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All-atom ab initio folding of a diverse set of proteins

Jae Shick Yang·William W. Chen·Jeffrey Skolnick·Eugene I. Shakhnovich
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Abstract

Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio folding of a representative diverse set of proteins, using a minimalist transferable energy model that consists of two-body atom-atom interactions, hydrogen-bonding, and a local sequence energy term that models sequence-specific chain stiffness. Starting from a random coil, the native-like structure was observed during replica exchange Monte Carlo (REMC) simulation for most proteins regardless of their structural classes; the lowest energy structure was close to native- in the range of 2-6 A root-mean-square deviation (RMSD). Our results demonstrate that the successful all-atom folding of a protein chain to its native state is governed by only a few crucial energetic terms.

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Jae Shick Yang, William W. Chen, Jeffrey Skolnick, Eugene I. Shakhnovich. 2006-11-27. All-atom ab initio folding of a diverse set of proteins. https://arxiv.org/abs/q-bio/0611086

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