中国物理B ›› 2009, Vol. 18 ›› Issue (11): 4852-4864.doi: 10.1088/1674-1056/18/11/040

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Modelling of a DNA packaging motor

钱钧1, 薛晓光2, 谢平3, 王鹏业3   

  1. (1)College of Physics Science, Nankai University, Tianjin 300071, China; (2)Department of Physics, Renmin University of China, Beijing 100872, China; (3)Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • 收稿日期:2009-04-06 修回日期:2009-05-07 出版日期:2009-11-20 发布日期:2009-11-20
  • 基金资助:
    Project supported by the National Natural Science Foundation of China (Grant Nos 10834014 and 10674173) and the National Basic Research Program of China (Grant No 2009CB930704).

Modelling of a DNA packaging motor

Qian Jun(钱钧)a),Xie Ping (谢平)b)†, Xue Xiao-Guang(薛晓光)c), and Wang Peng-Ye(王鹏业)b)   

  1. a College of Physics Science, Nankai University, Tianjin 300071, China; b Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; c Department of Physics, Renmin University of China, Beijing 100872, China
  • Received:2009-04-06 Revised:2009-05-07 Online:2009-11-20 Published:2009-11-20
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant Nos 10834014 and 10674173) and the National Basic Research Program of China (Grant No 2009CB930704).

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摘要： During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage φ 29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient \textitin vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the φ 29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.

Abstract: During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage $\phi$29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the $\phi$29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.

Key words: DNA translocation, pause, slip, molecular motor

中图分类号:  (Nucleic acids)

  • 87.14.G-
87.15.A- (Theory, modeling, and computer simulation) 87.15.B- (Structure of biomolecules) 87.15.H- (Dynamics of biomolecules) 36.20.Hb (Configuration (bonds, dimensions)) 87.15.R- (Reactions and kinetics)