Directional dependent dynamics of protein molecules on DNA

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 79, Issue 4, 2009, Pages

  Murugan, Rajamanickam ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY MADRAS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN DYNAMICS; CIS-ACTING ELEMENT; DNA CHAINS; ENERGY COST; ENERGY INPUTS; ENHANCING EFFECT; INITIAL POSITION; MECHANISM OF ACTION; PROTEIN MOLECULES; RANDOMLY DISTRIBUTED; RETARDING EFFECT; SEARCH SPACES; SITE-SPECIFIC; TARGET SITES; TRANSCRIPTIONAL FACTORS;

BINDING ENERGY; BINDING SITES; BROWNIAN MOVEMENT; DNA; DYNAMICS; FREE ENERGY; GENES; NUCLEIC ACIDS; TARGETS;

MOLECULES;

EID: 65649113213     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.79.041913     Document Type: Article

References (30)

1. B. Levin, Genes VIII (Prentice-Hall, Englewoods Cliff, NJ, 2003)
2. B. Alberts, D. Bray, J. Lewis, K. Roberts, and J. D. Watson, Molecular Biology of the Cell (Garland, New York, 1994)
3. M. Ptashne, A Genetic Switch (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2004).
4. A. D. Riggs, S. Bourgeois, and M. Cohn, J. Mol. Biol. 53, 401 (1970). 10.1016/0022-2836(70)90074-4
5. G. Adam and M. Delbruck, Structural Chemistry in Molecular Biology (Freeman, San Francisco, 1968)
6. R. F. Bruinsma, Physica A 313, 211 (2002). 10.1016/S0378-4371(02)01038-5
7. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20, 6929 (1981). 10.1021/bi00527a028
8. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20, 6961 (1981). 10.1021/bi00527a028
9. S. E. Halford and M. D. Szczelkun, Eur. Biophys. J. 31, 257 (2002) 10.1007/s00249-002-0224-4
10. S. E. Halford and J. F. Marko, Nucleic Acids Res. 32, 3040 (2004). 10.1093/nar/gkh624
11. M. Slutsky and L. A. Mirny, Biophys. J. 87, 4021 (2004) 10.1529/biophysj.104.050765
12. M. Slutsky, M. Kardar, and L. A. Mirny, Phys. Rev. E 69, 061903 (2004). 10.1103/PhysRevE.69.061903
13. G. Kolesov, Z. Wunderlich, O. N. Laikova, M. S. Gelfand, and L. A. Mirny, Proc. Natl. Acad. Sci. U.S.A. 104, 13948 (2007). 10.1073/pnas.0700672104
14. R. Murugan, Biophys. Chem. 120, 143 (2006). 10.1016/j.bpc.2005.10.014
15. M. Ptashne and A. Gann, Genes and Signals (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2001).
16. R. Murugan, J. Theor. Biol. 248, 696 (2007) 10.1016/j.jtbi.2007.06.003
17. E. M. Blackwood and J. T. Kadonaga, Science 281, 60 (1998). 10.1126/science.281.5373.60
18. G. Lan and S. X. Sun, Biophys. J. 88, 999 (2005). 10.1529/biophysj.104. 047662
19. M. O. Magnasco, Phys. Rev. Lett. 71, 1477 (1993) 10.1103/PhysRevLett.71. 1477
20. R. D. Astumian, Science 276, 917 (1997) 10.1126/science.276.5314.917
21. P. Reimann, Phys. Rep. 361, 57 (2002). 10.1016/S0370-1573(01)00081-3
22. I. M. Sokolov, R. Metzler, K. Pant, and M. C. Williams, Biophys. J. 89, 895 (2005). 10.1529/biophysj.104.057612
23. C. W. Gardiner, Handbook of Stochastic Methods (Springer, Berlin, 2004)
24. H. Risken, Fokker-Planck Equations (Springer, Berlin, 1996)
25. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 2004)
26. S. Redner, A Guide to First Passage Processes (Cambridge University Press, Cambridge, England, 2001).
27. R. Murugan, Phys. Rev. E 76, 011901 (2007) 10.1103/PhysRevE.76.011901
28. R. Murugan, Phys. Rev. E 69, 011911 (2004). 10.1103/PhysRevE.69.011911
29. C. G. Kalodimos, N. Biris, A. M. J. J. Bonvin, M. M. Levandoski, M. Guennuegues, R. Boelens, and R. Kaptein, Science 305, 386 (2004). 10.1126/science.1097064
30. L. Hu, A. Y. Grosberg, and R. Bruinsma, Biophys. J. 95, 1151 (2008). 10.1529/biophysj.108.129825