The influence of short-range interactions on protein conformation. 3. Dipeptide distributions in proteins of known sequence and structure.
A statistical analysis is made of the distribution into alpha-helical and non-alpha-helical regions of the various dipeptide types appearing in a sample of seven proteins of known sequence and structure. By considering as a group all dipeptide types occurring at a given location relative to the reported helix-coil boundaries and examining the percentage of cases in which these appear in non-alpha-helical regions throughout the protein sample, we find a sharp change in the nature of the observed dipeptide types when the helix-coil boundary is crossed. Furthermore, we find that dipeptide types which occur in the coil region near the C-terminal end of helical segments are non-alpha-helical in almost 90 per cent of the cases in which they appear throughout the sample. No similar effect is found in the coil region near the N-terminal end of helical segments. These results give evidence for the importance of short-range interactions in determining protein conformation. They are also consistent with predictions based on a model for helix formation given in the second paper of this series.(1)
D000595:Amino Acid Sequence; D002918:Chymotrypsin; D006454:Hemoglobins; D008956:Models, Chemical; D009113:Muramidase; D009211:Myoglobin; D010206:Papain; D010455:Peptides; D011506:Proteins; D012260:Ribonucleases; D013223:Statistics as Topic
D006454:Hemoglobins; D009211:Myoglobin; D010455:Peptides; D011506:Proteins; D012260:Ribonucleases; D009113:Muramidase; D002918:Chymotrypsin; D010206:Papain