Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.

ABSTRACT: We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity, yet releases it with ease in the cytoplasm for subsequent use. The observations fit the "conformational selection" model whereby the existence of a weakly populated, higher energy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized. The approach relies on the systematic use of computational perturbation/response techniques based on linear response theory, by sequentially applying directed forces on single-residues along the chain and recording the resulting r

SUBMITTER: Atilgan C 

PROVIDER: S-EPMC2758672 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature