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 ^3hJ_NC- 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 β-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 β-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.