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Volumn 119, Issue 44, 2015, Pages 14111-14119

DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MOLECULAR DYNAMICS; NUCLEIC ACIDS; NUCLEOTIDES; PROTEINS;

EID: 84946827690     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b08486     Document Type: Article
Times cited : (12)

References (48)
  • 1
    • 84946837767 scopus 로고    scopus 로고
    • John Wiley & Sons, Ltd: Chichester
    • Strauch, M. A. In eLS; John Wiley & Sons, Ltd: Chichester, 2001.
    • (2001) eLS
    • Strauch, M.A.1
  • 2
    • 0035930331 scopus 로고    scopus 로고
    • Recognition of Specific DNA Sequences
    • Garvie, C. W.; Wolberger, C. Recognition of Specific DNA Sequences Mol. Cell 2001, 8, 937-946 10.1016/S1097-2765(01)00392-6
    • (2001) Mol. Cell , vol.8 , pp. 937-946
    • Garvie, C.W.1    Wolberger, C.2
  • 3
    • 84877031756 scopus 로고    scopus 로고
    • How Do Proteins Locate Specific Targets in DNA?
    • Redding, S.; Greene, E. C. How Do Proteins Locate Specific Targets in DNA? Chem. Phys. Lett. 2013, 570, 1-11 10.1016/j.cplett.2013.03.035
    • (2013) Chem. Phys. Lett. , vol.570 , pp. 1-11
    • Redding, S.1    Greene, E.C.2
  • 4
    • 51249090299 scopus 로고    scopus 로고
    • Importance of Accurate DNA Structures in Solution: The Jun-Fos Model
    • Heddi, B.; Foloppe, N.; Oguey, C.; Hartmann, B. Importance of Accurate DNA Structures in Solution: The Jun-Fos Model J. Mol. Biol. 2008, 382, 956-970 10.1016/j.jmb.2008.07.047
    • (2008) J. Mol. Biol. , vol.382 , pp. 956-970
    • Heddi, B.1    Foloppe, N.2    Oguey, C.3    Hartmann, B.4
  • 5
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
    • Perez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92, 3817-3829 10.1529/biophysj.106.097782
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchán, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 7
    • 84877729731 scopus 로고    scopus 로고
    • Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
    • Zgarbova, M.; Luque, F. J.; Sponer, J.; Cheatham, T. E., III; Otyepka, M.; Jurecka, P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters J. Chem. Theory Comput. 2013, 9, 2339-2354 10.1021/ct400154j
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2339-2354
    • Zgarbova, M.1    Luque, F.J.2    Sponer, J.3    Cheatham, T.E.4    Otyepka, M.5    Jurecka, P.6
  • 8
    • 84860767348 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
    • Götz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born J. Chem. Theory Comput. 2012, 8, 1542-1555 10.1021/ct200909j
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 1542-1555
    • Götz, A.W.1    Williamson, M.J.2    Xu, D.3    Poole, D.4    Le Grand, S.5    Walker, R.C.6
  • 9
    • 84923133278 scopus 로고    scopus 로고
    • On the Absence of Intrahelical DNA Dynamics on the us to ms Timescale
    • Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E., III On the Absence of Intrahelical DNA Dynamics on the us to ms Timescale Nat. Commun. 2014, 5, 5152 10.1038/ncomms6152
    • (2014) Nat. Commun. , vol.5 , pp. 5152
    • Galindo-Murillo, R.1    Roe, D.R.2    Cheatham, T.E.3
  • 10
    • 84923206685 scopus 로고    scopus 로고
    • Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC)
    • Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E., III Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC) Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 1041-1058 10.1016/j.bbagen.2014.09.007
    • (2015) Biochim. Biophys. Acta, Gen. Subj. , vol.1850 , pp. 1041-1058
    • Galindo-Murillo, R.1    Roe, D.R.2    Cheatham, T.E.3
  • 11
    • 84884192184 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
    • Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9, 3878-3888 10.1021/ct400314y
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Götz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 13
    • 1242314385 scopus 로고    scopus 로고
    • DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations
    • Djuranovic, D.; Hartmann, B. DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations Biopolymers 2004, 73, 356-368 10.1002/bip.10528
    • (2004) Biopolymers , vol.73 , pp. 356-368
    • Djuranovic, D.1    Hartmann, B.2
  • 15
    • 33746074088 scopus 로고    scopus 로고
    • Quantification of DNA BI/BII Backbone States in Solution. Implications for DNA Overall Structure and Recognition
    • Heddi, B.; Foloppe, N.; Bouchemal, N.; Hantz, E.; Hartmann, B. Quantification of DNA BI/BII Backbone States in Solution. Implications for DNA Overall Structure and Recognition J. Am. Chem. Soc. 2006, 128, 9170-9177 10.1021/ja061686j
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 9170-9177
    • Heddi, B.1    Foloppe, N.2    Bouchemal, N.3    Hantz, E.4    Hartmann, B.5
  • 17
    • 0038118496 scopus 로고    scopus 로고
    • Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states
    • Djuranovic, D.; Hartmann, B. Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states J. Biomol. Struct. Dyn. 2003, 20, 771-788 10.1080/07391102.2003.10506894
    • (2003) J. Biomol. Struct. Dyn. , vol.20 , pp. 771-788
    • Djuranovic, D.1    Hartmann, B.2
  • 18
    • 0023350241 scopus 로고
    • Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology
    • Srinivasan, A. R.; Olson, W. K. Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology J. Biomol. Struct. Dyn. 1987, 4, 895-938 10.1080/07391102.1987.10507690
    • (1987) J. Biomol. Struct. Dyn. , vol.4 , pp. 895-938
    • Srinivasan, A.R.1    Olson, W.K.2
  • 19
    • 0034624091 scopus 로고    scopus 로고
    • BII Nucleotides in the B and C Forms of Natural-sequence Polymeric DNA: A New Model for the C Form of DNA
    • van Dam, L.; Levitt, M. H. BII Nucleotides in the B and C Forms of Natural-sequence Polymeric DNA: A New Model for the C Form of DNA J. Mol. Biol. 2000, 304, 541-561 10.1006/jmbi.2000.4194
    • (2000) J. Mol. Biol. , vol.304 , pp. 541-561
    • Van Dam, L.1    Levitt, M.H.2
  • 20
    • 0032755536 scopus 로고    scopus 로고
    • Helix Morphology Changes in B-DNA Induced By Spontaneous BI ⇌ BII Substate Interconversion
    • Winger, R. H.; Liedl, K. R.; Pichler, A.; Hallbrucker, A.; Mayer, E. Helix Morphology Changes in B-DNA Induced By Spontaneous BI ⇌ BII Substate Interconversion J. Biomol. Struct. Dyn. 1999, 17, 223-235 10.1080/07391102.1999.10508355
    • (1999) J. Biomol. Struct. Dyn. , vol.17 , pp. 223-235
    • Winger, R.H.1    Liedl, K.R.2    Pichler, A.3    Hallbrucker, A.4    Mayer, E.5
  • 21
    • 0030984104 scopus 로고    scopus 로고
    • Sensitivity of NMR Internucleotide Distances to B-DNA Conformation: Underlying Mechanics
    • Lefebvre, A.; Fermandjian, S.; Hartmann, B. Sensitivity of NMR Internucleotide Distances to B-DNA Conformation: Underlying Mechanics Nucleic Acids Res. 1997, 25, 3855-3862 10.1093/nar/25.19.3855
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3855-3862
    • Lefebvre, A.1    Fermandjian, S.2    Hartmann, B.3
  • 23
    • 0032417684 scopus 로고    scopus 로고
    • Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets
    • Rozenberg, H.; Rabinovich, D.; Frolow, F.; Hegde, R. S.; Shakked, Z. Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 15194-15199 10.1073/pnas.95.26.15194
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 15194-15199
    • Rozenberg, H.1    Rabinovich, D.2    Frolow, F.3    Hegde, R.S.4    Shakked, Z.5
  • 25
    • 84884354648 scopus 로고    scopus 로고
    • The Papillomavirus E2 Proteins
    • McBride, A. A. The Papillomavirus E2 Proteins Virology 2013, 445, 57-79 10.1016/j.virol.2013.06.006
    • (2013) Virology , vol.445 , pp. 57-79
    • McBride, A.A.1
  • 26
    • 79960861304 scopus 로고    scopus 로고
    • Evolutionary Variation of Papillomavirus E2 Protein and E2 Binding Sites
    • Rogers, A.; Waltke, M.; Angeletti, P. C. Evolutionary Variation of Papillomavirus E2 Protein and E2 Binding Sites Virol. J. 2011, 8, 379 10.1186/1743-422X-8-379
    • (2011) Virol. J. , vol.8 , pp. 379
    • Rogers, A.1    Waltke, M.2    Angeletti, P.C.3
  • 27
    • 0023178843 scopus 로고
    • Bovine Papillomavirus E2 Trans-Activating Gene Product Binds to Specific Sites in Papillomavirus DNA
    • Androphy, E. J.; Lowy, D. R.; Schiller, J. T. Bovine Papillomavirus E2 Trans-Activating Gene Product Binds to Specific Sites in Papillomavirus DNA Nature 1987, 325, 70-73 10.1038/325070a0
    • (1987) Nature , vol.325 , pp. 70-73
    • Androphy, E.J.1    Lowy, D.R.2    Schiller, J.T.3
  • 28
    • 0036086459 scopus 로고    scopus 로고
    • The Papillomavirus E2 Proteins: Structure, Function, and Biology
    • Hegde, R. S. The Papillomavirus E2 Proteins: Structure, Function, and Biology Annu. Rev. Biophys. Biomol. Struct. 2002, 31, 343-360 10.1146/annurev.biophys.31.100901.142129
    • (2002) Annu. Rev. Biophys. Biomol. Struct. , vol.31 , pp. 343-360
    • Hegde, R.S.1
  • 29
    • 0023958472 scopus 로고
    • The Specific DNA Recognition Sequence of the Bovine Papillomavirus E2 Protein is an E2-Dependent Enhancer
    • Hawley-Nelson, P.; Androphy, E. J.; Lowy, D. R.; Schiller, J. T. The Specific DNA Recognition Sequence of the Bovine Papillomavirus E2 Protein is an E2-Dependent Enhancer EMBO J. 1988, 7, 525-531
    • (1988) EMBO J. , vol.7 , pp. 525-531
    • Hawley-Nelson, P.1    Androphy, E.J.2    Lowy, D.R.3    Schiller, J.T.4
  • 30
    • 0026656038 scopus 로고
    • Crystal Structure at 1.7 A of the Bovine Papillomavirus-1 E2 DNA-binding Domain Bound to its DNA Target
    • Hegde, R. S.; Grossman, S. R.; Laimins, L. A.; Sigler, P. B. Crystal Structure at 1.7 A of the Bovine Papillomavirus-1 E2 DNA-binding Domain Bound to its DNA Target Nature 1992, 359, 505-512 10.1038/359505a0
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.S.1    Grossman, S.R.2    Laimins, L.A.3    Sigler, P.B.4
  • 31
    • 25844495843 scopus 로고    scopus 로고
    • Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism
    • Djuranovic, D.; Hartmann, B. Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism Biophys. J. 2005, 89, 2542-2551 10.1529/biophysj.104.057109
    • (2005) Biophys. J. , vol.89 , pp. 2542-2551
    • Djuranovic, D.1    Hartmann, B.2
  • 32
    • 51049122626 scopus 로고    scopus 로고
    • MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation
    • Falconi, M.; Oteri, F.; Eliseo, T.; Cicero, D. O.; Desideri, A. MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation Biophys. J. 2008, 95, 1108-1117 10.1529/biophysj.108.130849
    • (2008) Biophys. J. , vol.95 , pp. 1108-1117
    • Falconi, M.1    Oteri, F.2    Eliseo, T.3    Cicero, D.O.4    Desideri, A.5
  • 35
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
    • Zgarbová, M.; Otyepka, M.; Šponer, J.; Mládek, A.; Banáš, P.; Cheatham, T. E. I.; Jurečka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles J. Chem. Theory Comput. 2011, 7, 2886-2902 10.1021/ct200162x
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbová, M.1    Otyepka, M.2    Šponer, J.3    Mládek, A.4    Banáš, P.5    Cheatham, T.E.I.6    Jurečka, P.7
  • 37
    • 49449085241 scopus 로고    scopus 로고
    • Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
    • Joung, I. S.; Cheatham, T. E., III Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041 10.1021/jp8001614
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9020-9041
    • Joung, I.S.1    Cheatham, T.E.2
  • 38
    • 84927779536 scopus 로고    scopus 로고
    • Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning
    • Hopkins, C. W.; Le Grand, S.; Walker, R. C.; Roitberg, A. E. Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning J. Chem. Theory Comput. 2015, 11, 1864-1874 10.1021/ct5010406
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 1864-1874
    • Hopkins, C.W.1    Le Grand, S.2    Walker, R.C.3    Roitberg, A.E.4
  • 41
    • 33646940952 scopus 로고
    • Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
    • Ryckaert, J. P. J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes J. Comput. Phys. 1977, 23, 327-341 10.1016/0021-9991(77)90098-5
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 42
    • 84952104504 scopus 로고
    • An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms
    • Pastor, R. W.; Brooks, B. R.; Szabo, A. An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms Mol. Phys. 1988, 65, 1409-1419 10.1080/00268978800101881
    • (1988) Mol. Phys. , vol.65 , pp. 1409-1419
    • Pastor, R.W.1    Brooks, B.R.2    Szabo, A.3
  • 44
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
    • Roe, D. R.; Cheatham, T. E., III PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9, 3084-3095 10.1021/ct400341p
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 45
    • 84892604842 scopus 로고    scopus 로고
    • Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
    • Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Swails, J. M.; Roitberg, A. E.; Cheatham, T. E., III Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide J. Chem. Theory Comput. 2014, 10, 492-499 10.1021/ct400862k
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 492-499
    • Bergonzo, C.1    Henriksen, N.M.2    Roe, D.R.3    Swails, J.M.4    Roitberg, A.E.5    Cheatham, T.E.6
  • 46
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual Molecular Dynamics
    • Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
    • (1996) J. Mol. Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 47
    • 79957788878 scopus 로고    scopus 로고
    • ProDy: Protein Dynamics Inferred from Theory and Experiments
    • Bakan, A.; Meireles, L. M.; Bahar, I. ProDy: Protein Dynamics Inferred from Theory and Experiments Bioinformatics 2011, 27, 1575-1577 10.1093/bioinformatics/btr168
    • (2011) Bioinformatics , vol.27 , pp. 1575-1577
    • Bakan, A.1    Meireles, L.M.2    Bahar, I.3
  • 48
    • 20944449840 scopus 로고    scopus 로고
    • Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis
    • Madhumalar, A.; Bansal, M. Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis J. Biomol. Struct. Dyn. 2005, 23, 13-27 10.1080/07391102.2005.10507043
    • (2005) J. Biomol. Struct. Dyn. , vol.23 , pp. 13-27
    • Madhumalar, A.1    Bansal, M.2


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