Conformation-dependent sequence design: evolutionary approach

A. V. Chertovich; E. N. Govorun; V. A. Ivanov; P. G. Khalatur; A. R. Khokhlov

doi:10.1140/epje/e2004-00036-1

EPJ

Conformation-dependent sequence design: evolutionary approach

A. V. Chertovich¹^*, E. N. Govorun¹, V. A. Ivanov¹, P. G. Khalatur²^,3 and A. R. Khokhlov¹^,3

¹ Physics Department, Moscow State University, 119992, Moscow, Russia
² Department of Physical Chemistry, Tver State University, 170002, Tver, Russia
³ Department of Polymer Science, University of Ulm, 89069, Ulm, Germany

Abstract

A new modification of evolutionary approach to sequence design of copolymers has been proposed. A model of step-by-step evolution of a two-letter (HP) copolymer sequence has been studied by means of a coarse-grained Monte Carlo algorithm. The conditions for accepting a change in the primary sequence depend on the spatial conformation of HP-copolymer chain. This leads to a coupling between sequence and conformation and to formation of protein-like conformations and primary sequences (for some values of parameters of the model) independently of initial sequence and/or conformation. Simple theory describing these computer simulation observations is developed.