Discrete step model of helix-coil kinetics: Distribution of fluctuation times

• Published in: The Journal of Chemical Physics
• Main Author: Poland, Douglas
• Format: Article in Journal/Newspaper
• Language: English
• Published: AIP Publishing 1996
• Subjects: Physical and Theoretical Chemistry; General Physics and Astronomy; Sperm whale
• Online Access: http://dx.doi.org/10.1063/1.471965; https://pubs.aip.org/aip/jcp/article-pdf/105/3/1242/10781016/1242_1_online.pdf

A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo cellular automata approximation of the kinetics of this system in discrete time. This approximation is tested against a number of exact solutions for homopolymers and is then used to calculate moments of the distribution function for the time intervals between switches in conformational state at a given site (e.g., given a switch from coil to helix at zero time, how long will it take before the state switches back). The maximum-entropy method is used to construct the very broad distribution function from the moments. In heteropolymers the diffusion of helix-coil boundaries is reduced, helix being more localized on strong helix-forming residues. We investigate the effect of a specific sequence of amino acid residues on conformational fluctuations by using the known σ and s values for the naturally occurring amino acids to simulate the kinetics of helix formation (limiting the range of cooperativity to the α-helix) in sperm whale myoglobin, giving the time evolution to the equilibrium probability profile in this system.