Dynamic effects on j-couplings across hydrogen bonds in proteins.
We combine molecular dynamics simulation (MD) with density functional theory (DFT)/finite perturbation theory (FPT) to obtain the Fermi contact contributions to the 3hJNC' couplings in the SMN Tudor domain. Our results show that the effect of conformational motion needs to be considered for the accurate prediction of these scalar couplings. For hydrogen bonds in the beta-sheet regions, the calculated cumulative J-coupling averages remain constant after the first 200 ps. In the more flexible regions at the edges of the beta-sheets, the cumulative J-coupling averages vary over the 500-ps trajectory, providing a qualitative insight into the degree of conformational motion in different regions of the protein.
Markwick
Phineus R L
PR
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. markwick@embl.de
Sprangers
Remco
R
Sattler
Michael
M
D003198:Computer Simulation; D017362:Cyclic AMP Response Element-Binding Protein; D006860:Hydrogen Bonding; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins; D055532:SMN Complex Proteins; D013816:Thermodynamics
D017362:Cyclic AMP Response Element-Binding Protein; D009419:Nerve Tissue Proteins; D016601:RNA-Binding Proteins; D055532:SMN Complex Proteins