Premium
Use of residual dipolar couplings as restraints in ab initio protein structure prediction
Author(s) -
Haliloglu Turkan,
Kolinski Andrzej,
Skolnick Jeffrey
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10511
Subject(s) - chemistry , residual , ab initio , computational chemistry , dipole , residual dipolar coupling , protein structure prediction , ab initio quantum chemistry methods , chemical physics , protein structure , crystallography , molecule , organic chemistry , biochemistry , algorithm , computer science
NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, are used as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints are applied using a recently developed SICHO (SIde‐CHain‐Only) lattice protein model that employs a replica exchange Monte Carlo (MC) algorithm to search conformational space. Using a small number of RDC restraints, the quality of the predicted structures is improved as reflected by lower RMSD/dRMSD (root mean square deviation/distance root mean square deviation) values from the corresponding native structures and by the higher correlation of the most cooperative mode of motion of each predicted structure with that of the native structure. The latter, in particular, has possible implications for the structure‐based functional analysis of predicted structures. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 548–562, 2003