中国物理B ›› 2004, Vol. 13 ›› Issue (9): 1574-1581.doi: 10.1088/1009-1963/13/9/037

• 8000 CROSSDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇    下一篇

Folding of lattice protein model chains with fixed ends

吉高峰, 薛彬, 王炜   

  1. National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing 210093, China
  • 收稿日期:2004-02-19 修回日期:2004-05-18 出版日期:2005-06-21 发布日期:2005-06-21
  • 基金资助:
    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.

Folding of lattice protein model chains with fixed ends

Ji Gao-Feng (吉高峰), Xue Bin (薛彬), Wang Wei (王炜)   

  1. National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing 210093, China
  • Received:2004-02-19 Revised:2004-05-18 Online:2005-06-21 Published:2005-06-21
  • Supported by:
    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.

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摘要： 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.

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.

Key words: lattice protein model, Monte Carlo simulation, folding behaviour, constraints on the ends of chains

中图分类号:  (Folding: thermodynamics, statistical mechanics, models, and pathways)

  • 87.15.Cc