The influence of short-range interactions on protein conformation. 3. Dipeptide distributions in proteins of known sequence and structure

• Published in: Proceedings of the National Academy of Sciences - PNAS 1969-07, Vol.63 (3), p.615-622
• Main Authors: Kotelchuck, D, Dygert, M, Scheraga, H A
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Chymotrypsin; Hemoglobins; Models, Chemical; Muramidase; Myoglobin; Papain; Peptides; Proteins; Ribonucleases; Statistics as Topic
• ISSN: 0027-8424
• DOI: 10.1073/pnas.63.3.615

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)