RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

[1]  Michael Feig,et al.  Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase. , 2010, Biochimica et biophysica acta.

[2]  Michael Feig,et al.  RNA polymerase II flexibility during translocation from normal mode analysis , 2010, Proteins.

[3]  B. Coulombe,et al.  Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II. , 2010, Protein expression and purification.

[4]  Robert Landick,et al.  Role of the RNA polymerase trigger loop in catalysis and pausing , 2010, Nature Structural &Molecular Biology.

[5]  M. Kashlev,et al.  Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. , 2009, Methods.

[6]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[7]  J. Strathern,et al.  Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II*♦ , 2009, The Journal of Biological Chemistry.

[8]  Simone C. Wiesler,et al.  Bridge helix and trigger loop perturbations generate superactive RNA polymerases , 2008, Journal of biology.

[9]  Craig D. Kaplan,et al.  A bridge to transcription by RNA polymerase , 2008, Journal of biology.

[10]  Yuemin Liu,et al.  Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes , 2008, Proteins.

[11]  W. Greenleaf,et al.  Single-molecule studies of RNA polymerase: motoring along. , 2008, Annual review of biochemistry.

[12]  P. Cramer,et al.  Structure of eukaryotic RNA polymerases. , 2008, Annual review of biophysics.

[13]  Evgeny Nudler,et al.  RNA polymerase: the vehicle of transcription. , 2008, Trends in microbiology.

[14]  Jonathan Tennyson,et al.  Water vapour in the atmosphere of a transiting extrasolar planet , 2007, Nature.

[15]  Irina Artsimovitch,et al.  Structural basis for substrate loading in bacterial RNA polymerase , 2007, Nature.

[16]  Craig D. Kaplan,et al.  Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis , 2006, Cell.

[17]  T. Schlick,et al.  Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta. , 2006, Biochemical and biophysical research communications.

[18]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[19]  W. Greenleaf,et al.  Direct observation of base-pair stepping by RNA polymerase , 2005, Nature.

[20]  Michael Feig,et al.  NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[21]  Michael Feig,et al.  Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. , 2005, Molecular cell.

[22]  Arkady Mustaev,et al.  A Ratchet Mechanism of Transcription Elongation and Its Control , 2005, Cell.

[23]  P. Cramer,et al.  Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. , 2004, Molecular cell.

[24]  D. Bushnell,et al.  Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center , 2004, Cell.

[25]  Adam W Van Wynsberghe,et al.  Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. , 2004, Biochemistry.

[26]  Michael Feig,et al.  MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. , 2004, Journal of molecular graphics & modelling.

[27]  Thomas A Steitz,et al.  The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase , 2004, Cell.

[28]  Alexander D. MacKerell,et al.  Improved treatment of the protein backbone in empirical force fields. , 2004, Journal of the American Chemical Society.

[29]  M. Delarue,et al.  Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. , 2002, Journal of molecular biology.

[30]  A. Sali,et al.  Evolution and physics in comparative protein structure modeling. , 2002, Accounts of chemical research.

[31]  P. Cramer,et al.  RNA POLYMERASE II ELONGATION COMPLEX , 2001 .

[32]  P. Cramer,et al.  Architecture of RNA polymerase II and implications for the transcription mechanism. , 2000, Science.

[33]  Alexander D. MacKerell,et al.  All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000, J. Comput. Chem..

[34]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[35]  R. Kornberg,et al.  Eukaryotic transcriptional control. , 1999, Trends in cell biology.

[36]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[37]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[38]  M Karplus,et al.  Zinc binding in proteins and solution: A simple but accurate nonbonded representation , 1995, Proteins.

[39]  D. Beglov,et al.  Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .

[40]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[41]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[42]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .