

Author and Baker lab graduate student Yang Hsia spoke on a Nature podcast on the work. Have a listen to hear about this awesome work from the protein design experts themselves! Links below.

Paper

Podcast Under 16 June 2016 "Protein football"

We will post a PDF version of the paper to the Baker lab website. Once we have it up I will post that link here as well.