Simulation Studies of the Outer Membrane Protein Chaperone Skp

Abstract

Transmembrane outer membrane proteins (OMPs) from Gram-negative bacteria are associated with virulence, multidrug resistance, and general physiological function, and a deeper understanding of OMP biogenesis machinery may provide potential targets for combating diverse pathogens. Skp, a periplasmic chaperone, helps to protect nascent OMPs from degradation, and facilitates their transport to the outer membrane. Skp is a trimeric macromolecule whose structure resembles a “jellyfish”, with a small beta-sheet “head” forming the base for long protruding alpha-helical “tentacles” that are thought to sequester a diverse array of unfolded OMP substrates. To further understand the mechanisms of substrate binding by Skp, we have performed all-atom, fully-solvated molecular dynamics simulations, and characterized the inherent conformational flexibility of the trimer via sampling of hundreds of nanoseconds. In addition, Skp has been shown to interact stoichiometrically with bacterial lipopolysaccharide (LPS), a complex glycolipid from the outer membrane of Gram-negative bacteria that regulates release of OMP substrates by unknown mechanisms. Simulations were used to confirm that LPS molecules formed a stable complex with trimeric Skp, bound tightly via their glucosamine-linked phosphate groups to conserved cationic binding sites on the outer surface of the Skp tentacles. Bound LPS induced significant flexibility at glycine-containing hinge regions within the tentacles, leading to opening of the chaperone cavity. This may help to provide a structural basis for the experimentally observed regulation of Skp-bound substrate release by LPS.