Theoretical investigations on elucidating fundamental mechanisms of catalysis and dynamics involved in transcription by rna polymerase

Journal of Theoretical and Computational Chemistry

Volumn 12, Issue 8, 2013, Pages

  Pardo Avila, Fátima ^a   Da, Lin Tai ^a   Wang, Ying ^a   Huang, Xuhui ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Markov state models; Molecular dynamics; molecular motors

Indexed keywords

EID: 84880707426     PISSN: 02196336     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219633613410058     Document Type: Article

References (62)

1. Cramer P, Bushnell DA, Kornberg RD, Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution, Science 292:1863-1876, 2001.
2. Kornberg RD, The molecular basis of eukaryotic transcription, Proc Natl Acad Sci USA 104:12955-12961, 2007.
3. Westover KD, Bushnell DA, Kornberg RD, Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center, Cell 119:481-489, 2004.
4. Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD, Structural basis of transcription: Role of the trigger loop in substrate speciflucity and catalysis, Cell 127:941-954, 2006.
5. Brueckner F, Cramer P, Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation, Nature Struct Mol Biol 15:811-818, 2008.
6. Brueckner F, Ortiz J, Cramer P, A movie of the RNA polymerase nucleotide addition cycle, Curr Opin Struct Biol 19:294-299, 2009.
7. Bushnell DA, Cramer P, Kornberg RD, Structural basis of transcription: Alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution, Proc Natl Acad Sci USA 99:1218-1222, 2002.
8. Cramer P, Architecture of RNA polymerase II and implications for the transcription mechanism, Science 288:640-649, 2000.
9. Liu X, Bushnell DA, Silva D-A, Huang X, Kornberg RD, Initiation complex structure and promoter proofreading, Science 333:633-637, 2011.
10. Wang D et al., Structural basis of transcription: Backtracked RNA polymerase II at 3.4 angstrom resolution, Science 324:1203-1206, 2009.
11. Kaplan CD, Jin H, Zhang IL, Belyanin A, Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo, PLoS Genetics 8:e1002627, 2012.
12. Huang X et al., RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription, Proc Natl Acad Sci USA 107:15745-15750, 2010.
13. Nedialkov YA et al., The RNA polymerase bridge helix YFI motif in catalysis, fludelity and translocation, Biochim Biophys Acta 1829:187-198, 2012.
14. Malinen AM et al., Active site opening and closure control translocation of multisubunit RNA polymerase, Nucleic Acids Res 40:7442-7451, 2012.
15. Galburt EA, Grill SW, Bustamante C, Single molecule transcription elongation, Methods 48:323-332, 2009.
16. Bai L, Fulbright R, Wang M, Mechanochemical kinetics of transcription elongation, Phys Rev Lett 98:1-4, 2007.
17. Larson MH et al., Trigger loop dynamics mediate the balance between the transcriptional fludelity and speed of RNA polymerase II, Proc Natl Acad Sci USA 109:6555-6560, 2012.
18. Kireeva ML et al., Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase, BMC Biophys 5:11, 2012.
19. Feig M, Burton ZF, RNA polymerase II flexibility during translocation from normal mode analysis, Proteins 78:434-446, 2010.
20. Feig M, Burton ZF, RNA polymerase II with open and closed trigger loops: Active site dynamics and nucleic acid translocation, Biophys J 99:2577-2586, 2010.
21. Shaw D, Dror R, Salmon J, Millisecond-scale molecular dynamics simulations on Anton, Proc Conf High Performance Computing, Networking, Storage and Analysis (SC09), pp. 1-11, 2009, available at (accessed 13 July 2013).
22. Marrink SJ, Risselada HJ, Yeflumov S, Tieleman DP, De Vries AH, The MARTINI force flueld: Coarse grained model for biomolecular simulations, The J Phys Chem B 111:7812-7824, 2007.
23. Klein ML, Shinoda W, Large-scale molecular dynamics simulations of self-assembling systems, Science 321:798-800, 2008.
24. Shinoda W, DeVane R, Klein ML, Multi-property flutting and parameterization of a coarse grained model for aqueous surfactants, Mol Simul 33:27-36, 2007.
25. Wassenaar Ta, Ing-olfsson HI, Priess M, Marrink SJ, Schafer LV, Mixing MARTINI: Electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations, The J Phys Chem B 117:3516-3530, 2013.
26. Bowman GR, Beauchamp KA, Boxer G, Pande VS, Progress and challenges in the automated construction of Markov state models for full protein systems, J Chem Phys 131:124101, 2009.
27. Bowman GR, Voelz VA, Pande VS, Atomistic folding simulations of the fluve-helix bundle protein-(6-85), J Am Chem Soc 133:664-667, 2011.
28. Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC, Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics, J Chem Phys 126:155101, 2007.
29. Morcos F et al., Modeling conformational ensembles of slow functional motions in Pin1-WW, PLoS Comput Biol 6:e1001015, 2010.
30. No-e F, Schutte C, Vanden-Eijnden E, Reich L, Weikl TR, Constructing the equilibrium ensemble of folding pathways from short o -equilibrium simulations, Proc Natl Acad Sci USA 106:19011-19016, 2009.
31. Silva D-A, Bowman GR, Sosa-Peinado A, Huang X, A role for both conformational selection and induced flut in ligand binding by the LAO protein, PLoS Comput Biol 7:e1002054, 2011.
32. Voelz VA, Bowman GR, Beauchamp K, Pande VS, Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39), J Am Chem Soc 132:1526-1528, 2010.
33. Das M, Electron transfer through non-hydrogen and hydrogen bonded intermolecular tunnel junctions: A computational study, J Theoret Comput Chem 11:997-1004, 2012.
34. Liu J, Tsai M-D, DNA polymerase-: Pre-steady-state kinetic analyses of dATP-S stereoselectivity and alteration of the stereoselectivity by various metal ions and by site-directed mutagenesis, Biochemistry 40:9014-9022, 2001.
35. Castro C et al., Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA-and DNA-dependent RNA and DNA polymerases, Proc Natl Acad Sci USA 104:4267-4272, 2007.
36. Carvalho A, The catalytic mechanism of RNA polymerase II, J Chem Theor Comput 7:1177-1188, 2011.
37. Vassylyev DG et al., Structural basis for substrate loading in bacterial RNA polymerase, Nature 448:163-168, 2007.
38. Nedialkov YA et al., NTP-driven translocation by human RNA polymerase II, J Biol Chem 278:18303-18312, 2003.
39. Batada NN, Westover KD, Bushnell DA, Levitt M, Kornberg RD, Di usion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center, Proc Natl Acad Sci USA 101:17361-17364, 2004.
40. Zhang J, Palangat M, Landick R, Role of the RNA polymerase trigger loop in catalysis and pausing, Nature Struct Mol Biol 17:99-104, 2010.
41. QIN P-H et al., Interactions of the nucleotides with the metal ions Mg 2, Ca 2, Mn 2, Na , and K , J Theoret Comput Chem 11:1183-1199, 2012.
42. Tehrani ZA, Javan MJ, Fattahi A, Hashemi MM, E ect of cation radical formation on reactivity and acidity enhancement of cytosine nucleobase: Natural bond orbital and atom in molecule analysis, J Theoret Comput Chem 11:313-327, 2012.
43. Da L, Wang D, Huang X, Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II, J Am Chem Soc 134:2399-2406, 2012.
44. Yuzenkova Y et al., Stepwise mechanism for transcription fludelity, BMC Biol 8:54, 2010.
45. Yin YW, Steitz TA, The structural mechanism of translocation and helicase activity in T7 RNA polymerase, Cell 116:393-404, 2004.
46. Da L-T, Pardo-Avila F, Wang D, Huang X, A Two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase, PLOS Comput Biolo 9: E1003020, 2013.
47. Bar-Nahum G et al., A ratchet mechanism of transcription elongation and its control, Cell 120:183-193, 2005.
48. Guo Q, Sousa R, Translocation by T7 RNA polymerase: A sensitively poised Brownian ratchet, J Mol Biol 358:241-254, 2006.
49. Yu J, Oster G, A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription, Biophys J 102:532-541, 2012.
50. Kwak H, Fuda NJ, Core LJ, Lis JT, Precise maps of RNA polymerase reveal how promoters direct initiation and pausing, Science 339:950-953, 2013.
51. Landick R, Transcriptional pausing without backtracking, Proc Natl Acad Sci USA 106:8797-8798, 2009.
52. Kireeva ML, Kashlev M, Mechanism of sequence-specifluc pausing of bacterial RNA polymerase, Proc Natl Acad Sci USA 106:8900-8905, 2009.
53. Weixlbaumer A, Leon K, Landick R, Darst SA, Structural basis of transcriptional pausing in bacteria, Cell 152:431-441, 2013.
54. Cheung ACM, Cramer P, Structural basis of RNA polymerase II backtracking, arrest and reactivation, Nature 471:249-253, 2011.
55. Maoil-eidigh DO, Tadigotla VR, Nudler E, Ruckenstein AE, A uniflued model of transcription elongation: What have we learned from single-molecule experiments Biophys J 100:1157-1166, 2011.
56. Nedialkov YA, Nudler E, Burton ZF, RNA polymerase stalls in a post-translocated register and can hyper-translocate, Transcription 3:260-269, 2012.
57. Chakraborty A et al., Opening and closing of the bacterial RNA polymerase clamp, Science 337:591-595, 2012.
58. Kettenberger H, Armache K-J, Cramer P, Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage, Cell 114:347-357, 2003.
59. Kettenberger H, Armache K, Cramer P, Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS, Molecular Cell 16:955-965, 2004.
60. Chowdhury D, Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist's perspective, pp. 1-370, arXiv:1207.6070 [physics.bio-ph], 2012.
61. Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM, Direct observation of base-pair stepping by RNA polymerase, Nature 438:460-465, 2005.
62. Gelles J, Landick R, RNA polymerase as a molecular motor, Cell 93:13-16, 1998.