Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. Appendix: Testing a 1-Dimensional Diffusion Model for Peptide Dynamics

Abstract

Quenching of the triplet state of tryptophan by cysteine provides an important new tool for measuring the rate at which a specific intramolecular contact is formed in disordered polypeptides. By measuring the viscosity dependence of the quenching rate, both the reaction-limited and the diffusion-limited quenching rates can be determined. The diffusion-limited rate corresponds to the rate of forming a short-range contact. The reaction-limited rate, which depends solely on the equilibrium end-to-end distribution, becomes essentially length-independent for short chains, providing clear-cut evidence that the chain is stiff. The length dependence of the reaction-limited rate can be accurately calculated using the distance dependence of the quenching rate determined at room temperature in a rigid glass, together with the end-to-end distance distribution for a wormlike chain having a persistence length of 0.6−0.7 nm. In addition, the length dependence of the diffusion-limited rate can also be reproduced by treat...