A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
Tóm tắt
Từ khóa
Tài liệu tham khảo
NJ Fuda, 2009, Defining mechanisms that regulate RNA polymerase II transcription in vivo, Nature, 461, 186, 10.1038/nature08449
RD Kornberg, 2007, The molecular basis of eukaryotic transcription, Proc Natl Acad Sci USA, 104, 12955, 10.1073/pnas.0704138104
D Wang, 2006, Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis, Cell, 127, 941, 10.1016/j.cell.2006.11.023
P Cramer, 2000, Architecture of RNA polymerase II and implications for the transcription mechanism, Science, 288, 640, 10.1126/science.288.5466.640
S Tagami, 2010, Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein, Nature, 468, 978, 10.1038/nature09573
DG Vassylyev, 2007, Structural basis for substrate loading in bacterial RNA polymerase, Nature, 448, 163, 10.1038/nature05931
DG Vassylyev, 2007, Structural basis for transcription elongation by bacterial RNA polymerase, Nature, 448, 157, 10.1038/nature05932
DG Vassylyev, 2002, Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution, Nature, 417, 712, 10.1038/nature752
A Cheung, 2012, A Movie of RNA Polymerase II Transcription, Cell, 149, 1431, 10.1016/j.cell.2012.06.006
JF Sydow, 2009, RNA polymerase fidelity and transcriptional proofreading, Curr Opin Struc Biol, 19, 732, 10.1016/j.sbi.2009.10.009
V Svetlov, 2009, Macromolecular micromovements: how RNA polymerase translocates, Curr Opin Struc Biol, 19, 701, 10.1016/j.sbi.2009.10.002
R Landick, 2009, Transcriptional pausing without backtracking, Proc Natl Acad Sci USA, 106, 8797, 10.1073/pnas.0904373106
F Brueckner, 2009, A movie of the RNA polymerase nucleotide addition cycle, Curr Opin Struc Biol, 19, 294, 10.1016/j.sbi.2009.04.005
V Svetlov, 2012, Basic mechanism of transcription by RNA polymerase II, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1829, 20, 10.1016/j.bbagrm.2012.08.009
M Palangat, 2012, Efficient reconstitution of transcription elongation complexes for single-molecule studies of eukaryotic RNA polymerase II, Transcription, 3, 146, 10.4161/trns.20269
MH Larson, 2012, Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II, Proc Natl Acad Sci USA, 109, 6555, 10.1073/pnas.1200939109
X Huang, 2010, RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription, Proc Natl Acad Sci USA, 107, 15745, 10.1073/pnas.1009898107
CD Kaplan, 2012, Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo, PLoS Genet, 8, e1002627, 10.1371/journal.pgen.1002627
CD Kaplan, 2012, Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1829, 39, 10.1016/j.bbagrm.2012.09.007
J Zhang, 2009, Role of the RNA polymerase trigger loop in catalysis and pausing, Nat Struct Mol Biol, 17, 99, 10.1038/nsmb.1732
CD Kaplan, 2008, The RNA Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted by a-Amanitin, Mol Cell, 30, 547, 10.1016/j.molcel.2008.04.023
Y Yuzenkova, 2010, Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis, Proc Natl Acad Sci USA, 107, 10878, 10.1073/pnas.0914424107
ML Kireeva, 2012, Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase, BMC Biophysics, 5, 11, 10.1186/2046-1682-5-11
M Feig, 2010, RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation, Biophys J, 99, 2577, 10.1016/j.bpj.2010.08.010
LT Da, 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, 2399, 10.1021/ja210656k
ATP Carvalho, 2011, The Catalytic Mechanism of RNA Polymerase II, J Chem Theory and Comput, 7, 1177, 10.1021/ct100579w
P Maiuri, 2011, Fast transcription rates of RNA polymerase II in human cells, EMBO Rep, 12, 1280, 10.1038/embor.2011.196
C Castro, 2009, Nucleic acid polymerases use a general acid for nucleotidyl transfer, Nat Struct Mol Biol, 16, 212, 10.1038/nsmb.1540
V Sosunov, 2003, Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase, EMBO J, 22, 2234, 10.1093/emboj/cdg193
SA Seibold, 2010, Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1799, 575, 10.1016/j.bbagrm.2010.05.002
PP Hein, 2011, RNA Transcript 3′-Proximal Sequence Affects Translocation Bias of RNA Polymerase, Biochemistry, 50, 7002, 10.1021/bi200437q
M Feig, 2010, RNA polymerase II flexibility during translocation from normal mode analysis, Proteins: Structure, Function, and Bioinformatics, 78, 434, 10.1002/prot.22560
AM Malinen, 2012, Active site opening and closure control translocation of multisubunit RNA polymerase, Nucleic Acids Res, 40, 7442, 10.1093/nar/gks383
NN Batada, 2004, Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center, Proc Natl Acad Sci USA, 101, 17361, 10.1073/pnas.0408168101
XQ Gong, 2005, Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II, Mol Cell, 18, 461, 10.1016/j.molcel.2005.04.011
YW Yin, 2004, The structural mechanism of translocation and helicase activity in T7 RNA polymerase, Cell, 116, 393, 10.1016/S0092-8674(04)00120-5
EA Abbondanzieri, 2005, Direct observation of base-pair stepping by RNA polymerase, Nature, 438, 460, 10.1038/nature04268
GR Bowman, 2009, Progress and challenges in the automated construction of Markov state models for full protein systems, J Chem Phys, 131, 124101, 10.1063/1.3216567
F Noé, 2008, Transition networks for modeling the kinetics of conformational change in macromolecules, Curr Opin Struc Biol, 18, 154, 10.1016/j.sbi.2008.01.008
GR Bowman, 2010, Taming the complexity of protein folding, Curr Opin Struc Biol, 21, 4, 10.1016/j.sbi.2010.10.006
JD Chodera, 2007, Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics, J Chem Phys, 126, 155101, 10.1063/1.2714538
Y Duan, 2003, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J Comput Chem, 24, 1999, 10.1002/jcc.10349
KL Meagher, 2003, Development of polyphosphate parameters for use with the AMBER force field, J Comput Chem, 24, 1016, 10.1002/jcc.10262
D Van Der Spoel, 2005, GROMACS: fast, flexible, and free, J Comput Chem, 26, 1701, 10.1002/jcc.20291
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In B. Pullman, editor. Intermolecular forces. Dordrecht: Reidel Publishing Company.
T Darden, 1993, Particle mesh Ewald: An N log (N) method for Ewald sums in large systems, J Chem Phys, 98, 10089, 10.1063/1.464397
HJC Berendsen, 1984, Molecular dynamics with coupling to an external bath, J Chem Phys, 81, 3684, 10.1063/1.448118
G Bussi, 2007, Canonical sampling through velocity rescaling, J Chem Phys, 126, 014101, 10.1063/1.2408420
B Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J Comput Chem, 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
B Isralewitz, 2001, Steered molecular dynamics and mechanical functions of proteins, Curr Opin Struc Biol, 11, 224, 10.1016/S0959-440X(00)00194-9
GR Bowman, 2009, Using generalized ensemble simulations and Markov state models to identify conformational states, Methods, 49, 197, 10.1016/j.ymeth.2009.04.013
W Zhuang, 2011, Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach, J Phys Chem B, 115, 5415, 10.1021/jp109592b
DA Silva, 2011, A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein, PLoS Comput Biol, 7, e1002054, 10.1371/journal.pcbi.1002054
X Huang, 2009, Rapid equilibrium sampling initiated from nonequilibrium data, Proc Natl Acad Sci USA, 106, 19765, 10.1073/pnas.0909088106