Published in Biochim Biophys Acta on May 15, 2010
The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol Cell (2011) 1.49
RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J (2010) 1.14
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol (2010) 1.11
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase. BMC Biophys (2012) 0.99
Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. Biochim Biophys Acta (2012) 0.98
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation. J Biol Chem (2011) 0.96
Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J (2013) 0.95
Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase. Mol Cell (2013) 0.95
Activity map of the Escherichia coli RNA polymerase bridge helix. J Biol Chem (2011) 0.94
The bridge helix coordinates movements of modules in RNA polymerase. BMC Biol (2010) 0.92
A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase. PLoS Comput Biol (2013) 0.90
RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription (2012) 0.90
The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation. Biochim Biophys Acta (2012) 0.89
Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription (2014) 0.84
The Bridge Helix of RNA polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement. Archaea (2012) 0.84
Computational simulation strategies for analysis of multisubunit RNA polymerases. Chem Rev (2013) 0.82
Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase. Nucleic Acids Res (2014) 0.79
High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet (2016) 0.77
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods (2001) 15.37
Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science (2001) 8.24
Structural basis for transcription elongation by bacterial RNA polymerase. Nature (2007) 5.09
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell (2006) 4.49
A ratchet mechanism of transcription elongation and its control. Cell (2005) 4.48
Structural basis for substrate loading in bacterial RNA polymerase. Nature (2007) 4.40
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci U S A (2003) 3.67
The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell (2004) 3.33
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B (2009) 3.17
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell (2005) 2.88
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol Cell (2007) 2.80
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell (2008) 2.62
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol (2008) 2.47
Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell (2005) 2.40
Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci U S A (2002) 2.37
The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem (2000) 2.35
Development of polyphosphate parameters for use with the AMBER force field. J Comput Chem (2003) 2.33
Ssu72 Is an RNA polymerase II CTD phosphatase. Mol Cell (2004) 2.25
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell (2008) 2.21
The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli. Proc Natl Acad Sci U S A (1998) 2.21
Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+. Biochemistry (2004) 2.10
A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Mol Cell (2002) 2.06
Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination. Genes Dev (1990) 2.06
Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.92
Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol (2009) 1.86
Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell (2004) 1.80
Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. Genes Dev (1994) 1.69
Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell (2009) 1.68
Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol (2008) 1.60
Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell (2001) 1.51
Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn2+. Biochemistry (2004) 1.50
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J Mol Biol (2002) 1.43
Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell (2005) 1.43
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry (2006) 1.40
Modulation of DNA repair by mutations flanking the DNA channel through RNA polymerase. EMBO J (2002) 1.38
Accurate initiation by RNA polymerase II in a whole cell extract from Saccharomyces cerevisiae. J Biol Chem (1990) 1.26
Four contiguous amino acids define the target for streptolydigin resistance in the beta subunit of Escherichia coli RNA polymerase. J Biol Chem (1993) 1.21
Alpha-amanitin blocks translocation by human RNA polymerase II. J Biol Chem (2004) 1.20
Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae. Methods Enzymol (2003) 1.19
Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol (2006) 1.17
Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J Mol Biol (2004) 1.17
A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol (2009) 1.17
Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol Cell Biol (2000) 1.17
In silico evidence for DNA polymerase-beta's substrate-induced conformational change. Biophys J (2004) 1.14
Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations. J Phys Chem B (2006) 1.14
Translocation by multi-subunit RNA polymerases. Biochim Biophys Acta (2010) 1.13
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol (2005) 1.11
Rapid kinetic analysis of transcription elongation by Escherichia coli RNA polymerase. J Mol Biol (2008) 1.03
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods (2009) 1.03
Kinetic mechanism of fully activated S6K1 protein kinase. J Biol Chem (2008) 1.00
Hydration energy landscape of the active site cavity in cytochrome P450cam. Proteins (1998) 1.00
Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity. J Biol Chem (2006) 0.98
RNA polymerase II flexibility during translocation from normal mode analysis. Proteins (2010) 0.97
Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates. Proteins (2005) 0.97
Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase. J Mol Biol (1996) 0.96
Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization. J Am Chem Soc (2008) 0.95
A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors. J Biol Chem (2007) 0.91
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. Protein Expr Purif (2009) 0.90
Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes. Proteins (2008) 0.89
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2. J Mol Biol (2007) 0.88
A bridge to transcription by RNA polymerase. J Biol (2008) 0.87
Isolation, purification, and in vitro characterization of recessive-lethal-mutant RNA polymerases from Escherichia coli. J Bacteriol (1996) 0.86
Apo adenylate kinase encodes its holo form: a principal component and varimax analysis. J Phys Chem B (2009) 0.85
Computational delineation of the catalytic step of a high-fidelity DNA polymerase. Protein Sci (2010) 0.83
Structure and dynamics of RNA polymerase II elongation complex. Biochem Biophys Res Commun (2006) 0.82
A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase. J Biol Chem (2007) 0.82
A comparative molecular dynamics study of thermophilic and mesophilic ribonuclease HI enzymes. J Biomol Struct Dyn (2007) 0.82
An enhanced molecular dynamics study of HPPK-ATP conformation space exploration and ATP binding to HPPK. J Phys Chem A (2009) 0.77
Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase. J Am Chem Soc (2004) 0.76
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc (2004) 5.96
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol Cell (2002) 3.91
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem (2003) 3.81
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science (2009) 3.60
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature (2007) 2.64
Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell (2005) 2.55
A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev (2005) 2.49
A transcription-independent role for TFIIB in gene looping. Mol Cell (2007) 2.38
LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res (2008) 2.38
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Ssu72 Is an RNA polymerase II CTD phosphatase. Mol Cell (2004) 2.25
The RNA polymerase II machinery: structure illuminates function. Cell (2002) 2.24
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell (2008) 2.21
Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. Mol Cell (2012) 1.96
Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc Natl Acad Sci U S A (2009) 1.92
Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol Cell (2002) 1.83
Functional interactions between the transcription and mRNA 3' end processing machineries mediated by Ssu72 and Sub1. Genes Dev (2003) 1.79
A physiological role for gene loops in yeast. Genes Dev (2009) 1.73
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res (2002) 1.69
Highly accurate biomolecular electrostatics in continuum dielectric environments. J Comput Chem (2008) 1.66
Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. J Biol Chem (2004) 1.59
A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J Chem Phys (2005) 1.56
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol. Proc Natl Acad Sci U S A (2010) 1.55
Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev (2006) 1.51
Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics (2006) 1.47
Amino acid substitutions that specifically impair the transcriptional activity of papillomavirus E2 affect binding to the long isoform of Brd4. Virology (2006) 1.47
RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. Mol Cell Biol (2004) 1.46
Nucleosomal elements that control the topography of the barrier to transcription. Cell (2012) 1.46
Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell (2005) 1.43
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol (2010) 1.43
Chronic arthritis down-regulates peripheral mu-opioid receptor expression with concomitant loss of endomorphin 1 antinociception. Arthritis Rheum (2005) 1.42
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes. J Biol Chem (2003) 1.36
Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Mol Cell Biol (2004) 1.32
Engineering of elongation complexes of bacterial and yeast RNA polymerases. Methods Enzymol (2003) 1.31
Chromatin remodeling by RNA polymerases. Trends Biochem Sci (2004) 1.30
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 1.29
Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II. J Biol Chem (2009) 1.25
Control of eukaryotic gene expression: gene loops and transcriptional memory. Adv Enzyme Regul (2010) 1.24
NTP-driven translocation by human RNA polymerase II. J Biol Chem (2003) 1.24
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (2009) 1.24
Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases. J Biol Chem (2005) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex. Nucleic Acids Res (2005) 1.20
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins (2013) 1.20
Alpha-amanitin blocks translocation by human RNA polymerase II. J Biol Chem (2004) 1.20
Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae. Methods Enzymol (2003) 1.19
The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol (2011) 1.19
Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J Mol Biol (2004) 1.17
Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol (2006) 1.17
The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol (2005) 1.17
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. J Comput Chem (2006) 1.16
Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B (2006) 1.16
Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Mol Cell Biol (2004) 1.15
RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J (2010) 1.14
Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations. J Phys Chem B (2006) 1.14
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. Elife (2013) 1.14
Translocation by multi-subunit RNA polymerases. Biochim Biophys Acta (2010) 1.13
Reduced native state stability in crowded cellular environment due to protein-protein interactions. J Am Chem Soc (2013) 1.13
Water chain formation and possible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: a molecular dynamics comparison of the wild type and R481K mutant. Biochemistry (2005) 1.12
Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J Biol Chem (2003) 1.12
A human RNA polymerase II-containing complex associated with factors necessary for spliceosome assembly. J Biol Chem (2001) 1.12
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J (2012) 1.12
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol (2005) 1.11
Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides. PLoS Pathog (2012) 1.11
Aberrant activity of the DNA repair enzyme AlkB. J Inorg Biochem (2004) 1.10
Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. J Biol Chem (2012) 1.10
Protein crowding affects hydration structure and dynamics. J Am Chem Soc (2012) 1.08
Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. J Phys Chem B (2006) 1.07
Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes. J Virol (2007) 1.04
Conformational sampling of peptides in cellular environments. Biophys J (2007) 1.04
Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries. Mol Cell Biol (2009) 1.03
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Direct assessment of transcription fidelity by high-resolution RNA sequencing. Nucleic Acids Res (2013) 1.03
Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J (2008) 1.03
Prostaglandin endoperoxide H synthases: peroxidase hydroperoxide specificity and cyclooxygenase activation. J Biol Chem (2007) 1.03
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods (2009) 1.03