Modeling DNA loops using the theory of elasticity

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

Volumn 73, Issue 3, 2006, Pages

  Balaeff, Alexander ^a,c   Mahadevan, L ^b   Schulten, Klaus ^a,d  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b HARVARD UNIVERSITY   (United States)

^c DUKE UNIVERSITY   (United States)

^d University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELASTIC ROD MODEL; ELECTROSTATIC CHARGE; PROTEIN-BOUND DNA LOOP;

ANISOTROPY; ELASTICITY; ELECTROSTATICS; MATHEMATICAL MODELS; PARAMETER ESTIMATION; PROTEINS;

DNA;

DNA;

CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELASTICITY; MECHANICAL STRESS; ULTRASTRUCTURE;

COMPUTER SIMULATION; DNA; ELASTICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; STRESS, MECHANICAL;

EID: 33645086141     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.73.031919     Document Type: Article

References (76)

1. J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 5th ed. (W. H. Freeman and Co., New York, 2002).
2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed. (Garland Science, New York, 2002).
3. S. E. Halford, A. J. Welsh, and M. D. Szczelkun, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.33.110502.132711 33, 1 (2004).
4. J. Vilar and L. Saiz, Curr. Opin. Genet. Dev. COGDET 0959-437X 15, 136 (2005).
5. S. Semsey, K. Virnik, and S. Adhya, Trends Biochem. Sci. TBSCDB 0167-7640 30, 334 (2005).
6. K. Luger, Curr. Opin. Genet. Dev. COGDET 0959-437X 13, 127 (2003).
7. M. Thanbichler, P. H. Viollier, and L. Shapiro, Curr. Opin. Genet. Dev. COGDET 0959-437X 15, 153 (2005).
8. T. E. Cheatham III, Curr. Opin. Struct. Biol. COSBEF 0959-440X 14, 360 (2004);
9. J. Norberg and L. Nilsson, Q. Rev. Biophys. QURBAW 0033-5835 10.1017/S0033583503003895 36, 257 (2003).
10. W. K. Olson and V. B. Zhurkin, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00086-5 10, 286 (2000).
11. T. Schlick, D. A. Beard, and J. Huang, Comput. Sci. Eng. CSENFA 1521-9615 10.1109/5992.881706 2, 38 (2000).
12. R. Phillips, M. Dittrich, and K. Schulten, Annu. Rev. Mater. Res. ARMRCU 1531-7331 10.1146/annurev.matsci.32.122001.102202 32, 219 (2002).
13. A. A. Travers and J. M. T. Thompson, Philos. Trans. R. Soc. London, Ser. A PTRMAD 0962-8428 10.1098/rsta.2004.1392 362, 1265 (2004).
14. J. Huang and T. Schlick, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1511506 117, 8573 (2002).
15. G. R. Kirchhoff, Vorlesungen über Mathematische Physik, Mechanik, Vorlesung 28 (B.G. Teubner, Leipzig, 1977).
16. A. V. Vologodskii and N. R. Cozzarelli, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.23.1.609 23, 609 (1994).
17. T. Schlick, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/0959-440X(95)80083-2 5, 245 (1995).
18. Y. Shi, A. E. Borovik, and J. E. Hearst, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.470250 103, 3166 (1995).
19. A. Balaeff, L. Mahadevan, and K. Schulten, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.4900 83, 4900 (1999).
20. P. K. Purohit, J. Kondev, and R. Phillips, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0737893100 100, 3173 (2003).
21. W. K. Olson, in Oxford Handbook of Nucleic Acid Structure, edited by, S. Neidle, (Oxford University Press, Oxford, UK, 1999), Chap., pp. 499-531.
22. J. F. Marko and E. D. Siggia, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.52.2912 52, 2912 (1995).
23. P. B. Furrer, R. S. Manning, and J. H. Maddocks, Biophys. J. BIOJAU 0006-3495 79, 116 (2000).
24. W. K. Olson, D. Swigon, and B. D. Coleman, Philos. Trans. R. Soc. London, Ser. A PTRMAD 0962-8428 362, 1403 (2004).
25. B. D. Coleman and D. Swigon, Philos. Trans. R. Soc. London, Ser. A PTRMAD 0962-8428 362, 1281 (2004).
26. E. Villa, A. Balaeff, L. Mahadevan, and K. Schulten, Multiscale Model. Simul. MMSUBT 1540-3459 2, 527 (2004).
27. E. Villa, A. Balaeff, and K. Schulten, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409387102 102, 6783 (2005).
28. T. Schlick, B. Li, and W. Olson, Biophys. J. BIOJAU 0006-3495 67, 2146 (1994).
29. M. O. Fenley, W. K. Olson, I. Tobias, and G. S. Manning, Biophys. Chem. BICIAZ 0301-4622 10.1016/0301-4622(93)E0094-L 50, 255 (1994).
30. A. Vologodskii and N. R. Cozzarelli, Biopolymers BIPMAA 0006-3525 10.1002/bip.360350304 35, 289 (1995).
31. J. Ubbink and T. Odijk, Biophys. J. BIOJAU 0006-3495 76, 2502 (1999).
32. A. A. Travers, Philos. Trans. R. Soc. London, Ser. A PTRMAD 0962-8428 362, 1423 (2004).
33. W. K. Olson, A. A. Gorin, X.-J. Lu, L. M. Hock, and V. B. Zhurkin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.19.11163 95, 11163 (1998).
34. A. Matsumoto and W. K. Olson, Biophys. J. BIOJAU 0006-3495 83, 22 (2002).
35. W. K. Olson, N. L. Marky, R. L. Jernigan, and V. B. Zhurkin, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1993.1409 232, 530 (1993).
36. L. Mahadevan and J. B. Keller, Philos. Trans. R. Soc. London, Ser. A PTRMAD 0962-8428 440, 149 (1993).
37. M. Lewis, G. Chang, N. C. Horton, M. A. Kercher, H. C. Pace, M. A. Schumacher, R. G. Brennan, and P. Lu, Science SCIEAS 0036-8075 271, 1247 (1996).
38. B. Müller-Hill, The Lac Operon: A Short History of a Genetic Paradigm (Walter de Gruyter, Berlin, 1996).
39. S. Oehler, E. R. Eismann, H. Krämer, and B. Müller-Hill, EMBO J. EMJODG 0261-4189 9, 973 (1990).
40. A. E. H. Love, A Treatise on the Mathematical Theory of Elasticity (Dover Publications, Inc., New York, 1927).
41. L. D. Landau and E. M. Lifschitz, Theory of Elasticity, Vol. 7 of Course of Theoretical Physics (Pergamon Press, Oxford, New York, 1986), 3rd ed.
42. T. P. Westcott, I. Tobias, and W. K. Olson, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.474752 107, 3967 (1997).
43. B. D. Coleman, I. Tobias, and D. Swigon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.470021 103, 9101 (1995).
44. W. K. Olson, M. Bansal, S. K. Burley, R. E. Dickerson, M. Gerstein, S. C. Harvey, U. Heinemann, X.-J. Lu, S. Neidle, Z. Shakked, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.2001.4987 313, 229 (2001).
45. E. T. Whittaker, A Treatise on the Analytical Dynamics of Particles and Rigid Bodies, with an Introduction to the Problem of Three Bodies, 4th ed. (Cambridge University Press, Cambridge, UK, 1960).
46. M. E. Hogan and R. H. Austin, Nature (London) NATUAS 0028-0836 10.1038/329263a0 329, 263 (1987).
47. P. J. Hagerman, Annu. Rev. Biophys. Biophys. Chem. ARBCEY 0883-9182 10.1146/annurev.bb.17.060188.001405 17, 265 (1988).
48. T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.29.1.523 29, 523 (2000).
49. P. J. Heath, J. B. Clendenning, B. S. Fujimoto, and J. M. Schurr, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0432 260, 718 (1996).
50. S. G. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.12.6185 94, 6185 (1997).
51. Y. L. Zhang and D. M. Crothers, Biophys. J. BIOJAU 0006-3495 84, 136 (2003).
52. I. Tobias, D. Swigon, and B. D. Coleman, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.61.747 61, 747 (2000).
53. L. M. Edelman, R. Cheong, and J. D. Kahn, Biophys. J. BIOJAU 0006-3495 84, 1131 (2003).
54. G. Bader and U. Ascher, SIAM (Soc. Ind. Appl. Math.) J. Sci. Stat. Comput. SIJCD4 0196-5204 10.1137/0908047 8, 483 (1987).
55. A. Balaeff, L. Mahadevan, and K. Schulten, http://arxiv.org/abs/physics/ 0301006 (2003).
56. W. Hsieh, P. A. Whitson, K. S. Mathews, and R. D. Wells, J. Biol. Chem. JBCHA3 0021-9258 262, 14583 (1987).
57. B. D. Coleman, D. Swigon, and I. Tobias, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.61.759 61, 759 (2000).
58. Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Cozzarelli, and C. Bustamante, Nature (London) NATUAS 0028-0836 10.1038/nature01810 424, 338 (2003).
59. G. S. Manning, Q. Rev. Biophys. QURBAW 0033-5835 2, 179 (1978).
60. A. Balaeff, L. Mahadevan, and K. Schulten, Structure (London) STRUE6 0969-2126 12, 123 (2004).
61. T. R. Strick, J.-F. Allemand, D. Bensimon, A. Bensimon, and V. Croquette, Science SCIEAS 0036-8075 271, 1835 (1996);
62. S. B. Smith, Y. Cui, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.274.5288.795 271, 795 (1996).
63. V. V. Rybenkov, C. Ullsperger, A. Vologodskii, and N. R. Cozzarelli, Science SCIEAS 0036-8075 10.1126/science.277.5326.690 277, 690 (1997).
64. D. Swigon, B. D. Coleman, and I. Tobias, Biophys. J. BIOJAU 0006-3495 74, 2515 (1998).
65. B. Isralewitz, M. Gao, and K. Schulten, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00194-9 11, 224 (2001).
66. C. L. Lawson, D. Swigon, K. S. Murakami, S. A. Darst, H. M. Berman, and R. H. Ebright, Curr. Opin. Struct. Biol. COSBEF 0959-440X 14, 10 (2004).
67. J. M. Hudson and M. G. Fried, J. Mol. Biol. JMOBAK 0022-2836 214, 381 (1990);
68. M. Perros, T. A. Steitz, M. G. Fried, and J. M. Hudson, Science SCIEAS 0036-8075 274, 1929 (1996).
69. J. F. Marko, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i1997-00223-5 38, 183 (1997).
70. J. C. Reese, Curr. Opin. Genet. Dev. COGDET 0959-437X 13, 105 (2003).
71. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics JMGRDV 0263-7855 10.1016/0263-7855(96)00018-5 14, 33 (1996).
72. M. D. Barkley, and S. Bourgeois, in The Operon, edited by, J. H. Miller, and, W. S. Reznikoff, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1980), pp. 177-220.
73. Polygen, Quanta, Polygen Corporation, 200 Fifth Ave., Waltham, MA 02254 (1988).
74. L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1999.6201 151, 283 (1999).
75. A. D. MacKerell, Jr., J. Wiorkiewicz-Kuczera, and M. Karplus, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00153a017 117, 11946 (1995).
76. J. F. Marko and E. D. Siggia, Science SCIEAS 0036-8075 265, 506 (1994).