Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings.
An accurate description of hydrogen bonds is essential to identify the determinants of protein stability and function as well as folding and misfolding behavior. We describe a method of using J couplings through hydrogen bonds as ensemble-averaged restraints in molecular dynamics simulations. Applications to the cases of ubiquitin and protein G show that these scalar couplings provide powerful structural information that, when used through the methodology that we present here, enables the description of the geometry and energetics of hydrogen bonds with an accuracy approaching that of high-resolution X-ray structures.
Gsponer
Joerg
J
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Hopearuoho
Harri
H
Cavalli
Andrea
A
Dobson
Christopher M
CM
Vendruscolo
Michele
M
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry
C029152:G-substrate; D009419:Nerve Tissue Proteins; D011506:Proteins; D025801:Ubiquitin