title: Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
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.
authors.affiliation: Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA. fmarassi@sbmri.org.
authors.forename: Francesca M
authors.initials: FM
authors.lastname: Marassi
authors.affiliation: Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD, 20892-5624, USA.
authors.forename: Charles D
authors.initials: CD
authors.lastname: Schwieters
authors.affiliation: Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Yao
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D002462:Cell Membrane / Q000737:chemistry*; D003198:Computer Simulation; D008823:Micelles; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D010767:Phosphorylcholine / Q000737:chemistry; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry*; D037521:Virulence Factors / Q000737:chemistry*; D015010:Yersinia pestis / Q000737:chemistry*
chemical_list: C526543:Ail protein, Yersinia pestis; D001425:Bacterial Outer Membrane Proteins; D008823:Micelles; D012997:Solvents; D037521:Virulence Factors; D010767:Phosphorylcholine
keywords: Ail; Implicit solvation; Membrane protein; NMR; Structure; Yersinia pestis