Application of solid-state NMR restraint potentials in membrane protein modeling.
We have developed a set of orientational restraint potentials for solid-state NMR observables including (15)N chemical shift and (15)N-(1)H dipolar coupling. Torsion angle molecular dynamics simulations with available experimental (15)N chemical shift and (15)N-(1)H dipolar coupling as target values have been performed to determine orientational information of four membrane proteins and to model the structures of some of these systems in oligomer states. The results suggest that incorporation of the orientational restraint potentials into molecular dynamics provides an efficient means to the determination of structures that optimally satisfy the experimental observables without an extensive geometrical search.
Lee
Jinhyuk
J
Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.
Chen
Jianhan
J
Brooks
Charles L
CL
Im
Wonpil
W
D001426:Bacterial Proteins / Q000737:chemistry; D017104:Bacteriophage M13 / Q000737:chemistry; D027682:Cation Transport Proteins / Q000737:chemistry; D015497:HIV-1 / Q000737:chemistry; D006801:Humans; D009980:Influenza A virus / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation
D001426:Bacterial Proteins; D027682:Cation Transport Proteins; D008565:Membrane Proteins; C408446:MerF mercury transport protein, Pseudomonas fluorescens; D009587:Nitrogen Isotopes