Conformation-dependent sequence design: evolutionary approach
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
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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.
© EDP Sciences, Società Italiana di Fisica, and Springer-Verlag, 2004