메뉴 건너뛰기




Volumn 111, Issue 21, 2014, Pages 7665-7670

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

Author keywords

Markov state model; Molecular dynamics; Trigger loop

Indexed keywords

DNA; MAGNESIUM ION; MESSENGER RNA; NUCLEOTIDE; RNA; RNA POLYMERASE II;

EID: 84901684210     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1315751111     Document Type: Article
Times cited : (125)

References (49)
  • 2
    • 84862666457 scopus 로고    scopus 로고
    • A movie of RNA polymerase II transcription
    • Cheung AC, Cramer P (2012) A movie of RNA polymerase II transcription. Cell 149(7): 1431-1437.
    • (2012) Cell , vol.149 , Issue.7 , pp. 1431-1437
    • Cheung, A.C.1    Cramer, P.2
  • 3
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center
    • DOI 10.1016/j.cell.2004.10.016, PII S0092867404010013
    • Westover KD, Bushnell DA, Kornberg RD (2004) Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center. Cell 119(4): 481-489. (Pubitemid 39482348)
    • (2004) Cell , vol.119 , Issue.4 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 4
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • DOI 10.1016/j.molcel.2004.11.040, PII S1097276504007300
    • Kettenberger H, Armache KJ, Cramer P (2004) Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 16(6):955-965. (Pubitemid 40018405)
    • (2004) Molecular Cell , vol.16 , Issue.6 , pp. 955-965
    • Kettenberger, H.1    Armache, K.-J.2    Cramer, P.3
  • 5
    • 0035827332 scopus 로고    scopus 로고
    • Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 A resolution
    • DOI 10.1126/science.1059495
    • Gnatt AL, Cramer P, Fu JH, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 A resolution. Science 292(5523):1876-1882. (Pubitemid 32538357)
    • (2001) Science , vol.292 , Issue.5523 , pp. 1876-1882
    • Gnatt, A.L.1    Cramer, P.2    Fu, J.3    Bushnell, D.A.4    Kornberg, R.D.5
  • 6
  • 7
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis
    • DOI 10.1016/j.cell.2006.11.023, PII S0092867406014796
    • Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis. Cell 127(5):941-954. (Pubitemid 44792264)
    • (2006) Cell , vol.127 , Issue.5 , pp. 941-954
    • Wang, D.1    Bushnell, D.A.2    Westover, K.D.3    Kaplan, C.D.4    Kornberg, R.D.5
  • 8
    • 70549108206 scopus 로고    scopus 로고
    • Macromolecular micromovements: How RNA polymerase translocates
    • Svetlov V, Nudler E (2009) Macromolecular micromovements: How RNA polymerase translocates. Curr Opin Struct Biol 19(6):701-707.
    • (2009) Curr Opin Struct Biol , vol.19 , Issue.6 , pp. 701-707
    • Svetlov, V.1    Nudler, E.2
  • 9
    • 84863069608 scopus 로고    scopus 로고
    • Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II
    • Da LT, Wang D, Huang X (2012) 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(4):2399-2406.
    • (2012) J Am Chem Soc , vol.134 , Issue.4 , pp. 2399-2406
    • Da, L.T.1    Wang, D.2    Huang, X.3
  • 10
    • 28544432440 scopus 로고    scopus 로고
    • Direct observation of base-pair stepping by RNA polymerase
    • DOI 10.1038/nature04268, PII N04268
    • Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM (2005) Direct observation of base-pair stepping by RNA polymerase. Nature 438(7067):460-465. (Pubitemid 41742012)
    • (2005) Nature , vol.438 , Issue.7067 , pp. 460-465
    • Abbondanzieri, E.A.1    Greenleaf, W.J.2    Shaevitz, J.W.3    Landick, R.4    Block, S.M.5
  • 11
    • 55249117324 scopus 로고    scopus 로고
    • Core structure of the yeast spt4-spt5 complex: A conserved module for regulation of transcription elongation
    • Guo M, et al. (2008) Core structure of the yeast spt4-spt5 complex: A conserved module for regulation of transcription elongation. Structure 16(11):1649-1658.
    • (2008) Structure , vol.16 , Issue.11 , pp. 1649-1658
    • Guo, M.1
  • 12
    • 79960966899 scopus 로고    scopus 로고
    • Initiation complex structure and promoter proofreading
    • Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) Initiation complex structure and promoter proofreading. Science 333(6042):633-637.
    • (2011) Science , vol.333 , Issue.6042 , pp. 633-637
    • Liu, X.1    Bushnell, D.A.2    Silva, D.A.3    Huang, X.4    Kornberg, R.D.5
  • 13
    • 77953112483 scopus 로고    scopus 로고
    • X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct
    • Wang D, Zhu G, Huang X, Lippard SJ (2010) X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct. Proc Natl Acad Sci USA 107(21):9584-9589.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.21 , pp. 9584-9589
    • Wang, D.1    Zhu, G.2    Huang, X.3    Lippard, S.J.4
  • 14
    • 84872376551 scopus 로고    scopus 로고
    • Basic mechanism of transcription by RNA polymerase II
    • Svetlov V, Nudler E (2013) Basic mechanism of transcription by RNA polymerase II. Biochim Biophys Acta 1829(1):20-28.
    • (2013) Biochim Biophys Acta , vol.1829 , Issue.1 , pp. 20-28
    • Svetlov, V.1    Nudler, E.2
  • 15
    • 1342313235 scopus 로고    scopus 로고
    • The structural mechanism of translocation and helicase activity in T7 RNA polymerase
    • DOI 10.1016/S0092-8674(04)00120-5, PII S0092867404001205
    • Yin YW, Steitz TA (2004) The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116(3):393-404. (Pubitemid 38366316)
    • (2004) Cell , vol.116 , Issue.3 , pp. 393-404
    • Yin, Y.W.1    Steitz, T.A.2
  • 16
    • 84863082064 scopus 로고    scopus 로고
    • A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription
    • Yu J, Oster G (2012) A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription. Biophys J 102(3):532-541.
    • (2012) Biophys J , vol.102 , Issue.3 , pp. 532-541
    • Yu, J.1    Oster, G.2
  • 17
  • 18
    • 84872386768 scopus 로고    scopus 로고
    • Structural basis of transcription elongation
    • Martinez-Rucobo FW, Cramer P (2013) Structural basis of transcription elongation. Biochim Biophys Acta 1829(1):9-19.
    • (2013) Biochim Biophys Acta , vol.1829 , Issue.1 , pp. 9-19
    • Martinez-Rucobo, F.W.1    Cramer, P.2
  • 19
    • 79953855317 scopus 로고    scopus 로고
    • A unified model of transcription elongation: What have we learned from single-molecule experiments?
    • Maoiléidigh DO, Tadigotla VR, Nudler E, Ruckenstein AE (2011) A unified model of transcription elongation: What have we learned from single-molecule experiments? Biophys J 100(5):1157-1166.
    • (2011) Biophys J , vol.100 , Issue.5 , pp. 1157-1166
    • Maoiléidigh, D.O.1    Tadigotla, V.R.2    Nudler, E.3    Ruckenstein, A.E.4
  • 20
    • 78049347876 scopus 로고    scopus 로고
    • RNA polymerase II with open and closed trigger loops: Active site dynamics and nucleic acid translocation
    • Feig M, Burton ZF (2010) RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J 99(8):2577-2586.
    • (2010) Biophys J , vol.99 , Issue.8 , pp. 2577-2586
    • Feig, M.1    Burton, Z.F.2
  • 21
    • 84870983295 scopus 로고    scopus 로고
    • Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
    • Kireeva ML, et al. (2012) Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC Biophys 5(1):11.
    • (2012) BMC Biophys , vol.5 , Issue.1 , pp. 11
    • Kireeva, M.L.1
  • 22
    • 77957678214 scopus 로고    scopus 로고
    • RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription
    • Huang X, et al. (2010) RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription. Proc Natl Acad Sci USA 107(36):15745-15750.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.36 , pp. 15745-15750
    • Huang, X.1
  • 23
    • 84867297989 scopus 로고    scopus 로고
    • Active site opening and closure control translocation of multisubunit RNA polymerase
    • Malinen AM, et al. (2012) Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res 40(15):7442-7451.
    • (2012) Nucleic Acids Res , vol.40 , Issue.15 , pp. 7442-7451
    • Malinen, A.M.1
  • 24
    • 84884682805 scopus 로고    scopus 로고
    • Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism
    • Dangkulwanich M, et al. (2013) Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife 2: e00971.
    • (2013) ELife , vol.2
    • Dangkulwanich, M.1
  • 28
    • 34247338100 scopus 로고    scopus 로고
    • Automatic discovery of metastable states for the construction of Markov models of macromolecular con-formational dynamics
    • Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC (2007) Automatic discovery of metastable states for the construction of Markov models of macromolecular con-formational dynamics. J Chem Phys 126(15):155101.
    • (2007) J Chem Phys , vol.126 , Issue.15 , pp. 155101
    • Chodera, J.D.1    Singhal, N.2    Pande, V.S.3    Dill, K.A.4    Swope, W.C.5
  • 29
    • 70349631761 scopus 로고    scopus 로고
    • Progress and challenges in the automated construction of Markov state models for full protein systems
    • Bowman GR, Beauchamp KA, Boxer G, Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131(12):124101.
    • (2009) J Chem Phys , vol.131 , Issue.12 , pp. 124101
    • Bowman, G.R.1    Beauchamp, K.A.2    Boxer, G.3    Pande, V.S.4
  • 30
    • 70450255797 scopus 로고    scopus 로고
    • Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
    • Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA 106(45):19011-19016.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.45 , pp. 19011-19016
    • Noé, F.1    Schütte, C.2    Vanden-Eijnden, E.3    Reich, L.4    Weikl, T.R.5
  • 31
    • 78651242947 scopus 로고    scopus 로고
    • Modeling conformational ensembles of slow functional motions in Pin1-WW
    • Morcos F, et al. (2010) Modeling conformational ensembles of slow functional motions in Pin1-WW. PLOS Comput Biol 6(12):e1001015.
    • (2010) PLOS Comput Biol , vol.6 , Issue.12
    • Morcos, F.1
  • 32
    • 76149136021 scopus 로고    scopus 로고
    • Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
    • Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 132(5): 1526-1528.
    • (2010) J Am Chem Soc , vol.132 , Issue.5 , pp. 1526-1528
    • Voelz, V.A.1    Bowman, G.R.2    Beauchamp, K.3    Pande, V.S.4
  • 33
    • 79851482740 scopus 로고    scopus 로고
    • Atomistic folding simulations of the five-helix bundle protein λ(6-85)
    • Bowman GR, Voelz VA, Pande VS (2011) Atomistic folding simulations of the five-helix bundle protein λ(6-85). J Am Chem Soc 133(4):664-667.
    • (2011) J Am Chem Soc , vol.133 , Issue.4 , pp. 664-667
    • Bowman, G.R.1    Voelz, V.A.2    Pande, V.S.3
  • 35
    • 79958136745 scopus 로고    scopus 로고
    • A role for both conforma-tional selection and induced fit in ligand binding by the LAO protein
    • Silva DA, Bowman GR, Sosa-Peinado A, Huang X (2011) A role for both conforma-tional selection and induced fit in ligand binding by the LAO protein. PLOS Comput Biol 7(5):e1002054.
    • (2011) PLOS Comput Biol , vol.7 , Issue.5
    • Silva, D.A.1    Bowman, G.R.2    Sosa-Peinado, A.3    Huang, X.4
  • 36
    • 58149089145 scopus 로고    scopus 로고
    • Can morphing methods predict intermediate structures?
    • Weiss DR, Levitt M (2009) Can morphing methods predict intermediate structures? J Mol Biol 385(2):665-674.
    • (2009) J Mol Biol , vol.385 , Issue.2 , pp. 665-674
    • Weiss, D.R.1    Levitt, M.2
  • 37
    • 49449102926 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation
    • Brueckner F, Cramer P (2008) Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 15(8):811-818.
    • (2008) Nat Struct Mol Biol , vol.15 , Issue.8 , pp. 811-818
    • Brueckner, F.1    Cramer, P.2
  • 38
    • 84860111277 scopus 로고    scopus 로고
    • Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo
    • Kaplan CD, Jin H, Zhang IL, Belyanin A (2012) Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo. PLoS Genet 8(4): e1002627.
    • (2012) PLoS Genet , vol.8 , Issue.4
    • Kaplan, C.D.1    Jin, H.2    Zhang, I.L.3    Belyanin, A.4
  • 39
    • 84873323216 scopus 로고    scopus 로고
    • Structural basis of transcriptional pausing in bacteria
    • Weixlbaumer A, Leon K, Landick R, Darst SA (2013) Structural basis of transcriptional pausing in bacteria. Cell 152(3):431-441.
    • (2013) Cell , vol.152 , Issue.3 , pp. 431-441
    • Weixlbaumer, A.1    Leon, K.2    Landick, R.3    Darst, S.A.4
  • 40
    • 57249108333 scopus 로고    scopus 로고
    • Bridge helix and trigger loop perturbations generate superactive RNA polymerases
    • Tan L, Wiesler S, Trzaska D, Carney HC, Weinzierl RO (2008) Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 7(10):40.
    • (2008) J Biol , vol.7 , Issue.10 , pp. 40
    • Tan, L.1    Wiesler, S.2    Trzaska, D.3    Carney, H.C.4    Weinzierl, R.O.5
  • 41
    • 82455199223 scopus 로고    scopus 로고
    • Structural basis of initial RNA polymerase II transcription
    • Cheung AC, Sainsbury S, Cramer P (2011) Structural basis of initial RNA polymerase II transcription. EMBO J 30(23):4755-4763.
    • (2011) EMBO J , vol.30 , Issue.23 , pp. 4755-4763
    • Cheung, A.C.1    Sainsbury, S.2    Cramer, P.3
  • 42
    • 84872407990 scopus 로고    scopus 로고
    • The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation
    • Nedialkov YA, et al. (2013) The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. Biochim Biophys Acta 1829(2):187-198.
    • (2013) Biochim Biophys Acta , vol.1829 , Issue.2 , pp. 187-198
    • Nedialkov, Y.A.1
  • 43
    • 84869783692 scopus 로고    scopus 로고
    • RNA polymerase stalls in a post-translocated register and can hyper-translocate
    • Nedialkov YA, Nudler E, Burton ZF (2012) RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription 3(5):260-269.
    • (2012) Transcription , vol.3 , Issue.5 , pp. 260-269
    • Nedialkov, Y.A.1    Nudler, E.2    Burton, Z.F.3
  • 46
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999-2012.
    • (2003) J Comput Chem , vol.24 , Issue.16 , pp. 1999-2012
    • Duan, Y.1
  • 47
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435-447.
    • (2008) J Chem Theory Comput , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 48
    • 63449118443 scopus 로고    scopus 로고
    • Using generalized ensemble simulations and Markov state models to identify conformational states
    • Bowman GR, Huang X, Pande VS (2009) Using generalized ensemble simulations and Markov state models to identify conformational states. Methods 49(2):197-201.
    • (2009) Methods , vol.49 , Issue.2 , pp. 197-201
    • Bowman, G.R.1    Huang, X.2    Pande, V.S.3
  • 49
    • 0034704229 scopus 로고    scopus 로고
    • A global geometric framework for nonlinear dimensionality reduction
    • DOI 10.1126/science.290.5500.2319
    • Tenenbaum JB, de Silva V, Langford JC (2000) A global geometric framework for nonlinear dimensionality reduction. Science 290(5500):2319-2323. (Pubitemid 32041577)
    • (2000) Science , vol.290 , Issue.5500 , pp. 2319-2323
    • Tenenbaum, J.B.1    De Silva, V.2    Langford, J.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.