Conformational properties and dynamics of protein-like chains confined in an infinite cylinder

Abstract

In this paper the conformational properties and dynamics of protein-like lattice chains confined in an infinite cylinder are investigated by using Monte Carlo simulation method and the hybrid (3 1 0) lattice model. When the diameter of infinite cylinder D is greater than 0.5–0.7 R F, the shape of protein-like chains remains unchanged, here Flory radius R F is R F = 3.0 N 0.6. When D < 0.5 R F, the confinement of the cylinder help to form the helices, however, it hinders to form the coils, and the shape of protein-like chains changes from sphere-like structure to rod-like one. Different confinements affect distinctly to form the secondary structure of proteins. There exist a different dynamics behavior between protein-like chains confined in an infinite cylinder and general protein-like chains without confinement. These investigations may provide some insights into the influence of crowding condition to the conformation properties and dynamics of proteins.