Optimal bundling of transmembrane helices using sparse distance constraints.

ABSTRACT: We present a two-step approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only sparse distance constraints, such as those derived from chemical cross-linking, dipolar EPR and FRET experiments. In Step 1, using an algorithm, we developed, the conformational space of membrane protein folds matching a set of distance constraints is explored to provide initial structures for local conformational searches. In Step 2, these structures refined against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. We begin by describing the statistical analysis of the solved membrane protein structures from which the theoretical port

SUBMITTER: Sale K 

PROVIDER: S-EPMC2286557 | biostudies-literature | 2004 Oct

REPOSITORIES: biostudies-literature