HIV design challenge

One of the biggest challenges facing protein design today is to model protein backbones. Unlike prediction, where a sequence is given, a design puzzle has more hidden traps since amino acids can change, allowing multiple (potentially false) answers to nearly identical problems. We are not at a stage where we know definitively how to choose the solutions that will work when produced and tested in the lab. Historically the complexity of a design problem is reduced by holding the backbones fixed. With the FoldIt game, we are asking users to sample flexible backbone designs with score-guided intuition to tackle this problem: how do we build one protein segment at a time under the constraint of a native scaffolding while maintaining the "foldability" of a sequence? Similar to prediction puzzles, we set up scores based on known metrics for assessing the quality of these models, and ultimately try to correlate these measures with experimental data to understand the underlying design principles, while iteratively improving them at the same time.

Using GP120, the HIV protein responsible for entry into host cells, as a model system is significant in that 1) it remains a viable candidate as an AIDS vaccine, and 2) it has an unusual topology. Having the tools to understand and engineer this molecule would contribute greatly to both AIDS research and protein engineering. Among several mechanisms used, the molecule uses a number of variable loops to distract the immune system from forging an effective response. In a nutshell, GP120s are located on the very outside of a viral particle, the envelope, and when the immune system sees it, a wave of antibodies are produced to try to neutralize the pathogen. The problem, however, is that although we make antibodies against this molecule, they are mostly directed to attack loops that are not related to the central machinery (which is hidden) responsible for invading host cells. To focus the response, our strategy in designing the vaccine is to expose the elements directly responsible (marked with CD4bs in the attached figure) by creating viral free proteins that resemble GP120 but lack its cloaking machineries (by editing structural regions marked with A,B,C,D in the figure, for example). In other words, we are interested in trimming away these loops while preserving the area on the surface vulnerable to neutralizing antibodies. We are hopeful because antibodies that can neutralize a wide variety of HIV strains do exist. The idea is to create a "mold" based on the known broadly neutralizing antibodies and present it to the immune system for the production of similar antibodies. The term "reverse vaccinology" has been coined to describe this strategy -- we know some antibodies work; now we try to produce copies of them by guiding the human body to make them.

As described previously, maintaining a protein structure while doing extensive remodeling work remains a challenge. However, one can intuitively imagine "protein sculpting" being useful in many applications of protein design. Besides the AIDS challenge presented above, we can apply the same shaping strategy to improve enzyme actives sites to make them more active, to alter cellular signaling by modulating the strength of proteins interacting with each other, and to create protein chimeras by shaping different parts to fit together for new functions, just to name a few. We are starting to address these problems with FoldIt. Designs that are judged plausible will be systematically studied by actually making them in the lab and testing for their (hopefully improved) functions. The goal is to learn enough about proteins through this process: to fundamentally improve our understanding of protein biochemistry and potentially create a vaccine or an enzyme along the way.

( Posted by  possu 76 2145  |  Thu, 05/21/2009 - 18:20  |  1 comment )
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Joined: 05/26/2008
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/***~~~ THIS IS GREAT NEWS ~~~***\

So happy to see this become implemented in the game. Great work! and thanks to everyone involved :)

So a couple of questions..

a) Since changing the the shape of a portion of the puzzle such as the helix in this first puzzle, could potentially change the shape of the remainder of the structure, will you presenting these puzzles again after the design target as folding only targets ?

b) Is the FoldIt software capable of displaying more than one protein, or other objects ? If so, is there any plans to present two proteins, and to model one to dock to the other, or is the intention just to model small areas where the remainder of the structure is locked such as in the first puzzle we are working on?

Thanks,
-Steve

:)

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons