Abstract
Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N–H, Cα–Hα, C′–N, and Cα–C′ bonds, as well as for the two-bond C′–H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5–3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.
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Case, D.A. Calculations of NMR dipolar coupling strengths in model peptides. J Biomol NMR 15, 95–102 (1999). https://doi.org/10.1023/A:1008349812613
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DOI: https://doi.org/10.1023/A:1008349812613