Statistical mechanics of noncovalent bonds in polyamino acids. V. Treatment of long chains by the method of sequence‐generating functions: Hydrophobic bonding in random coil, and interactions between helical segments

Abstract

AbstractThe method of sequence‐generating functions is applied to long polypeptide chains to describe various types of hydrophobic bonding in the random coil. These results are then combined with a similar treatment of the α‐helix in order to discuss the helix–coil transition in single helices and in molecules whose helical segments interact by side‐chain hydrophobic bonding. Numerical calculations, based on the equations derived in this and preceding papers, are presented to show the relative probabilities of occurrence in the random coil of neighbor–neighbor hydrophobic bonds and pockets of hydrophobic bonding, and the relative probabilities of occurrence of the various states in a system of interacting helices. A discussion is also presented of the dependence of the helix–coil nucleation and growth parameters on solvent and side chain.