Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
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.
Haliloglu
Turkan
T
Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek 80815, Istanbul, Turkey.
Kolinski
Andrzej
A
Skolnick
Jeffrey
J
D000213:Acyl Carrier Protein / Q000737:chemistry; D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy; D009010:Monte Carlo Method; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012416:Rubredoxins / Q000737:chemistry
D000213:Acyl Carrier Protein; D001426:Bacterial Proteins; D011506:Proteins; D012416:Rubredoxins; C068605:nodF protein, Rhizobium