Molecular dynamics simulations of a bacterial autotransporter: Na1P from Neisseria meningitidis


Khalid, Syma and Samsom, Mark S.P. (2006) Molecular dynamics simulations of a bacterial autotransporter: Na1P from Neisseria meningitidis. Molecular Membrane Biology, 23, (6), 499-508. (doi:10.1080/09687860600849531).

Download

[img] PDF - Publishers print
Restricted to System admin

Download (490Kb) | Request a copy

Description/Abstract

NalP is an autotransporter secretory protein found in the outer membrane of Neisseria meningitidis. The crystal structure of the NalP translocator domain revealed a transmembrane beta-barrel containing a central alpha-helix. The role of this alpha-helix, and of the conformational dynamics of the beta-barrel pore have been studied via atomistic molecular dynamics simulations. Three simulations, each of 10 ns duration, of NalP embedded within a solvated DMPC bilayer were performed. The helix was removed from the barrel interior in one simulation. The conformational stability of the protein is similar to that of other outer membrane proteins, e.g., OmpA, in comparable simulations. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a 'plug'. Water molecules entering the resultant pore form hydrogen bonds with the barrel lining that compensate for the loss of helix-barrel hydrogen bonds. The dimensions of the pore fluctuate over the course of the simulation revealing it to be flexible, but only wide enough to allow transport of the passenger domain in an unfolded or extended conformation. The simulations help us to understand the role of the central helix in plugging the pore and in maintaining the width of the barrel, and show that the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation.

Item Type: Article
ISSNs: 0968-7688 (print)
Related URLs:
Keywords: autotransporter, molecular dynamics, outer membrane protein
Subjects: Q Science > QR Microbiology
Divisions: University Structure - Pre August 2011 > School of Chemistry
ePrint ID: 48164
Date Deposited: 31 Aug 2007
Last Modified: 27 Mar 2014 18:31
URI: http://eprints.soton.ac.uk/id/eprint/48164

Actions (login required)

View Item View Item