Calculations of NMR dipolar coupling strengths in model peptides.
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, C alpha-H alpha, C'-N, and C alpha-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.
Case
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Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA. case@scripps.edu
D000081:Acetamides / Q000737:chemistry; D000409:Alanine / Q000737:chemistry; D019281:Dimerization; D006860:Hydrogen Bonding; D008432:Mathematical Computing; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011522:Protons; D011789:Quantum Theory; D013696:Temperature; D014732:Vibration; D014867:Water / Q000737:chemistry
D000081:Acetamides; D010455:Peptides; D011522:Protons; D014867:Water; D000409:Alanine; C018595:N-methylacetamide