Interplay between peptide bond geometrical parameters in nonglobular structural contexts

Biomed Res Int. 2013:2013:326914. doi: 10.1155/2013/326914. Epub 2013 Dec 26.

Abstract

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-C(α)-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-C(α)-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amyloidogenic Proteins / chemistry
  • Collagen / chemistry
  • Hydrogen Bonding
  • Models, Molecular
  • Protein Conformation*
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Water / chemistry

Substances

  • Amyloidogenic Proteins
  • Proteins
  • Water
  • Collagen