Analysis of proton chemical shifts in regular secondary structure of proteins.
The contribution of peptide groups to H alpha and H beta proton chemical shifts can be modeled with empirical equations that represent magnetic anisotropy and electrostatic interactions [Osapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436-9444]. Using these, a model for the 'random coil' reference state can be generated by averaging a dipeptide over energetically allowed regions of torsion-angle space. Such calculations support the notion that the empirical constant used in earlier studies arises from neighboring peptide contributions in the reference state, and suggest that special values be used for glycine and proline residues, which differ significantly from other residues in their allowed phi, psi-ranges. New constants for these residues are reported that provide significant improvements in predicted backbone shifts. To illustrate how secondary structure affects backbone chemical shifts we report calculations on oligopeptide models for helices, sheets and turns. In addition to suggesting a physical mechanism for the widely recognized average difference between alpha and beta secondary structures, these models suggest several additional regularities that should be expected: (a) H alpha protons at the edges of beta-sheets will have a two-residue periodicity; (b) the H alpha 2 and H alpha 3 protons of glycine residues will exhibit different shifts, particularly in sheets; (c) H beta protons will also be sensitive to local secondary structure, but in different directions and to a smaller extent than H alpha protons; (d) H alpha protons in turns will generally be shifted upfield, except those in position 3 of type I turns. Examples of observed shift patterns in several proteins illustrate the application of these ideas.
Osapay
K
K
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.
Case
D A
DA
D000818:Animals; D004798:Enzymes / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
D004798:Enzymes; D010455:Peptides; D011506:Proteins