Protein Dynamics

Protein structures provide clues to the mechanisms of biological processes and inspiration for new biological hypotheses. Surprisingly, half of all protein families are not represented by any solved structure. Even less is known about how protein structures behave in complex cellular environments or what structural motions they undergo to achieve their functions. We are approaching these problems using creative chemistry, rewiring of the genetic code and advances in computational structure prediction.

The primary reason why so many protein families are currently intractable is that they do not behave well under the conditions required for crystallographic or NMR structural analysis. We are developing an approach that uses conditions amiable to all proteins: the inside of the living native cell. This is done by covalently capturing protein structural features in the cell and reading this information out by high-throughput mass spectrometry (collaboration with the lab of Josh Elias).

Proteins undergo constant structural fluctuations which are often important to their function. These fluctuations expose normally burried residues to the surrounding environment. The rate constants and equilibrium constants of these fluctuations constitute the folding energy landscape of the protein. By a novel approach to chemically modifying exposed amino acids and reading out the modifications by high-throughput mass spectrometry, we can reveal important parts of this landscape. We are currently working to identify the motions of the NSF machine, which should help to reveal how it unfolds SNARE complexes.

 

Selected Publications

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.
Bernstein R, Schmidt KL, Harbury PB, Marqusee S
Proc. Natl. Acad. Sci. U.S.A. 108: 10532-7 (2011)

PDF | PubMED

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The equilibrium unfolding pathway of a (beta/alpha)8 barrel.
Silverman JA, Harbury PB
J. Mol. Biol. 324: 1031-40 (2002)

PDF | PubMED

 

 

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