Conformation-dependent sequence design: evolutionary approach.
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.
Chertovich
A V
AV
Physics Department, Moscow State University, 119992, Moscow, Russia. chertov@polly.phys.msu.ru
Govorun
E N
EN
Ivanov
V A
VA
Khalatur
P G
PG
Khokhlov
A R
AR
D000465:Algorithms; D003198:Computer Simulation; D019277:Entropy; D019143:Evolution, Molecular; D008024:Ligands; D008958:Models, Molecular; D008962:Models, Theoretical; D009010:Monte Carlo Method; D011108:Polymers / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D017422:Sequence Analysis, DNA; D013816:Thermodynamics
D008024:Ligands; D011108:Polymers; D011506:Proteins