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

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Conformation-dependent sequence design: evolutionary approach.

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

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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.

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Algorithms Computer Simulation Entropy Evolution, Molecular Ligands Models, Molecular Models, Theoretical Monte Carlo Method Polymers Protein Conformation Protein Folding Proteins Sequence Analysis, DNA Thermodynamics Journal Article

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A V Chertovich, E N Govorun, V A Ivanov, P G Khalatur, A R Khokhlov. 2004. Conformation-dependent sequence design: evolutionary approach.. https://doi.org/10.1140/epje%2Fe2004-00036-1

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