The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations.

ABSTRACT: Solid-state NMR study shows that the 22-residue K3 peptide (Ser(20)-Lys(41)) from beta(2)-microglobulin (beta(2)m) adopts a beta-strand-loop-beta-strand conformation in its fibril state. Residue Pro(32) has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state of full-length beta(2)m. To get insights into the structural properties of the K3 peptide, and determine whether the strand-loop-strand conformation is encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular dynamics on both the cis and trans variants. Our simulations show that the conformational space of the trans- and cis-K3 peptides is very different, with 1% of the sampled conformations in common at room temperature. In addition, both va

SUBMITTER: Liang C 

PROVIDER: S-EPMC2440456 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature