Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain

Journal of Chemical Physics

Volumn 136, Issue 15, 2012, Pages

  Zheng, Wenjun ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

C-TERMINUS; COARSE-GRAINED MODELING; COILED COIL; CONFORMATIONAL TRANSITIONS; COUPLED MOTIONS; DOMAIN ROTATIONS; DYNEIN MOTORS; DYNEINS; FLUORESCENCE RESONANCE ENERGY TRANSFER; MECHANOCHEMICAL COUPLINGS; MICROTUBULES; MOTOR FUNCTION; NORMAL MODE ANALYSIS; NORMAL MODES; NUCLEOTIDE BINDING; PRODUCT RELEASE; SINGLE-MOLECULE; STRUCTURAL INSIGHTS; STRUCTURAL STATE; X-RAY STRUCTURE;

ELECTRON MICROSCOPY; ENERGY TRANSFER;

CONFORMATIONS;

DYNEIN ADENOSINE TRIPHOSPHATASE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DYNEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 84860176470     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4704661     Document Type: Article

References (76)

1. T. Shima, K. Imamula, T. Kon, R. Ohkura, and K. Sutoh, J. Struct. Biol. 156, 182 (2006). 10.1016/j.jsb.2006.03.014
2. S. L. Reck-Peterson, A. Yildiz, A. P. Carter, A. Gennerich, N. Zhang, and R. D. Vale, Cell 126, 335 (2006). 10.1016/j.cell.2006.05.046
3. I. R. Gibbons and A. J. Rowe, Science 149, 424 (1965). 10.1126/science.149.3682.424
4. S. Karki and E. L. Holzbaur, Curr. Opin. Cell. Biol. 11, 45 (1999). 10.1016/S0955-0674(99)80006-4
5. L. M. DiBella and S. M. King, Int. Rev. Cytol. 210, 227 (2001). 10.1016/S0074-7696(01)10007-0
6. R. D. Vale, Cell 112, 467 (2003). 10.1016/S0092-8674(03)00111-9
7. R. B. Vallee, J. C. Williams, D. Varma, and L. E. Barnhart, J. Neurobiol. 58, 189 (2004). 10.1002/neu.10314
8. K. A. Johnson, Annu. Rev. Biophys. Biophys. Chem. 14, 161 (1985). 10.1146/annurev.bb.14.060185.001113
9. K. Imamula, T. Kon, R. Ohkura, and K. Sutoh, Proc. Natl. Acad. Sci. U.S.A. 104, 16134 (2007). 10.1073/pnas.0702370104
10. T. Kon, T. Mogami, R. Ohkura, M. Nishiura, and K. Sutoh, Nat. Struct. Mol. Biol. 12, 513 (2005). 10.1038/nsmb930
11. E. L. Holzbaur and K. A. Johnson, Biochemistry 28, 7010 (1989). 10.1021/bi00443a034
12. E. L. Holzbaur and K. A. Johnson, Biochemistry 28, 5577 (1989). 10.1021/bi00439a036
13. T. Mogami, T. Kon, K. Ito, and K. Sutoh, J. Biol. Chem. 282, 21639 (2007). 10.1074/jbc.M701914200
14. A. Habura, I. Tikhonenko, R. L. Chisholm, and M. P. Koonce, J. Biol. Chem. 274, 15447 (1999). 10.1074/jbc.274.22.15447
15. S. H. Tynan, M. A. Gee, and R. B. Vallee, J. Biol. Chem. 275, 32769 (2000). 10.1074/jbc.M001537200
16. S. A. Burgess, M. L. Walker, H. Sakakibara, P. J. Knight, and K. Oiwa, Nature (London) 421, 715 (2003). 10.1038/nature01377
17. N. Numata, T. Kon, T. Shima, K. Imamula, T. Mogami, R. Ohkura, and K. Sutoh, Biochem. Soc. Trans. 36, 131 (2008). 10.1042/BST0360131
18. A. J. Roberts, N. Numata, M. L. Walker, Y. S. Kato, B. Malkova, T. Kon, R. Ohkura, F. Arisaka, P. J. Knight, K. Sutoh, and S. A. Burgess, Cell 136, 485 (2009). 10.1016/j.cell.2008.11.049
19. I. R. Gibbons, B. H. Gibbons, G. Mocz, and D. J. Asai, Nature (London) 352, 640 (1991). 10.1038/352640a0
20. K. Ogawa, Nature (London) 352, 643 (1991). 10.1038/352643a0
21. M. Samso, M. Radermacher, J. Frank, and M. P. Koonce, J. Mol. Biol. 276, 927 (1998). 10.1006/jmbi.1997.1584
22. A. F. Neuwald, L. Aravind, J. L. Spouge, and E. V. Koonin, Genome Res. 9, 27 (1999). 10.1101/gr.9.1.27
23. M. A. Gee, J. E. Heuser, and R. B. Vallee, Nature (London) 390, 636 (1997). 10.1038/37663
24. M. Nishiura, T. Kon, K. Shiroguchi, R. Ohkura, T. Shima, Y. Y. Toyoshima, and K. Sutoh, J. Biol. Chem. 279, 22799 (2004). 10.1074/jbc.M313362200
25. G. Mocz and I. R. Gibbons, Biochemistry 35, 9204 (1996). 10.1021/bi960662u
26. Y. Takahashi, M. Edamatsu, and Y. Y. Toyoshima, Proc. Natl. Acad. Sci. U.S.A. 101, 12865 (2004). 10.1073/pnas.0403429101
27. T. Kon, M. Nishiura, R. Ohkura, Y. Y. Toyoshima, and K. Sutoh, Biochemistry 43, 11266 (2004). 10.1021/bi048985a
28. A. Silvanovich, M. G. Li, M. Serr, S. Mische, and T. S. Hays, Mol. Biol. Cell 14, 1355 (2003). 10.1091/mbc.E02-10-0675
29. S. L. Reck-Peterson and R. D. Vale, Proc. Natl. Acad. Sci. U.S.A. 101, 14305 (2004). 10.1073/pnas.0404506101
30. C. Cho, S. L. Reck-Peterson, and R. D. Vale, J. Biol. Chem. 283, 25839 (2008). 10.1074/jbc.M802951200
31. K. Shiroguchi and Y. Y. Toyoshima, Cell Motil Cytoskeleton 49, 189 (2001). 10.1002/cm.1032
32. T. Shima, T. Kon, K. Imamula, R. Ohkura, and K. Sutoh, Proc. Natl. Acad. Sci. U.S.A. 103, 17736 (2006). 10.1073/pnas.0606794103
33. T. Kon, K. Sutoh, and G. Kurisu, Nat. Struct. Mol. Biol. 18, 638 (2011). 10.1038/nsmb.2074
34. A. P. Carter, C. Cho, L. Jin, and R. D. Vale, Science 331, 1159 (2011). 10.1126/science.1202393
35. V. Tozzini, Curr. Opin. Struct. Biol. 15, 144 (2005). 10.1016/j.sbi.2005.02.005
36. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar, Biophys. J. 80, 505 (2001). 10.1016/S0006-3495(01)76033-X
37. F. Tama and Y. H. Sanejouand, Protein Eng. 14, 1 (2001). 10.1093/protein/14.1.1
38. K. Hinsen, Proteins 33, 417 (1998). 10.1002/(SICI)1097-0134(19981115)33: 3417::AID-PROT103.0.CO;2-8
39. M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996). 10.1103/PhysRevLett.77. 1905
40. W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein, Proteins 48, 682 (2002). 10.1002/prot.10168
41. I. Bahar and A. J. Rader, Curr. Opin. Struct. Biol. 15, 586 (2005). 10.1016/j.sbi.2005.08.007
42. F. Tama and C. L. Brooks, Annu. Rev. Biophys. Biomol. Struct. 35, 115 (2006). 10.1146/annurev.biophys.35.040405.102010
43. W. Zheng and S. Doniach, Proc. Natl. Acad. Sci. U.S.A. 100, 13253 (2003). 10.1073/pnas.2235686100
44. W. Zheng and B. R. Brooks, Biophys. J. 89, 167 (2005). 10.1529/biophysj.105.063305
45. W. Zheng and B. Brooks, J. Mol. Biol. 346, 745 (2005). 10.1016/j.jmb.2004.12.020
46. H. Yu, L. Ma, Y. Yang, and Q. Cui, PLOS Comput. Biol. 3, e23 (2007). 10.1371/journal.pcbi.0030023
47. I. Navizet, R. Lavery, and R. L. Jernigan, Proteins 54, 384 (2004). 10.1002/prot.10476
48. W. Zheng, B. R. Brooks, and G. Hummer, Proteins 69, 43 (2007). 10.1002/prot.21465
49. M. Cecchini, A. Houdusse, and M. Karplus, PLOS Comput. Biol. 4, e1000129 (2008). 10.1371/journal.pcbi.1000129
50. W. Zheng, B. R. Brooks, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 103, 7664 (2006). 10.1073/pnas.0510426103
51. W. Zheng, Proteins 78, 638 (2010). 10.1002/prot.22594
52. W. Zheng and M. Tekpinar, BMC Struct. Biol. 9, 45 (2009). 10.1186/1472-6807-9-45
53. W. Zheng and D. Thirumalai, Biophys. J. 96, 2128 (2009). 10.1016/j.bpj.2008.12.3897
54. M. Tekpinar and W. Zheng, Proteins 78, 2469 (2010). 10.1002/prot.22755
55. F. Tama, M. Feig, J. Liu, C. L. Brooks III, and K. A. Taylor, J. Mol. Biol. 345, 837 (2005). 10.1016/j.jmb.2004.10.084
56. A. W. Serohijos, Y. Chen, F. Ding, T. C. Elston, and N. V. Dokholyan, Proc. Natl. Acad. Sci. U.S.A. 103, 18540 (2006). 10.1073/pnas.0602867103
57. D. Tsygankov, A. W. Serohijos, N. V. Dokholyan, and T. C. Elston, J. Chem. Phys. 130, 025101 (2009). 10.1063/1.3050098
58. A. W. Serohijos, D. Tsygankov, S. Liu, T. C. Elston, and N. V. Dokholyan, Phys. Chem. Chem. Phys. 11, 4840 (2009). 10.1039/b902028d
59. J. Hafner and W. Zheng, J. Chem. Phys. 132, 014111 (2010). 10.1063/1.3288503
60. D. Ming and M. E. Wall, Phys. Rev. Lett. 95, 198103 (2005). 10.1103/PhysRevLett.95.198103
61. W. Zheng, Proteins 79, 2291 (2011). 10.1002/prot.23055
62. F. Zhu and G. Hummer, Biophys. J. 97, 2456 (2009). 10.1016/j.bpj.2009.08. 020
63. W. Zheng, J. C. Liao, B. R. Brooks, and S. Doniach, Proteins 67, 886 (2007). 10.1002/prot.21326
64. H. Wang and G. Oster, Nature (London) 396, 279 (1998). 10.1038/24409
65. S. Fischer, B. Windshugel, D. Horak, K. C. Holmes, and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 102, 6873 (2005). 10.1073/pnas.0408784102
66. G. Li and Q. Cui, Biophys. J. 86, 743 (2004). 10.1016/S0006-3495(04) 74152-1
67. A. P. Carter, J. E. Garbarino, E. M. Wilson-Kubalek, W. E. Shipley, C. Cho, R. A. Milligan, R. D. Vale, and I. R. Gibbons, Science 322, 1691 (2008). 10.1126/science.1164424
68. I. R. Gibbons, J. E. Garbarino, C. E. Tan, S. L. Reck-Peterson, R. D. Vale, and A. P. Carter, J. Biol. Chem. 280, 23960 (2005). 10.1074/jbc.M501636200
69. T. Kon, K. Imamula, A. J. Roberts, R. Ohkura, P. J. Knight, I. R. Gibbons, S. A. Burgess, and K. Sutoh, Nat. Struct. Mol. Biol. 16, 325 (2009). 10.1038/nsmb.1555
70. A. P. Carter and R. D. Vale, Biochem. Cell Biol. 88, 15 (2010). 10.1139/O09-127
71. H. Ueno, T. Yasunaga, C. Shingyoji, and K. Hirose, Proc. Natl. Acad. Sci. U.S.A. 105, 19702 (2008). 10.1073/pnas.0808194105
72. N. Mizuno, A. Narita, T. Kon, K. Sutoh, and M. Kikkawa, Proc. Natl. Acad. Sci. U.S.A. 104, 20832 (2007). 10.1073/pnas.0710406105
73. A. Gennerich, A. P. Carter, S. L. Reck-Peterson, and R. D. Vale, Cell 131, 952 (2007). 10.1016/j.cell.2007.10.016
74. R. D. Vale, J. Cell Biol. 150, F13 (2000). 10.1083/jcb.150.1.F13
75. P. Hook, A. Mikami, B. Shafer, B. T. Chait, S. S. Rosenfeld, and R. B. Vallee, J. Biol. Chem. 280, 33045 (2005). 10.1074/jbc.M504693200
76. See supplementary material at http://dx.doi.org/10.1063/1.4704661 E-JCPSA6-136-041216 for two supplemental tables, two supplemental figures, two movies, and two Ca coordinate files in PDB format.