Direct Comparison of Experimental and Calculated NMR Scalar Coupling Constants for Force Field Validation and Adaptation

• Published in: Journal of chemical theory and computation 2008-11, Vol.4 (11), p.1949-1958
• Main Authors: Schmid, Franziska F.-F, Meuwly, Markus
• Format: Article
• Language: English
• Subjects: Biomolecular Systems
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/ct800241d

The ability to measure scalar coupling constants across hydrogen bonds (3h J NC′) from high-resolution NMR experiments allows the characterization of detailed structural properties of biomolecules. To analyze those, a parametrized model based on the linear combination of atomic orbitals relates H-bond geometries with the measured 3h J NC′ coupling magnitude. In the present study the dependence of calculated 3h J NC′ coupling constants on force field parameters is assessed. It is shown that increased polarity of the hydrogen bond improves the calculated 3h J NC′ coupling constants and shifts the conformational ensemble sampled from the molecular dynamics (MD) simulations toward the experimentally measured one. Increased charges lead to more narrow distance and angle distributions and improve the agreement between calculated and measured 3h J NC′ couplings. However, different secondary structures are better represented by different magnitudes of electrostatic interactionsdifferent atomic partial charges in the present workas indicated by root-mean square deviations (rsmds) between observed and calculated coupling constants 3h J NC′. The parametrization of the empirical formula is found to be meaningful and robust, but the parameter values are not universal across different proteins and different secondary structural elements (α-helices, β-sheets and loops). Using standard and slightly increased CHARMM charges, predictions for the as-yet unknown scalar coupling constants for the V54A and I6A mutants of protein G are made.