Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature

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Abstract

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two dimensional and has two different "amino acids." Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.

Detaljer

Författare
Enheter & grupper
Originalspråkengelska
Sidor (från-till)10298-10305
Antal sidor8
TidskriftJournal of Chemical Physics
Volym103
Utgivningsnummer23
StatusPublished - 1995
PublikationskategoriForskning
Peer review utfördJa