Local interactions in bends of proteins.

Abstract

Calculated probabilities of bend formation in 47 amino acid sequences of N-acetyl-N'-methylamide dipeptides, determined from a statistical mechanical analysis using empirical conformational energies, were compared with the observed fraction of bends formed in the same 47 dipeptide sequences in the x-ray structures of 20 globular proteins. Agreement between the calculated and observed fraction of bends was found for 26 dipeptides, suggesting that, for those particular dipeptide sequences, local interactions dominate over long-range interactions in determining conformational preference. Seven dipeptide sequences, all of which contained a Gly residue, had a significantly higher calculated than observed bend preference, indicating the strong influence of long-range and/or solvent interactions in those sequences. Of the 14 sequences for which the calculated was significantly less than the observed bend fraction, 13 dipeptide sequences contained at least one polar residue (Ser, Asn, or Asp) and/or an aromatic residue (Phe or Tyr), suggesting that solvent effects may play an important role in dictating the conformation in these sequences. The analysis of dipeptide sequences in the twenty globular proteins also indicated that the 4 leads to 1 hydrogen bond is not a dominant factor in stabilizing bends in proteins, and that most dipeptide sequences are capable of forming several types of bend conformations.

• Authors: S S Zimmerman, H A Scheraga
• Journal: Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci U S A) Vol. 74 Issue 10 Pg. 4126-9 (Oct 1977) ISSN: 0027-8424 [Print] United States
• PMID: 270658 (Publication Type: Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S.)

Chemical References

• Dipeptides
• Proteins

Topics

• Chemical Phenomena
• Chemistry
• Dipeptides (analysis)
• Models, Chemical
• Probability
• Protein Conformation
• Proteins
• X-Ray Diffraction