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

By Jae-Shick Yang, William W. Chen, Jeffrey Skolnick, Eugene I. Shakhnovich. 2006

94 citations recorded by the source corpus.

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 by 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 folding of a protein chain to its native state is governed by only a few crucial energetic terms.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “libraries [22,23] or other strategies to search conformational space [24,25], followed by sophisticated energy optimization or”
The protein folding problem. (2008, background): “Because native proteins are only 5–10 kcal/mol more stable than their denatured states, it is clear that no type of intermolecular force can be neglected in folding and structure prediction (238).”
3D Protein Structure Predicted from Sequence (2011, unknown): “to-‐structure problem remains unsolved, methods that use fragment libraries [20,21] or other strategies to search conformational space [22,23], followed by sophisticated energy optimization or molecular d”
Prediction of protein structure from ideal forms (2008, background): “1–4 (This approach is referred to as de-novo since it can no longer be considered to build strictly from first principles).”
Mimicking the folding pathway to improve homology-free protein structure prediction (2009, methodology): “Although others have integrated 2° and 3° structure determination (11, 12) with an iterative fixing (ItFix) of 2° structure (13–15), our approach differs by ( i ) not using any exogenous 2° structure prediction or homology; ( ii ) removing side-chain degrees of freedom from the model, which greatly…”
Protein knots and fold complexity: Some new twists (2007, background): “…implications for structure rediction are already well known: that the definition of secndary and tertiary structure must interact (Meiler and Baker, 003) and when this is done, good results can be obtained at east for proteins under 100 residues in length (Bradley et al., 005; Yang et al., 2007).”