Abstract Using Monte Carlo simulations, we have studied the folding dynamics and thermodynamics of geometrically constrained lattice protein model chains. The constraints are realized by fixing one or both terminals of the chains. By comparing the results with that of the free-end chains, we find that the folding behaviours of the end-constrained chains are not completely similar to that of the free-end chains. Both kinds of constraints on the chain ends affect the folding dynamics of the chains: i.e., the folding rate, but not the thermodynamics. The thermodynamic behaviour of the one-end-fixed chains shows less difference from that of the free-end chains, while the thermodynamic behaviour of the two-end-fixed chains has obvious difference from that of the free-end chains. The origin of these differences comes from the differences of the ergodicity of the chains in the conformational space.
Received: 19 February 2004
Revised: 18 May 2004
Accepted manuscript online:
PACS:
87.15.Cc
(Folding: thermodynamics, statistical mechanics, models, and pathways)
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos 90103031, 10074030, 10021001 and 10204013), and the Nonlinear Project of the State Key Development Program for Basic Research of the NSM of China.
Cite this article:
Ji Gao-Feng (吉高峰), Xue Bin (薛彬), Wang Wei (王炜) Folding of lattice protein model chains with fixed ends 2004 Chinese Physics 13 1574
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