DISTANCE GEOMETRY GENERATES NATIVE-LIKE FOLDS FOR SMALL HELICAL PROTEINS USING THE CONSENSUS DISTANCES OF PREDICTED PROTEIN STRUCTURES

Citation
Es. Huang et al., DISTANCE GEOMETRY GENERATES NATIVE-LIKE FOLDS FOR SMALL HELICAL PROTEINS USING THE CONSENSUS DISTANCES OF PREDICTED PROTEIN STRUCTURES, Protein science, 7(9), 1998, pp. 1998-2003
Citations number
37
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biology
Journal title
ISSN journal
0961-8368
Volume
7
Issue
9
Year of publication
1998
Pages
1998 - 2003
Database
ISI
SICI code
0961-8368(1998)7:9<1998:DGGNFF>2.0.ZU;2-H
Abstract
For successful ab initio protein structure prediction, a method is nee ded to identify native-like structures from a set containing both nati ve and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue dis tances are available. We describe a method by which distance geometry restraints are culled from sets of 500 protein-like conformations for four small helical proteins generated by the method of Simons et al. ( 1997). A consensus-based approach was applied in which every inter-C a lpha distance was measured, and the most frequently occurring distance s were used as input restraints for distance geometry. For each protei n, a structure with lower coordinate root-mean-square (RMS) error than the mean of the original set was constructed; in three cases the topo logy of the fold resembled that of the native protein. When the fold s ets were filtered for the best scoring conformations with respect to a n all-atom knowledge-based scoring function, the remaining subset of 5 0 structures yielded restraints of higher accuracy. A second round of distance geometry using these restraints resulted in an average coordi nate RMS error of 4.38 Angstrom.