Exploring the conformational space of membrane protein folds matching distance constraints.

ABSTRACT: Herein we present a computational technique for generating helix-membrane protein folds matching a predefined set of distance constraints, such as those obtained from NMR NOE, chemical cross-linking, dipolar EPR, and FRET experiments. The purpose of the technique is to provide initial structures for local conformational searches based on either energetic considerations or ad-hoc scoring criteria. In order to properly screen the conformational space, the technique generates an exhaustive list of conformations within a specified root-mean-square deviation (RMSD) where the helices are positioned in order to match the provided distances. Our results indicate that the number of structures decreases exponentially as the number of distances increases, and increases exponentially as the errors ass

SUBMITTER: Faulon JL 

PROVIDER: S-EPMC2323961 | biostudies-literature | 2003 Aug

REPOSITORIES: biostudies-literature