Formation of secondary structures in polypetides. A Monte Carlo simulation.
The lattice approximation of a polypetide chain was used in the computer simulation. The residues of a model polypetide were represented by the chain of a-carbons located on a very flexible [310] lattice. The force field contained the long-range contact potential between the residues as well as the local preferences in forming helical structures. The chain consisted of two types of residues: hydrophillic (P) and hydrophobic (H), forming a typical repeatable helical septet -HHPPHPP-. The simulations were performed by means of the Replica Exchange Monte Carlo method combined with th e Histogram method. A series of simulations were performed enabling one to investigate the influence of both components of the force field on the transition temperature and the characteristics of the coil-to-globule transition. The properties of low-temperature ordered structures were determined. The thermodynamical description of the mod el polypeptide was also given. The phase transition was found to be sharp and cooperative for longer chains and strong helical potential.
Sikorski
Andrzej
A
Department of Chemistry, University of Warsaw, 1 Pasteura Str., 02-093 Warsaw, Poland. sikorski@chem.uw.edu.pl
Romiszowski
Piotr
P
D000465:Algorithms; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D010455:Peptides