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Ab initio protein structure prediction using physicochemical potentials and a simplified off‐lattice model
Author(s) -
Gibbs Nick,
Clarke Anthony R.,
Sessions Richard B.
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20010501)43:2<186::aid-prot1030>3.0.co;2-l
Subject(s) - ab initio , protein structure prediction , lattice (music) , lattice protein , computational chemistry , statistical physics , computer science , materials science , chemistry , protein structure , physics , nuclear magnetic resonance , organic chemistry , acoustics
This study describes a computational method for ab inito protein structure prediction. Protein conformation has been modeled by using six optimized backbone torsion angles and fixed side chains approximating rotationally averaged real side chains. The approximations aim to keep complexity of the structure description to a minimum without seriously compromising the accuracy of the structural representation. An evolutionary Monte Carlo algorithm has been developed to search through this restricted conformational space to locate low‐energy protein structures. A simple physicochemical force field has been developed to assess the energies of different conformations within this structural description. The corresponding residue interaction energies are based on hydrophobic, hydrophilic, steric, and hydrogen‐bonding potentials. The search procedure has been used to locate native energy minima from primary sequence alone. The 3‐D structures of polypeptides up to 38 residues with both β and α secondary structural elements have been accurately predicted. The search procedure has been found to be highly efficient and follows an energetically and structurally plausible pathway to locate native populations. The simple force field described in the study has been compared with a more complex all‐atom model and been found to be similarly effective in predicting the structures of proposed independent folding units. Proteins 2001;43:186–202. © 2001 Wiley‐Liss, Inc.