Molecular simulation uncovers the conformational space of the λ Cro dimer in solution.

ABSTRACT: The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Inters

SUBMITTER: Ahlstrom LS 

PROVIDER: S-EPMC3218345 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature