Incorporation of pairwise interactions into the Lifson-Roig model for helix prediction.
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 delta G value for a pairwise apolar interaction is dependent upon the spacing and orientation but not the sequential location of the participating residues. The apparent delta G values for such interactions are about 40% greater than the corresponding apparent delta delta G values obtained from difference measurements.
Shalongo
W
W
Department of Biochemistry, University of Iowa, Iowa City 52242, USA.
Stellwagen
E
E
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
D010455:Peptides