Modeling stochastic kinetics of molecular machines at multiple levels: From molecules to modules

Biophysical Journal

Volumn 104, Issue 11, 2013, Pages 2331-2341

  Chowdhury, Debashish ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MOTOR;

BIOLOGICAL MODEL; BIOMECHANICS; BIOPHYSICS; KINETICS; METABOLISM; REVIEW; STATISTICS;

BIOMECHANICAL PHENOMENA; BIOPHYSICAL PROCESSES; KINETICS; MODELS, BIOLOGICAL; MOLECULAR MOTOR PROTEINS; STOCHASTIC PROCESSES;

EID: 84878838994     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.04.042     Document Type: Review

References (89)

1. M. Piccolino Biological machines: from mills to molecules Nat. Rev. Mol. Cell Biol. 1 2000 149 153
2. C. Mavroidis, A. Dubey, and M.L. Yarmush Molecular machines Annu. Rev. Biomed. Eng. 6 2004 363 395
3. A. Baumgaertner Biomolecular machines M. Rieth, W. Schommers, Handbook of Theoretical and Computational Nanotechnology 2005 American Scientific Publishers Stevenson Ranch, CA 1 89
4. N.R. Cozzarelli, and G.J. Cost J.E. Stray Giant proteins that move DNA: bullies of the genomic playground Nat. Rev. Mol. Cell Biol. 7 2006 580 588
5. B. Alberts The cell as a collection of protein machines: preparing the next generation of molecular biologists Cell 92 1998 291 294
6. M.F. Carlier, and E. Helfer F. Haraux Living nanomachines P. Boisseau, P. Houdy, M. Lahmani, Nanoscience 2010 Springer New York
7. J. Frank Molecular Machines in Biology: Workshop of the Cell 2011 Cambridge University Press Cambridge
8. B. Roux Molecular Machines 2011 World Scientific River Edge, NJ
9. M.G. Rossmann, and V.B. Rao Viral Molecular Machines 2012 Springer New York
10. A.K. Sharma, and D. Chowdhury Template-directed biopolymerization: tape-copying Turing machines Biophys. Rev. Lett. 7 2012 1 41
11. J. Howard Mechanics of Motor Proteins and the Cytoskeleton 2001 Sinauer Associates Sunderland, MA
12. R.D. Vale, and R.A. Milligan The way things move: looking under the hood of molecular motor proteins Science 288 2000 88 95
13. M. Schliwa Molecular Motors 2003 Wiley-VCH New York
14. D.D. Hackney, and F. Tanamoi The Enzymes, Vol. 23. Energy Coupling and Molecular Motors 2004 Elsevier New York
15. J.M. Squire, and D.A.D. Parry Fibrous Proteins: Muscle and Molecular Motors 2005 Elsevier New York
16. A.B. Kolomeisky, and M.E. Fisher Molecular motors: a theorist's perspective Annu. Rev. Phys. Chem. 58 2007 675 695
17. H. Wang Several issues in modeling molecular motors J. Comput. Theoret. Nanosci. 5 2008 1 35
18. W. Hwang, and M.J. Lang Mechanical design of translocating motor proteins Cell Biochem. Biophys. 54 2009 11 22
19. C. Veigel, and C.F. Schmidt Moving into the cell: single-molecule studies of molecular motors in complex environments Nat. Rev. Mol. Cell Biol. 12 2011 163 176
20. Y.E. Goldman, and E.M. Ostap Molecular Motors and Motility, Vol. 4. Comprehensive Biophysics 2012 Elsevier New York
21. D. Chowdhury Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective Phys. Rep. 2013 10.1016/j.physrep.2013.03.005 (Author-edited final version is available also at http://arxiv.org/abs/1207.6070)
22. D. Dulin, and J. Lipfert N.H. Dekker Studying genomic processes at the single-molecule level: introducing the tools and applications Nat. Rev. Genet. 14 2013 9 22
23. L.H. Hartwell, and J.J. Hopfield A.W. Murray From molecular to modular cell biology Nature 402 6761, Suppl 1999 C47 C52
24. A. Mogilner, R. Wollman, and W.F. Marshall Quantitative modeling in cell biology: what is it good for? Dev. Cell 11 2006 279 287
25. S. Leibler, and D.A. Huse Porters versus rowers: a unified stochastic model of motor proteins J. Cell Biol. 121 1993 1357 1368
26. J. Howard, and A.A. Hyman Microtubule polymerases and depolymerases Curr. Opin. Cell Biol. 19 2007 31 35
27. J.R. McIntosh, and V. Volkov E.L. Grishchuk Tubulin depolymerization may be an ancient biological motor J. Cell Sci. 123 2010 3425 3434
28. E. Lorentzen, and E. Conti The exosome and the proteasome: nano-compartments for degradation Cell 125 2006 651 654
29. G. Oster, and H. Wang Rotary protein motors Trends Cell Biol. 13 2003 114 121
30. Y. Sowa, and R.M. Berry Bacterial flagellar motor Q. Rev. Biophys. 41 2008 103 132
31. U. Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines Rep. Prog. Phys. 75 2012 126001
32. F. Jülicher, A. Ajdari, and J. Prost Modeling molecular motors Rev. Mod. Phys. 69 1997 1269 1281
33. J. Howard Protein power strokes Curr. Biol. 16 2006 R517 R519
34. J.J. Hopfield Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity Proc. Natl. Acad. Sci. USA 71 1974 4135 4139
35. J. Ninio Kinetic amplification of enzyme discrimination Biochimie 57 1975 587 595
36. M.A. Welte, and S.P. Gross Molecular motors: a traffic cop within? HFSP J 2 2008 178 182
37. F. Berger, and C. Keller R. Lipowsky Co-operative transport by molecular motors Biochem. Soc. Trans. 39 2011 1211 1215
38. C. Leduc, and O. Campàs P. Bassereau Mechanism of membrane nanotube formation by molecular motors Biochim. Biophys. Acta 1798 2010 1418 1426
39. T.A. Baker, and S.P. Bell Polymerases and the replisome: machines within machines Cell 92 1998 295 305
40. J.R. McIntosh, M.I. Molodtsov, and F.I. Ataullakhanov Biophysics of mitosis Q. Rev. Biophys. 45 2012 147 207
41. A. Mogilner, and E. Craig Towards a quantitative understanding of mitotic spindle assembly and mechanics J. Cell Sci. 123 2010 3435 3445
42. E.C. Dykeman, and O.F. Sankey Normal mode analysis and applications in biological physics J. Phys. Condens. Matter 22 2010 423202
43. D. Keller, and C. Bustamante The mechanochemistry of molecular motors Biophys. J. 78 2000 541 556
44. G. Lan, and S.X. Sun Mechanochemical models of processive molecular motors Mol. Phys. 110 2012 1017 1034
45. T. Ha, A.G. Kozlov, and T.M. Lohman Single-molecule views of protein movement on single-stranded DNA Annu. Rev. Biophys 41 2012 295 319
46. L. Bai, T.J. Santangelo, and M.D. Wang Single-molecule analysis of RNA polymerase transcription Annu. Rev. Biophys. Biomol. Struct. 35 2006 343 360
47. J.R. Platt Strong inference: certain systematic methods of scientific thinking may produce much more rapid progress than others Science 146 1964 347 353
48. T.C. Chamberlin The method of multiple working hypotheses Science 15 1965 92 96
49. J. Frank Single-particle reconstruction of biological macromolecules in electron microscopy - 30 years Q. Rev. Biophys. 42 2009 139 158
50. G.C. Lander, H.R. Saibil, and E. Nogales Go hybrid: EM, crystallography, and beyond Curr. Opin. Struct. Biol. 22 2012 627 635
51. W.J. Greenleaf, M.T. Woodside, and S.M. Block High-resolution, single-molecule measurements of biomolecular motion Annu. Rev. Biophys. Biomol. Struct. 36 2007 171 190
52. J.R. Moffitt, and Y.R. Chemla C. Bustamante Recent advances in optical tweezers Annu. Rev. Biochem. 77 2008 205 228
53. K.C. Neuman, T. Lionnet, and J.F. Allemand Single-molecule micromanipulation techniques Annu. Rev. Mater. Res. 37 2007 33 67
54. S.J. Lord, H.L. Lee, and W.E. Moerner Single-molecule spectroscopy and imaging of biomolecules in living cells Anal. Chem. 82 2010 2192 2203
55. M.J. Lang, and S.M. Block Resource Letter: LBOT-1: laser-based optical tweezers Am. J. Phys. 71 2003 201 215
56. B.G. Hosu, and J. Jacob G. Forgacs Magnetic tweezers for intracellular applications Rev. Sci. Instrum. 74 2003 4158 4163
57. K. Kim, and O.A. Saleh A high-resolution magnetic tweezer for single-molecule measurements Nucleic Acids Res. 37 2009 e136
58. I. De Vlaminck, and C. Dekker Recent advances in magnetic tweezers Annu. Rev. Biophys 41 2012 453 472
59. R. Peters Single-molecule fluorescence analysis of cellular nanomachinery components Annu. Rev. Biophys. Biomol. Struct. 36 2007 371 394
60. C. Bustamante, W. Cheng, and Y.X. Mejia Revisiting the central dogma one molecule at a time Cell 144 2011 480 497 (Erratum in Cell. 2011. 145:160)
61. K.M. Herbert, W.J. Greenleaf, and S.M. Block Single-molecule studies of RNA polymerase: motoring along Annu. Rev. Biochem. 77 2008 149 176
62. A.M. van Oijen, and J.J. Loparo Single-molecule studies of the replisome Annu. Rev. Biophys 39 2010 429 448
63. M. Manosas, and T. Lionnet V. Croquette Studies of DNA-replication at the single molecule level using magnetic tweezers Biol. Phys. 60 2010 89 122
64. C.E. Aitken, A. Petrov, and J.D. Puglisi Single ribosome dynamics and the mechanism of translation Annu. Rev. Biophys 39 2010 491 513
65. S. Uemura, and J.D. Puglisi Real-time monitoring of single-molecule translation M.V. Rodnina, Ribosomes 2011 Springer New York 295 302
66. I. Tinoco Jr., and R.L. Gonzalez Jr. Biological mechanisms, one molecule at a time Genes Dev. 25 2011 1205 1231
67. W.H. Roos, and I.L. Ivanovska G.J.L. Wuite Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms Cell. Mol. Life Sci. 64 2007 1484 1497
68. M.J. Schnitzer, and S.M. Block Statistical kinetics of processive enzymes Cold Spring Harb. Symp. Quant. Biol. 60 1995 793 802
69. S. Redner A Guide to First-Passage Processes 2001 Cambridge University Press Cambridge
70. M.J. Lang Lighting up the Mechanome The Bridge 34 2007 12 16
71. R. Lipowsky The physics of bio-systems: from molecules to networks Biophys. Rev. Lett. 1 2006 223 230
72. A.C. Forster, and G.M. Church Towards synthesis of a minimal cell Mol. Syst. Biol. 2 2006 45
73. J.A. Hammer 3rd, and J.R. Sellers Walking to work: roles for class V myosins as cargo transporters Nat. Rev. Mol. Cell Biol. 13 2012 13 26
74. J.A. Spudich, and S. Sivaramakrishnan Myosin VI: an innovative motor that challenged the swinging lever arm hypothesis Nat. Rev. Mol. Cell Biol. 11 2010 128 137
75. H.L. Sweeney, and A. Houdusse Myosin VI rewrites the rules for myosin motors Cell 141 2010 573 582
76. S.M. Block Kinesin motor mechanics: binding, stepping, tracking, gating, and limping Biophys. J. 92 2007 2986 2995
77. A. Gennerich, and R.D. Vale Walking the walk: how kinesin and dynein coordinate their steps Curr. Opin. Cell Biol. 21 2009 59 67
78. R.B. Vallee, R.J. McKenney, and K.M. Ori-McKenney Multiple modes of cytoplasmic dynein regulation Nat. Cell Biol. 14 2012 224 230
79. J.A. Spudich The myosin swinging cross-bridge model Nat. Rev. Mol. Cell Biol. 2 2001 387 392
80. E.J.G. Peterman, and J.M. Scholey Mitotic microtubule crosslinkers: insights from mechanistic studies Curr. Biol. 19 2009 R1089 R1094
81. C.B. Lindemann, and K.A. Lesich Flagellar and ciliary beating: the proven and the possible J. Cell Sci. 123 2010 519 528
82. J.N. Thon, and J.E. Italiano Platelet formation Semin. Hematol. 47 2010 220 226
83. M. Dogterom, and J. Husson C. Tischer Microtubule forces and organization P. Lenz, Cell Motility 2007 Springer New York 93 115
84. A. Kornberg, and T. Baker DNA Replication 2nd ed. 1992 W.H. Freeman and Co. New York
85. J. Gelles, and R. Landick RNA polymerase as a molecular motor Cell 93 1998 13 16
86. H. Buc, and T. Strick RNA Polymerases as Molecular Motors 2009 RSC Publishing London
87. A. Herschhorn, and A. Hizi Retroviral reverse transcriptases Cell. Mol. Life Sci. 67 2010 2717 2747
88. J. Ortín, and F. Parra Structure and function of RNA replication Annu. Rev. Microbiol. 60 2006 305 326
89. M.V. Rodnina, W. Wintermeyer, and R. Green Ribosomes 2011 Springer New York