Format

Send to

Choose Destination
J Biomol NMR. 2015 Sep;63(1):59-65. doi: 10.1007/s10858-015-9963-2. Epub 2015 Jul 5.

Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.

Author information

1
Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA. fmarassi@sbmri.org.
2
Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
3
Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD, 20892-5624, USA.

Abstract

The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

KEYWORDS:

Ail; Implicit solvation; Membrane protein; NMR; Structure; Yersinia pestis

PMID:
26143069
PMCID:
PMC4577439
DOI:
10.1007/s10858-015-9963-2
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Springer Icon for PubMed Central
Loading ...
Support Center