Incorporation of pairwise interactions into the Lifson-Roig model for helix prediction

✍ Scribed by William Shalongo; Earle Stellwagen

• Book ID: 105356310
• Publisher: Cold Spring Harbor Laboratory Press
• Year: 1995
• Tongue: English
• Weight: 539 KB
• Volume: 4
• Category: Article
• ISSN: 0961-8368
• DOI: 10.1002/pro.5560040614

✦ Synopsis

Abstract

The helix/coil equilibrium of a peptide in solution can be modulated by a variety of side‐chain interactions that are not incorporated into the standard statistical mechanical models for prediction of peptide helical content. In this report, we describe a recursive formulation of the Lifson‐Roig model that facilitates incorporation of specific pairwise side‐chain interactions as well as nonspecific individual side‐chain capping interactions. Application of this extended model to a series of host/guest peptides indicates that the apparent AG value for a pairwise apolar interaction is dependent upon the spacing and orientation but not the sequential location of the participating residues. The apparent AG values for such interactions are about 40% greater than the corresponding apparent ΔΔG values obtained from difference measurements.