Backbone Structure of Yersinia Pestis Ail Determined in Micelles by NMR-restrained Simulated Annealing With Implicit Membrane Solvation

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry*
  • Cell Membrane / chemistry*
  • Computer Simulation*
  • Micelles*
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular*
  • Phosphorylcholine / chemistry
  • Reproducibility of Results
  • Solvents / chemistry*
  • Virulence Factors / chemistry*
  • Yersinia pestis / chemistry*

Substances

  • Ail protein, Yersinia pestis
  • Bacterial Outer Membrane Proteins
  • Micelles
  • Solvents
  • Virulence Factors
  • Phosphorylcholine