Observation of residual dipolar couplings in short peptides.
Residual dipolar couplings provide information on the orientation of individual bond vectors with respect to a unique set of molecular axes. We report that short peptides from 2 to 15 amino acids in length of arbitrary sequence exhibit a modest range of residual dipolar couplings when aligned in either strained polyacrylamide gels or alkyl-PEG bicelles. The absence of significant line broadening in gels suggests peptides align predominantly through steric interactions with the polyacrylamide matrix. However, broadening of NMR lines for a subset of residues aligned in bicelles indicates some peptides bind weakly to these lipid disks, yet a weak negative correlation between the couplings measured in gels and bicelles is consistent with steric hindrance playing a role in both media. The observation of dipolar couplings for peptides of length 10-15 suggests the statistical segment lengths of polypeptide chains must often be >10-15 residues, with data from denatured proteins indicating even larger values. Presumably, local side-chain backbone interactions severely restrict chain flexibility, with the cumulative effect of many such restrictions giving rise to biases in chain direction that may persist for the entire length of a protein chain. Comparison of experimental dipolar couplings for peptides with couplings calculated for ensembles of conformations generated by molecular dynamics should permit evaluation of the accuracy of molecular mechanics potentials in reproducing sequence-specific preferences for phi and psi angles.
Ohnishi
Satoshi
S
Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Shortle
David
D
D000595:Amino Acid Sequence; D004591:Electrophoresis, Polyacrylamide Gel; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D006180:Proton-Translocating ATPases / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*
D009842:Oligopeptides; D010455:Peptides; D006180:Proton-Translocating ATPases