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Volumn 105, Issue 3, 2013, Pages 767-775

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEOTIDE; RNA POLYMERASE II; RPB1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84881425547     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.05.060     Document Type: Article
Times cited : (30)

References (65)
  • 1
    • 0033370108 scopus 로고    scopus 로고
    • Eukaryotic transcriptional control
    • R.D. Kornberg Eukaryotic transcriptional control Trends Cell Biol. 9 1999 M46 M49
    • (1999) Trends Cell Biol. , vol.9
    • Kornberg, R.D.1
  • 2
    • 0034507632 scopus 로고    scopus 로고
    • Transcription of eukaryotic protein-coding genes
    • T.I. Lee, and R.A. Young Transcription of eukaryotic protein-coding genes Annu. Rev. Genet. 34 2000 77 137
    • (2000) Annu. Rev. Genet. , vol.34 , pp. 77-137
    • Lee, T.I.1    Young, R.A.2
  • 3
    • 39849097831 scopus 로고    scopus 로고
    • RNA polymerase: The vehicle of transcription
    • S. Borukhov, and E. Nudler RNA polymerase: the vehicle of transcription Trends Microbiol. 16 2008 126 134
    • (2008) Trends Microbiol. , vol.16 , pp. 126-134
    • Borukhov, S.1    Nudler, E.2
  • 4
    • 66549126163 scopus 로고    scopus 로고
    • A movie of the RNA polymerase nucleotide addition cycle
    • F. Brueckner, J. Ortiz, and P. Cramer A movie of the RNA polymerase nucleotide addition cycle Curr. Opin. Struct. Biol. 19 2009 294 299
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 294-299
    • Brueckner, F.1    Ortiz, J.2    Cramer, P.3
  • 5
    • 84862666457 scopus 로고    scopus 로고
    • A movie of RNA polymerase II transcription
    • A.C.M. Cheung, and P. Cramer A movie of RNA polymerase II transcription Cell 149 2012 1431 1437
    • (2012) Cell , vol.149 , pp. 1431-1437
    • Cheung, A.C.M.1    Cramer, P.2
  • 6
    • 10944232674 scopus 로고    scopus 로고
    • Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    • H. Kettenberger, K.J. Armache, and P. Cramer Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS Mol. Cell 16 2004 955 965
    • (2004) Mol. Cell , vol.16 , pp. 955-965
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 7
    • 34447513771 scopus 로고    scopus 로고
    • Structural basis for substrate loading in bacterial RNA polymerase
    • D.G. Vassylyev, and M.N. Vassylyeva R. Landick Structural basis for substrate loading in bacterial RNA polymerase Nature 448 2007 163 168
    • (2007) Nature , vol.448 , pp. 163-168
    • Vassylyev, D.G.1    Vassylyeva, M.N.2    Landick, R.3
  • 8
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis
    • D. Wang, and D.A. Bushnell R.D. Kornberg Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Cell 127 2006 941 954
    • (2006) Cell , vol.127 , pp. 941-954
    • Wang, D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 9
    • 78049347876 scopus 로고    scopus 로고
    • RNA polymerase II with open and closed trigger loops: Active site dynamics and nucleic acid translocation
    • M. Feig, and Z.F. Burton RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation Biophys. J. 99 2010 2577 2586
    • (2010) Biophys. J. , vol.99 , pp. 2577-2586
    • Feig, M.1    Burton, Z.F.2
  • 10
    • 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
    • L.T. Da, D. Wang, and X.H. Huang 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 2012 2399 2406
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 2399-2406
    • Da, L.T.1    Wang, D.2    Huang, X.H.3
  • 11
    • 49449102926 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation
    • F. Brueckner, and P. Cramer Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation Nat. Struct. Mol. Biol. 15 2008 811 818
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 811-818
    • Brueckner, F.1    Cramer, P.2
  • 12
    • 77955653271 scopus 로고    scopus 로고
    • Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
    • S.A. Seibold, and B.N. Singh Z.F. Burton Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase Biochim. Biophys. Acta 1799 2010 575 587
    • (2010) Biochim. Biophys. Acta , vol.1799 , pp. 575-587
    • Seibold, S.A.1    Singh, B.N.2    Burton, Z.F.3
  • 13
    • 84870983295 scopus 로고    scopus 로고
    • Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
    • M.L. Kireeva, and K. Opron Z.F. Burton Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase BMC Biophys 5 2012 11
    • (2012) BMC Biophys , vol.5 , pp. 11
    • Kireeva, M.L.1    Opron, K.2    Burton, Z.F.3
  • 14
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • I. Toulokhonov, and J.W. Zhang R. Landick A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing Mol. Cell 27 2007 406 419
    • (2007) Mol. Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.1    Zhang, J.W.2    Landick, R.3
  • 15
    • 44449103640 scopus 로고    scopus 로고
    • The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by α-amanitin
    • C.D. Kaplan, K.M. Larsson, and R.D. Kornberg The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by α-amanitin Mol. Cell 30 2008 547 556
    • (2008) Mol. Cell , vol.30 , pp. 547-556
    • Kaplan, C.D.1    Larsson, K.M.2    Kornberg, R.D.3
  • 16
    • 77957678214 scopus 로고    scopus 로고
    • RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription
    • X.H. Huang, and D. Wang M. Levitt RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription Proc. Natl. Acad. Sci. USA 107 2010 15745 15750
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 15745-15750
    • Huang, X.H.1    Wang, D.2    Levitt, M.3
  • 17
    • 77954655593 scopus 로고    scopus 로고
    • Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis
    • Y. Yuzenkova, and N. Zenkin Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis Proc. Natl. Acad. Sci. USA 107 2010 10878 10883
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 10878-10883
    • Yuzenkova, Y.1    Zenkin, N.2
  • 18
    • 77449093660 scopus 로고    scopus 로고
    • Role of the RNA polymerase trigger loop in catalysis and pausing
    • J.W. Zhang, M. Palangat, and R. Landick Role of the RNA polymerase trigger loop in catalysis and pausing Nat. Struct. Mol. Biol. 17 2010 99 104
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 99-104
    • Zhang, J.W.1    Palangat, M.2    Landick, R.3
  • 19
    • 81155132249 scopus 로고    scopus 로고
    • Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop
    • I. Artsimovitch, and V. Svetlov E. Nudler Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop J. Biol. Chem. 286 2011 40395 40400
    • (2011) J. Biol. Chem. , vol.286 , pp. 40395-40400
    • Artsimovitch, I.1    Svetlov, V.2    Nudler, E.3
  • 20
    • 79961184265 scopus 로고    scopus 로고
    • Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre
    • M. Roghanian, Y. Yuzenkova, and N. Zenkin Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre Nucleic Acids Res. 39 2011 4352 4359
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4352-4359
    • Roghanian, M.1    Yuzenkova, Y.2    Zenkin, N.3
  • 21
    • 84860211901 scopus 로고    scopus 로고
    • Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II
    • M.H. Larson, and J. Zhou S.M. Block Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II Proc. Natl. Acad. Sci. USA 109 2012 6555 6560
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 6555-6560
    • Larson, M.H.1    Zhou, J.2    Block, S.M.3
  • 22
    • 34447499995 scopus 로고    scopus 로고
    • Structural basis for transcription elongation by bacterial RNA polymerase
    • D.G. Vassylyev, and M.N. Vassylyeva I. Artsimovitch Structural basis for transcription elongation by bacterial RNA polymerase Nature 448 2007 157 162
    • (2007) Nature , vol.448 , pp. 157-162
    • Vassylyev, D.G.1    Vassylyeva, M.N.2    Artsimovitch, I.3
  • 23
    • 12944324227 scopus 로고    scopus 로고
    • A ratchet mechanism of transcription elongation and its control
    • G. Bar-Nahum, and V. Epshtein E. Nudler A ratchet mechanism of transcription elongation and its control Cell 120 2005 183 193
    • (2005) Cell , vol.120 , pp. 183-193
    • Bar-Nahum, G.1    Epshtein, V.2    Nudler, E.3
  • 24
    • 44449094019 scopus 로고    scopus 로고
    • Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation
    • M.L. Kireeva, and Y.A. Nedialkov M. Kashlev Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation Mol. Cell 30 2008 557 566
    • (2008) Mol. Cell , vol.30 , pp. 557-566
    • Kireeva, M.L.1    Nedialkov, Y.A.2    Kashlev, M.3
  • 25
    • 24044497229 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by antibiotic streptolydigin
    • D. Temiakov, and N. Zenkin D.G. Vassylyev Structural basis of transcription inhibition by antibiotic streptolydigin Mol. Cell 19 2005 655 666
    • (2005) Mol. Cell , vol.19 , pp. 655-666
    • Temiakov, D.1    Zenkin, N.2    Vassylyev, D.G.3
  • 26
    • 77951973031 scopus 로고    scopus 로고
    • Stepwise mechanism for transcription fidelity
    • Y. Yuzenkova, and A. Bochkareva N. Zenkin Stepwise mechanism for transcription fidelity BMC Biol. 8 2010 54
    • (2010) BMC Biol. , vol.8 , pp. 54
    • Yuzenkova, Y.1    Bochkareva, A.2    Zenkin, N.3
  • 27
    • 0037022279 scopus 로고    scopus 로고
    • Structural basis of transcription: α-amanitin-RNA polymerase II cocrystal at 2.8 Å resolution
    • D.A. Bushnell, P. Cramer, and R.D. Kornberg Structural basis of transcription: α-amanitin-RNA polymerase II cocrystal at 2.8 Å resolution Proc. Natl. Acad. Sci. USA 99 2002 1218 1222
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1218-1222
    • Bushnell, D.A.1    Cramer, P.2    Kornberg, R.D.3
  • 28
    • 33645119890 scopus 로고    scopus 로고
    • Structural perspective on mutations affecting the function of multisubunit RNA polymerases
    • V. Trinh, and M.F. Langelier B. Coulombe Structural perspective on mutations affecting the function of multisubunit RNA polymerases Microbiol. Mol. Biol. Rev. 70 2006 12 36
    • (2006) Microbiol. Mol. Biol. Rev. , vol.70 , pp. 12-36
    • Trinh, V.1    Langelier, M.F.2    Coulombe, B.3
  • 29
    • 84860111277 scopus 로고    scopus 로고
    • Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo
    • C.D. Kaplan, and H.Y. Jin A. Belyanin Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo PLoS Genet. 8 2012 e1002627
    • (2012) PLoS Genet. , vol.8 , pp. 1002627
    • Kaplan, C.D.1    Jin, H.Y.2    Belyanin, A.3
  • 30
    • 57249108333 scopus 로고    scopus 로고
    • Bridge helix and trigger loop perturbations generate superactive RNA polymerases
    • L. Tan, and S. Wiesler R.O. Weinzierl Bridge helix and trigger loop perturbations generate superactive RNA polymerases J. Biol. 7 2008 40
    • (2008) J. Biol. , vol.7 , pp. 40
    • Tan, L.1    Wiesler, S.2    Weinzierl, R.O.3
  • 31
    • 33646188087 scopus 로고    scopus 로고
    • Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil
    • F. Malagon, and M.L. Kireeva J.N. Strathern Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil Genetics 172 2006 2201 2209
    • (2006) Genetics , vol.172 , pp. 2201-2209
    • Malagon, F.1    Kireeva, M.L.2    Strathern, J.N.3
  • 32
    • 0043244876 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
    • H. Kettenberger, K.J. Armache, and P. Cramer Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage Cell 114 2003 347 357
    • (2003) Cell , vol.114 , pp. 347-357
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 33
    • 67249164174 scopus 로고    scopus 로고
    • Schizosacharomyces pombe RNA polymerase II at 3.6-Å resolution
    • H. Spåhr, and G. Calero R.D. Kornberg Schizosacharomyces pombe RNA polymerase II at 3.6-Å resolution Proc. Natl. Acad. Sci. USA 106 2009 9185 9190
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 9185-9190
    • Spåhr, H.1    Calero, G.2    Kornberg, R.D.3
  • 34
    • 67449116330 scopus 로고    scopus 로고
    • Structural basis of transcription: Mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
    • J.F. Sydow, and F. Brueckner P. Cramer Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA Mol. Cell 34 2009 710 721
    • (2009) Mol. Cell , vol.34 , pp. 710-721
    • Sydow, J.F.1    Brueckner, F.2    Cramer, P.3
  • 35
    • 78650310283 scopus 로고    scopus 로고
    • Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
    • S. Tagami, and S. Sekine S. Yokoyama Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein Nature 468 2010 978 982
    • (2010) Nature , vol.468 , pp. 978-982
    • Tagami, S.1    Sekine, S.2    Yokoyama, S.3
  • 36
    • 79952440464 scopus 로고    scopus 로고
    • Structural basis of RNA polymerase II backtracking, arrest and reactivation
    • A.C.M. Cheung, and P. Cramer Structural basis of RNA polymerase II backtracking, arrest and reactivation Nature 471 2011 249 253
    • (2011) Nature , vol.471 , pp. 249-253
    • Cheung, A.C.M.1    Cramer, P.2
  • 37
    • 82455199223 scopus 로고    scopus 로고
    • Structural basis of initial RNA polymerase II transcription
    • A.C.M. Cheung, S. Sainsbury, and P. Cramer Structural basis of initial RNA polymerase II transcription EMBO J. 30 2011 4755 4763
    • (2011) EMBO J. , vol.30 , pp. 4755-4763
    • Cheung, A.C.M.1    Sainsbury, S.2    Cramer, P.3
  • 38
    • 77449145343 scopus 로고    scopus 로고
    • RNA polymerase II flexibility during translocation from normal mode analysis
    • M. Feig, and Z.F. Burton RNA polymerase II flexibility during translocation from normal mode analysis Proteins 78 2010 434 446
    • (2010) Proteins , vol.78 , pp. 434-446
    • Feig, M.1    Burton, Z.F.2
  • 39
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Karplus, M.3
  • 40
    • 1642576012 scopus 로고    scopus 로고
    • Improved treatment of the protein backbone in empirical force fields
    • A.D. MacKerell Jr., M. Feig, and C.L. Brooks 3rd Improved treatment of the protein backbone in empirical force fields J. Am. Chem. Soc. 126 2004 698 699
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 698-699
    • MacKerell, Jr.A.D.1    Feig, M.2    Brooks III, C.L.3
  • 41
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • N. Foloppe, and A.D. MacKerell All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 21 2000 86 104
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, A.D.2
  • 42
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 43
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system-solvent boundary potential for computer-simulations
    • D. Beglov, and B. Roux Finite representation of an infinite bulk system-solvent boundary potential for computer-simulations J. Chem. Phys. 100 1994 9050 9063
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 44
    • 0029115487 scopus 로고
    • Zinc binding in proteins and solution: A simple but accurate nonbonded representation
    • R.H. Stote, and M. Karplus Zinc binding in proteins and solution: a simple but accurate nonbonded representation Proteins 23 1995 12 31
    • (1995) Proteins , vol.23 , pp. 12-31
    • Stote, R.H.1    Karplus, M.2
  • 45
    • 33846823909 scopus 로고
    • Particle mesh ewald - An N×log(N) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle mesh ewald - an N×log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 46
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water model
    • S. Miyamoto, and P.A. Kollman SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water model J. Comput. Chem. 13 1992 952 962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 47
    • 36449003554 scopus 로고
    • Constant-pressure molecular-dynamics algorithms
    • G.J. Martyna, D.J. Tobias, and M.L. Klein Constant-pressure molecular-dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 48
    • 36449007836 scopus 로고
    • Constant pressure molecular-dynamics simulation: The Langevin piston method
    • S.E. Feller, and Y.H. Zhang B.R. Brooks Constant pressure molecular-dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613 4621
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Brooks, B.R.3
  • 50
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • M. Feig, J. Karanicolas, and C.L. Brooks 3rd MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology J. Mol. Graph. Model. 22 2004 377 395
    • (2004) J. Mol. Graph. Model. , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 51
    • 0037157317 scopus 로고    scopus 로고
    • On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
    • H. Fukunishi, O. Watanabe, and S. Takada On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction J. Chem. Phys. 116 2002 9058 9067
    • (2002) J. Chem. Phys. , vol.116 , pp. 9058-9067
    • Fukunishi, H.1    Watanabe, O.2    Takada, S.3
  • 52
    • 84864254504 scopus 로고    scopus 로고
    • Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations
    • A.V. Predeus, and S. Gul M. Feig Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations J. Phys. Chem. B 116 2012 8610 8620
    • (2012) J. Phys. Chem. B , vol.116 , pp. 8610-8620
    • Predeus, A.V.1    Gul, S.2    Feig, M.3
  • 53
  • 54
    • 0027794972 scopus 로고
    • Targeted molecular-dynamics simulation of conformational change: Application to the TR transition in insulin
    • J. Schlitter, and M. Engels A. Wollmer Targeted molecular-dynamics simulation of conformational change: application to the TR transition in insulin Mol. Simul. 10 1993 291 308
    • (1993) Mol. Simul. , vol.10 , pp. 291-308
    • Schlitter, J.1    Engels, M.2    Wollmer, A.3
  • 57
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
    • S. Kumar, and D. Bouzida J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. 1. the method J. Comput. Chem. 13 1992 1011 1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Rosenberg, J.M.3
  • 58
    • 18644368600 scopus 로고    scopus 로고
    • Free energy landscape of A-DNA to B-DNA conversion in aqueous solution
    • N.K. Banavali, and B. Roux Free energy landscape of A-DNA to B-DNA conversion in aqueous solution J. Am. Chem. Soc. 127 2005 6866 6876
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 6866-6876
    • Banavali, N.K.1    Roux, B.2
  • 60
    • 59649110607 scopus 로고    scopus 로고
    • Nucleic acid polymerases use a general acid for nucleotidyl transfer
    • C. Castro, and E.D. Smidansky C.E. Cameron Nucleic acid polymerases use a general acid for nucleotidyl transfer Nat. Struct. Mol. Biol. 16 2009 212 218
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 212-218
    • Castro, C.1    Smidansky, E.D.2    Cameron, C.E.3
  • 62
    • 0034703474 scopus 로고    scopus 로고
    • Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability
    • E. Cota, and S.J. Hamill J. Clarke Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability J. Mol. Biol. 302 2000 713 725
    • (2000) J. Mol. Biol. , vol.302 , pp. 713-725
    • Cota, E.1    Hamill, S.J.2    Clarke, J.3
  • 63
    • 45449112338 scopus 로고    scopus 로고
    • Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations
    • R. Zhu, and F. Janetzko D.R. Salahub Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations Theor. Chem. Acc. 120 2008 479 489
    • (2008) Theor. Chem. Acc. , vol.120 , pp. 479-489
    • Zhu, R.1    Janetzko, F.2    Salahub, D.R.3
  • 64
    • 84866095413 scopus 로고    scopus 로고
    • A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II
    • Y. Zhang, and D. Salahub A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II Sci. China Chem. 55 2012 1887 1894
    • (2012) Sci. China Chem. , vol.55 , pp. 1887-1894
    • Zhang, Y.1    Salahub, D.2


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