ANALYSIS OF PROTON CHEMICAL-SHIFTS IN REGULAR SECONDARY STRUCTURE OF PROTEINS

The contribution of peptide groups to H(alpha) and H(beta) proton chem ical shifts can be modeled with empirical equations that represent mag netic anisotropy and electrostatic interactions [Osapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436-9444]. Using these, a model f or the 'random coil' reference state can be generated by averaging a d ipeptide over energetically allowed regions of torsion-angle space. Su ch 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 a nd proline residues, which differ significantly from other residues in their allowed phi,psi-ranges. New constants for these residues are re ported that provide significant improvements in predicted backbone shi fts. To illustrate how secondary structure affects backbone chemical s hifts we report calculations on oligopeptide models for helices, sheet s and turns. In addition to suggesting a physical mechanism for the wi dely recognized average difference between alpha and beta secondary st ructures, these models suggest several additional regularities that sh ould be expected: (a) H(alpha) protons at the edges of beta-sheets wil l have a two-residue periodicity; (b) the H(alpha) and H(alpha3) proto ns 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 shifte d upfield, except those in position 3 of type I turns. Examples of obs erved shift patterns in several proteins illustrate the application of these ideas.