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Volumn 160, Issue 1, 2012, Pages 54-61

What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences

Author keywords

Fluctuation; Hydration; Kinetics; Lifetime; Sequence dependence; Water molecule

Indexed keywords

ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; DISSOCIATION; DNA SEQUENCE; DNA STRUCTURE; ELECTRIC POTENTIAL; HYDRATION; HYDROGEN BOND; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SURFACE PROPERTY; TRANSPORT KINETICS; WATER TRANSPORT;

EID: 80455176888     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.09.006     Document Type: Article
Times cited : (20)

References (50)
  • 3
    • 25444514520 scopus 로고    scopus 로고
    • Water dynamics in the hydration layer around proteins and micelles
    • DOI 10.1021/cr020661+
    • B. Bagchi Water dynamics in the hydration layer around proteins and micelles Chemical Reviews 105 2005 3197 3219 (Pubitemid 41430808)
    • (2005) Chemical Reviews , vol.105 , Issue.9 , pp. 3197-3219
    • Bagchi, B.1
  • 5
    • 2342527858 scopus 로고    scopus 로고
    • Dynamics of water in biological recognition
    • S.K. Pal, and A.H. Zewail Dynamics of water in biological recognition Chemical Reviews 104 2004 2099 2123
    • (2004) Chemical Reviews , vol.104 , pp. 2099-2123
    • Pal, S.K.1    Zewail, A.H.2
  • 7
    • 0027058824 scopus 로고
    • NMR observation of individual molecules of hydration water bound to DNA duplexes: Direct evidence for a spine of hydration water present in aqueous solution
    • E. Liepinsh, G. Otting, and K. Wüthrich NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution Nucleic Acids Research 20 1992 6549 6553 (Pubitemid 23052674)
    • (1992) Nucleic Acids Research , vol.20 , Issue.24 , pp. 6549-6553
    • Liepinsh, E.1    Otting, G.2    Wuthrich, K.3
  • 8
    • 0033582598 scopus 로고    scopus 로고
    • Determination of the residence time of water molecules hydrating B'-DNA and B-DNA, by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy
    • DOI 10.1006/jmbi.1998.2467
    • A.T. Phan, J.-L. Leroy, and M. Guéron Determination of the residence time of water molecules hydrating B′-DNA and B-DNA, by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy Journal of Molecular Biology 286 1999 505 519 (Pubitemid 29090166)
    • (1999) Journal of Molecular Biology , vol.286 , Issue.2 , pp. 505-519
    • Phan, A.T.1    Leroy, J.-L.2    Gueron, M.3
  • 9
    • 0032475964 scopus 로고    scopus 로고
    • Water molecules in DNA recognition I: Hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy
    • DOI 10.1006/jmbi.1998.2033
    • M. Sunnerhagen, V.P. Denisov, K. Venu, A.M.J.J. Bonvin, J. Carey, B. Halle, and G. Otting Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy Journal of Molecular Biology 282 1998 847 858 (Pubitemid 28442351)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.4 , pp. 847-858
    • Sunnerhagen, M.1    Denisov, V.P.2    Venu, K.3    Bonvin, A.M.J.J.4    Carey, J.5    Halle, B.6    Otting, G.7
  • 13
    • 0034725528 scopus 로고    scopus 로고
    • Water and ion binding around RNA and DNA (C, G) oligomers
    • P. Auffinger, and E. Westhof Water and ion binding around RNA and DNA (C, G) oligomers Journal of Molecular Biology 300 2000 1113 1131
    • (2000) Journal of Molecular Biology , vol.300 , pp. 1113-1131
    • Auffinger, P.1    Westhof, E.2
  • 15
    • 0027304152 scopus 로고
    • Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
    • DOI 10.1006/jmbi.1993.1350
    • R.M. Brunne, E. Liepinsh, G. Otting, K. Wüthrich, and W.F. van Gunsteren Hydration of proteins: a comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations Journal of Molecular Biology 231 1993 1040 1048 (Pubitemid 23209878)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.4 , pp. 1040-1048
    • Brunne, R.M.1    Liepinsh, E.2    Otting, G.3    Wuthrich, K.4    Van Gunsteren, W.F.5
  • 17
    • 0033995767 scopus 로고    scopus 로고
    • Molecular dynamics simulation of solvated azurin: Correlation between surface solvent accessibility and water residence times
    • DOI 10.1002/(SICI)1097-0134(20000401)39:1<56::AID-PROT6>3.0.CO;2-5
    • A. Luise, M. Falconi, and A. Desideri Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times Proteins 39 2000 56 67 (Pubitemid 30124131)
    • (2000) Proteins: Structure, Function and Genetics , vol.39 , Issue.1 , pp. 56-67
    • Luise, A.1    Falconi, M.2    Desideri, A.3
  • 18
    • 0033636839 scopus 로고    scopus 로고
    • Residence times of water molecules in the hydration sites of myoglobin
    • V.A. Makarov, B.K. Andrews, P.E. Smith, and B.M. Pettitt Residence times of water molecules in the hydration sites of myoglobin Biophysical Journal 79 2000 2966 2974
    • (2000) Biophysical Journal , vol.79 , pp. 2966-2974
    • Makarov, V.A.1    Andrews, B.K.2    Smith, P.E.3    Pettitt, B.M.4
  • 19
    • 33845727429 scopus 로고    scopus 로고
    • Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation
    • S. Pal, P.K. Maiti, and B. Bagchi Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation The Journal of Chemical Physics 125 2006 234903
    • (2006) The Journal of Chemical Physics , vol.125 , pp. 234903
    • Pal, S.1    Maiti, P.K.2    Bagchi, B.3
  • 20
    • 0031568141 scopus 로고    scopus 로고
    • Water residence times around copper plastocyanin: A molecular dynamics simulation approach
    • C. Rocchi, A.R. Bizzarri, and S. Cannistraro Water residence times around copper plastocyanin: a molecular dynamics simulation approach Chemical Physics 214 1997 261 276
    • (1997) Chemical Physics , vol.214 , pp. 261-276
    • Rocchi, C.1    Bizzarri, A.R.2    Cannistraro, S.3
  • 21
    • 33745326750 scopus 로고    scopus 로고
    • Simulation studies of the protein-water interface. I. Properties at the molecular resolution
    • C. Schröder, T. Rudas, S. Boresch, and O. Steinhauser Simulation studies of the protein-water interface. I. Properties at the molecular resolution The Journal of Chemical Physics 124 2006 234907
    • (2006) The Journal of Chemical Physics , vol.124 , pp. 234907
    • Schröder, C.1    Rudas, T.2    Boresch, S.3    Steinhauser, O.4
  • 22
    • 0036707992 scopus 로고    scopus 로고
    • Structural and dynamic properties of water around acetylcholinesterase
    • DOI 10.1110/ps.0214002
    • R.H. Henchman, and J.A. McCammon Structural and dynamic properties of water around acetylcholinesterase Protein Science 11 2002 2080 2090 (Pubitemid 34919612)
    • (2002) Protein Science , vol.11 , Issue.9 , pp. 2080-2090
    • Henchman, R.H.1    Andrew McCammon, J.2
  • 23
    • 0001520216 scopus 로고
    • Computation of the mean residence time of water in the hydration shells of biomolecules
    • A.E. García, and L. Stiller Computation of the mean residence time of water in the hydration shells of biomolecules Journal of Computational Chemistry 14 1993 1396 1406
    • (1993) Journal of Computational Chemistry , vol.14 , pp. 1396-1406
    • García, A.E.1    Stiller, L.2
  • 24
    • 0037438967 scopus 로고    scopus 로고
    • A microscopic view of peptide and protein solvation
    • DOI 10.1016/S0301-4622(02)00283-1, PII S0301462202002831
    • D.A.C. Beck, D.O.V. Alonso, and V. Daggett A microscopic view of peptide and protein solvation Biophysical Chemistry 100 2003 221 237 (Pubitemid 36342275)
    • (2003) Biophysical Chemistry , vol.100 , Issue.1-3 , pp. 221-237
    • Beck, D.A.C.1    Alonso, D.O.V.2    Daggett, V.3
  • 25
    • 0036286851 scopus 로고    scopus 로고
    • Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
    • V. Makarov, M. Pettitt, and M. Feig Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment Accounts of Chemical Research 35 2002 376 384
    • (2002) Accounts of Chemical Research , vol.35 , pp. 376-384
    • Makarov, V.1    Pettitt, M.2    Feig, M.3
  • 26
    • 28444456034 scopus 로고    scopus 로고
    • Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer
    • DOI 10.1021/ja054462u
    • S. Bandyopadhyay, S. Chakraborty, and B. Bagchi Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer Journal of the American Chemical Society 127 2005 16660 16667 (Pubitemid 41740417)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.47 , pp. 16660-16667
    • Bandyopadhyay, S.1    Chakraborty, S.2    Bagchi, B.3
  • 28
    • 33644886316 scopus 로고    scopus 로고
    • Dynamics of water confined in the interdomain region of a multidomain protein
    • L. Hua, X. Huang, R. Zhou, and B.J. Berne Dynamics of water confined in the interdomain region of a multidomain protein The Journal of Physical Chemistry. B 110 2006 3704 3711
    • (2006) The Journal of Physical Chemistry. B , vol.110 , pp. 3704-3711
    • Hua, L.1    Huang, X.2    Zhou, R.3    Berne, B.J.4
  • 29
    • 2542633488 scopus 로고    scopus 로고
    • Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study
    • DOI 10.1002/prot.20114
    • B.S. Sanjeev, and S. Vishveshwara Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study Proteins 55 2004 915 923 (Pubitemid 38702950)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.4 , pp. 915-923
    • Sanjeev, B.S.1    Vishveshwara, S.2
  • 30
    • 51649131252 scopus 로고    scopus 로고
    • Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces
    • M.H. Priya, J.K. Shah, D. Asthagiri, and M.E. Paulaitis Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces Biophysical Journal 95 2008 2219 2225
    • (2008) Biophysical Journal , vol.95 , pp. 2219-2225
    • Priya, M.H.1    Shah, J.K.2    Asthagiri, D.3    Paulaitis, M.E.4
  • 31
    • 0027957222 scopus 로고
    • Distribution function implied dynamics versus residence times and correlations: Solvation shells of myoglobin
    • V. Lounnas, and B.M. Pettitt Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin Proteins 18 1994 148 160 (Pubitemid 24055077)
    • (1994) Proteins: Structure, Function and Genetics , vol.18 , Issue.2 , pp. 148-160
    • Lounnas, V.1    Pettitt, B.M.2
  • 32
    • 32444440762 scopus 로고    scopus 로고
    • A molecular jump mechanism of water reorientation
    • DOI 10.1126/science.1122154
    • D. Laage, and J.T. Hynes A molecular jump mechanism of water reorientation Science 311 2006 832 835 (Pubitemid 43228843)
    • (2006) Science , vol.311 , Issue.5762 , pp. 832-835
    • Laage, D.1    Hynes, J.T.2
  • 34
    • 69449095355 scopus 로고    scopus 로고
    • Sequence dependencies of DNA deformability and hydration in the minor groove
    • Y. Yonetani, and H. Kono Sequence dependencies of DNA deformability and hydration in the minor groove Biophysical Journal 97 2009 1138 1147
    • (2009) Biophysical Journal , vol.97 , pp. 1138-1147
    • Yonetani, Y.1    Kono, H.2
  • 35
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • T.E. Cheatham III, P. Cieplak, and P.A. Kollman A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat Journal of Biomolecular Structure & Dynamics 16 1999 845 862 (Pubitemid 29157655)
    • (1999) Journal of Biomolecular Structure and Dynamics , vol.16 , Issue.4 , pp. 845-862
    • Cheatham III, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 36
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • J. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry 21 2000 1049 1074
    • (2000) Journal of Computational Chemistry , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 39
    • 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 The Journal of Chemical Physics 98 1993 10089 10092
    • (1993) The Journal of Chemical Physics , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 40
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Journal of Computational Physics 23 1977 327 341
    • (1977) Journal of Computational Physics , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 41
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • H.R. Drew, and R.E. Dickerson Structure of a B-DNA dodecamer III. Geometry of hydration Journal of Molecular Biology 151 1981 535 556 (Pubitemid 12252694)
    • (1981) Journal of Molecular Biology , vol.151 , Issue.3 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 42
    • 33947372094 scopus 로고    scopus 로고
    • DNA deformability and hydration studied by molecular dynamics simulation
    • DOI 10.1080/08927020601052971, PII 773408833
    • Y. Yonetani, H. Kono, S. Fujii, A. Sarai, and N. Go DNA deformability and hydration studied by molecular dynamics simulation Molecular Simulation 33 2007 103 107 (Pubitemid 46446378)
    • (2007) Molecular Simulation , vol.33 , Issue.1-2 , pp. 103-107
    • Yonetani, Y.1    Kono, H.2    Fujii, S.3    Sarai, A.4    Go, N.5
  • 43
    • 4243422452 scopus 로고    scopus 로고
    • Effect of environment on hydrogen bond dynamics in liquid water
    • A. Luzar, and D. Chandler Effect of environment on hydrogen bond dynamics in liquid water Physical Review Letters 76 1996 928 931 (Pubitemid 126618501)
    • (1996) Physical Review Letters , vol.76 , Issue.6 , pp. 928-931
    • Luzar, A.1    Chandler, D.2
  • 44
    • 35548987996 scopus 로고    scopus 로고
    • Sequence-dependent DNA deformability studied using molecular dynamics simulations
    • DOI 10.1093/nar/gkm627
    • S. Fujii, H. Kono, S. Takenaka, N. Go, and A. Sarai Sequence-dependent DNA deformability studied using molecular dynamics simulations Nucleic Acids Research 35 2007 6063 6074 (Pubitemid 350018570)
    • (2007) Nucleic Acids Research , vol.35 , Issue.18 , pp. 6063-6074
    • Fujii, S.1    Kono, H.2    Takenaka, S.3    Go, N.4    Sarai, A.5
  • 46
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • DOI 10.1093/nar/gkg680
    • X.-J. Lu, and W.K. Olson 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Research 31 2003 5108 5121 (Pubitemid 37441878)
    • (2003) Nucleic Acids Research , vol.31 , Issue.17 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 47
    • 34547485422 scopus 로고    scopus 로고
    • How protein surfaces induce anomalous dynamics of hydration water
    • DOI 10.1021/jp0717185
    • F. Pizzitutti, M. Marchi, F. Sterpone, and P.J. Rossky How protein surfaces induce anomalous dynamics of hydration water The Journal of Physical Chemistry. B 111 2007 7584 7590 (Pubitemid 47166814)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.26 , pp. 7584-7590
    • Pizzitutti, F.1    Marchi, M.2    Sterpone, F.3    Rossky, P.J.4
  • 48
    • 67149126766 scopus 로고    scopus 로고
    • Does the dynamic Stokes shift report on slow protein hydration dynamics?
    • B. Halle, and L. Nilsson Does the dynamic Stokes shift report on slow protein hydration dynamics? The Journal of Physical Chemistry. B 113 2009 8210 8213
    • (2009) The Journal of Physical Chemistry. B , vol.113 , pp. 8210-8213
    • Halle, B.1    Nilsson, L.2


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