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Volumn 10, Issue 11, 2014, Pages 4765-4776

Adaptive-partitioning QM/MM dynamics simulations: 3. Solvent molecules entering and leaving protein binding sites

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EID: 84909638703     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500553x     Document Type: Article
Times cited : (39)

References (57)
  • 1
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 1976, 103, 227-249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 2
    • 84988053595 scopus 로고
    • - exchange reaction and gas phase protonation of polyethers
    • - exchange reaction and gas phase protonation of polyethers J. Comput. Chem. 1986, 7, 718-730
    • (1986) J. Comput. Chem. , vol.7 , pp. 718-730
    • Singh, U.C.1    Kollmann, P.A.2
  • 3
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field, M. J.; Bash, P. A.; Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 1990, 11, 700-733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 4
    • 84962367344 scopus 로고    scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • Gao, J. Methods and applications of combined quantum mechanical and molecular mechanical potentials Rev. Comput. Chem. 1996, 7, 119-185
    • (1996) Rev. Comput. Chem. , vol.7 , pp. 119-185
    • Gao, J.1
  • 5
    • 0032054613 scopus 로고    scopus 로고
    • Quantum mechanical calculations on biological systems
    • Friesner, R. A.; Beachy, M. D. Quantum mechanical calculations on biological systems Curr. Opin. Struct. Biol. 1998, 8, 257-262
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 257-262
    • Friesner, R.A.1    Beachy, M.D.2
  • 7
    • 0001135663 scopus 로고    scopus 로고
    • Combined quantum mechanics and molecular mechanics approaches to chemical and biochemical reactivity
    • In, von Ragué Schleyer, P. Wiley: Chichester, Vol.
    • Ruiz-López, M. F.; Rivail, J. L. Combined quantum mechanics and molecular mechanics approaches to chemical and biochemical reactivity In Encyclopedia of Computational Chemistry, von Ragué Schleyer, P., Ed.; Wiley: Chichester, 1998; Vol. 1, pp 437-448.
    • (1998) Encyclopedia of Computational Chemistry , vol.1 , pp. 437-448
    • Ruiz-López, M.F.1    Rivail, J.L.2
  • 8
    • 0032711930 scopus 로고    scopus 로고
    • Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
    • Monard, G.; Merz, K. M., Jr. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems Acc. Chem. Res. 1999, 32, 904-911
    • (1999) Acc. Chem. Res. , vol.32 , pp. 904-911
    • Monard, G.1    Merz, K.M.2
  • 9
    • 0033597059 scopus 로고    scopus 로고
    • Chemical reactivity studied by hybrid QM/MM methods
    • Hillier, I. H. Chemical reactivity studied by hybrid QM/MM methods THEOCHEM 1999, 463, 45-52
    • (1999) THEOCHEM , vol.463 , pp. 45-52
    • Hillier, I.H.1
  • 10
    • 0034859929 scopus 로고    scopus 로고
    • Theoretical perspectives on proton-coupled electron transfer reactions
    • Hammes-Schiffer, S. Theoretical perspectives on proton-coupled electron transfer reactions Acc. Chem. Res. 2000, 34, 273-281
    • (2000) Acc. Chem. Res. , vol.34 , pp. 273-281
    • Hammes-Schiffer, S.1
  • 11
    • 0012576082 scopus 로고    scopus 로고
    • Hybrid quantum mechanics/molecular mechanics approaches
    • In, Grotendorst, J. John von Neumann-Instituts: Jülich, Vol.
    • Sherwood, P. Hybrid quantum mechanics/molecular mechanics approaches. In Modern Methods and Algorithms of Quantum Chemistry, Grotendorst, J., Ed.; John von Neumann-Instituts: Jülich, 2000; Vol. 3, pp 285-305.
    • (2000) Modern Methods and Algorithms of Quantum Chemistry , vol.3 , pp. 285-305
    • Sherwood, P.1
  • 12
    • 0036025446 scopus 로고    scopus 로고
    • Quantum mechanical methods for enzyme kinetics
    • Gao, J.; Truhlar, D. G. Quantum mechanical methods for enzyme kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-505
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 467-505
    • Gao, J.1    Truhlar, D.G.2
  • 13
    • 0037098212 scopus 로고    scopus 로고
    • New challenges in quantum chemistry: Quests for accurate calculations for large molecular systems
    • Morokuma, K. New challenges in quantum chemistry: Quests for accurate calculations for large molecular systems Philos. Trans. R. Soc. A 2002, 360, 1149-1164
    • (2002) Philos. Trans. R. Soc. A , vol.360 , pp. 1149-1164
    • Morokuma, K.1
  • 14
    • 33846570818 scopus 로고    scopus 로고
    • QM/MM: What have we learned, where are we, and where do we go from here?
    • Lin, H.; Truhlar, D. G. QM/MM: What have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 2007, 117, 185-199
    • (2007) Theor. Chem. Acc. , vol.117 , pp. 185-199
    • Lin, H.1    Truhlar, D.G.2
  • 15
    • 34547507515 scopus 로고    scopus 로고
    • QM/MM methods for biological systems
    • Senn, H. M.; Thiel, W. QM/MM methods for biological systems Top. Curr. Chem. 2007, 268, 173-290
    • (2007) Top. Curr. Chem. , vol.268 , pp. 173-290
    • Senn, H.M.1    Thiel, W.2
  • 16
    • 84926135997 scopus 로고    scopus 로고
    • Recent developments in QM/MM methods towards open-boundary multi-scale simulations
    • Pezeshki, S.; Lin, H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations Mol. Simul. 2014, 10.1080/08927022.2014.911870
    • (2014) Mol. Simul.
    • Pezeshki, S.1    Lin, H.2
  • 17
    • 0009662619 scopus 로고    scopus 로고
    • ONIOM-XS: An extension of the ONIOM method for molecular simulation in condensed phase
    • Kerdcharoen, T.; Morokuma, K. ONIOM-XS: An extension of the ONIOM method for molecular simulation in condensed phase Chem. Phys. Lett. 2002, 355, 257-262
    • (2002) Chem. Phys. Lett. , vol.355 , pp. 257-262
    • Kerdcharoen, T.1    Morokuma, K.2
  • 18
    • 0037530063 scopus 로고    scopus 로고
    • 2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology
    • 2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology J. Chem. Phys. 2003, 118, 8856-8862
    • (2003) J. Chem. Phys. , vol.118 , pp. 8856-8862
    • Kerdcharoen, T.1    Morokuma, K.2
  • 19
    • 33947392043 scopus 로고    scopus 로고
    • Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations
    • Heyden, A.; Lin, H.; Truhlar, D. G. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations J. Phys. Chem. B 2007, 111, 2231-2241
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2231-2241
    • Heyden, A.1    Lin, H.2    Truhlar, D.G.3
  • 20
    • 80755185247 scopus 로고    scopus 로고
    • Adaptive-partitioning redistributed charge and dipole schemes for QM/MM dynamics simulations: On-the-fly relocation of boundaries that pass through covalent bonds
    • Pezeshki, S.; Lin, H. Adaptive-partitioning redistributed charge and dipole schemes for QM/MM dynamics simulations: On-the-fly relocation of boundaries that pass through covalent bonds J. Chem. Theory Comput. 2011, 7, 3625-3634
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3625-3634
    • Pezeshki, S.1    Lin, H.2
  • 22
    • 84865065466 scopus 로고    scopus 로고
    • Application of adaptive QM/MM methods to molecular dynamics simulations of aqueous systems
    • Park, K.; Gotz, A. W.; Walker, R. C.; Paesani, F. Application of adaptive QM/MM methods to molecular dynamics simulations of aqueous systems J. Chem. Theory Comput. 2012, 8, 2868-2877
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2868-2877
    • Park, K.1    Gotz, A.W.2    Walker, R.C.3    Paesani, F.4
  • 25
    • 84885600912 scopus 로고    scopus 로고
    • Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution
    • Várnai, C.; Bernstein, N.; Mones, L.; Csányi, G. Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution J. Phys. Chem. B 2013, 117, 12202-12211
    • (2013) J. Phys. Chem. B , vol.117 , pp. 12202-12211
    • Várnai, C.1    Bernstein, N.2    Mones, L.3    Csányi, G.4
  • 26
    • 26944480734 scopus 로고    scopus 로고
    • Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "umbrella integration"
    • Kästner, J.; Thiel, W. Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration" J. Chem. Phys. 2005, 123, 144104/1-5
    • (2005) J. Chem. Phys. , vol.123 , pp. 144104/1-5
    • Kästner, J.1    Thiel, W.2
  • 27
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Constrained reaction coordinate dynamics for the simulation of rare events Chem. Phys. Lett. 1989, 156, 472-477
    • (1989) Chem. Phys. Lett. , vol.156 , pp. 472-477
    • Carter, E.A.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 29
    • 0035935802 scopus 로고    scopus 로고
    • Calculating free energies using average force
    • Darve, E.; Pohorille, A. Calculating free energies using average force J. Chem. Phys. 2001, 115, 9169-9183
    • (2001) J. Chem. Phys. , vol.115 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 30
    • 58049208953 scopus 로고    scopus 로고
    • Conservative algorithm for an adaptive change of resolution in mixed atomistic/coarse-grained multiscale simulations
    • Heyden, A.; Truhlar, D. G. Conservative algorithm for an adaptive change of resolution in mixed atomistic/coarse-grained multiscale simulations J. Chem. Theory Comput. 2008, 4, 217-221
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 217-221
    • Heyden, A.1    Truhlar, D.G.2
  • 31
    • 80052228936 scopus 로고    scopus 로고
    • Comment on "adaptive multiscale molecular dynamics of macromolecular fluids"
    • Praprotnik, M.; Poblete, S.; Delle Site, L.; Kremer, K. Comment on "Adaptive multiscale molecular dynamics of macromolecular fluids" Phys. Rev. Lett. 2011, 107, 099801/1-2
    • (2011) Phys. Rev. Lett. , vol.107 , pp. 099801/1-2
    • Praprotnik, M.1    Poblete, S.2    Delle Site, L.3    Kremer, K.4
  • 33
    • 0018801493 scopus 로고
    • A voltage-gated anion channel from the electric organ of Torpedo-Californica
    • White, M. M.; Miller, C. A voltage-gated anion channel from the electric organ of Torpedo-Californica J. Biol. Chem. 1979, 254, 161-166
    • (1979) J. Biol. Chem. , vol.254 , pp. 161-166
    • White, M.M.1    Miller, C.2
  • 34
    • 0033873930 scopus 로고    scopus 로고
    • A decade of ClC chloride channels: Structure, mechanism, and many unsettled questions
    • Maduke, M.; Miller, C.; Mindell, J. A. A decade of ClC chloride channels: Structure, mechanism, and many unsettled questions Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 411-438
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 411-438
    • Maduke, M.1    Miller, C.2    Mindell, J.A.3
  • 35
    • 0035033206 scopus 로고    scopus 로고
    • Ion permeation and selectivity in ClC-type chloride channels
    • Fahlke, C. Ion permeation and selectivity in ClC-type chloride channels Am. J. Physiol. Renal. Physiol. 2001, 280, F748-757
    • (2001) Am. J. Physiol. Renal. Physiol. , vol.280 , pp. 748-757
    • Fahlke, C.1
  • 36
    • 33746641711 scopus 로고    scopus 로고
    • The ClC family of chloride channels and transporters
    • Dutzler, R. The ClC family of chloride channels and transporters Curr. Opin. Struct. Biol. 2006, 16, 439-446
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 439-446
    • Dutzler, R.1
  • 37
    • 39849092445 scopus 로고    scopus 로고
    • CLC chloride channels and transporters: From genes to protein structure, pathology, and physiology
    • Jentsch, T. J. CLC chloride channels and transporters: From genes to protein structure, pathology, and physiology Crit. Rev. Biochem. Mol. Biol. 2008, 43, 3-36
    • (2008) Crit. Rev. Biochem. Mol. Biol. , vol.43 , pp. 3-36
    • Jentsch, T.J.1
  • 39
    • 0037122805 scopus 로고    scopus 로고
    • X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
    • Dutzler, R.; Campbell, E. B.; Cadene, M.; Chait, B. T.; MacKinnon, R. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity Nature 2002, 415, 287-294
    • (2002) Nature , vol.415 , pp. 287-294
    • Dutzler, R.1    Campbell, E.B.2    Cadene, M.3    Chait, B.T.4    Mackinnon, R.5
  • 40
    • 0037418859 scopus 로고    scopus 로고
    • Gating the selectivity filter in ClC chloride channels
    • Dutzler, R.; Campbell, E. B.; MacKinnon, R. Gating the selectivity filter in ClC chloride channels Science 2003, 300, 108-112
    • (2003) Science , vol.300 , pp. 108-112
    • Dutzler, R.1    Campbell, E.B.2    Mackinnon, R.3
  • 41
    • 78651241836 scopus 로고    scopus 로고
    • Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters
    • Smith, M.; Lin, H. Charge delocalization upon chloride ion binding in ClC chloride ion channels/transporters Chem. Phys. Lett. 2011, 502, 112-117
    • (2011) Chem. Phys. Lett. , vol.502 , pp. 112-117
    • Smith, M.1    Lin, H.2
  • 42
    • 2542437774 scopus 로고    scopus 로고
    • Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli
    • Faraldo-Gómez, J. D.; Roux, B. Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli J. Mol. Biol. 2004, 339, 981-1000
    • (2004) J. Mol. Biol. , vol.339 , pp. 981-1000
    • Faraldo-Gómez, J.D.1    Roux, B.2
  • 44
    • 4444366193 scopus 로고    scopus 로고
    • Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the ClC chloride channel
    • Bostick, D. L.; Berkowitz, M. L. Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the ClC chloride channel Biophys. J. 2004, 87, 1686-1696
    • (2004) Biophys. J. , vol.87 , pp. 1686-1696
    • Bostick, D.L.1    Berkowitz, M.L.2
  • 45
    • 1142291714 scopus 로고    scopus 로고
    • Mechanism of anionic conduction across ClC
    • Cohen, J.; Schulten, K. Mechanism of anionic conduction across ClC Biophys. J. 2004, 86, 836-845
    • (2004) Biophys. J. , vol.86 , pp. 836-845
    • Cohen, J.1    Schulten, K.2
  • 46
    • 33746228476 scopus 로고    scopus 로고
    • Exploring the gating mechanism in the ClC chloride channel via metadynamics
    • Gervasio, F. L.; Parrinello, M.; Ceccarelli, M.; Klein, M. L. Exploring the gating mechanism in the ClC chloride channel via metadynamics J. Mol. Biol. 2006, 361, 390-398
    • (2006) J. Mol. Biol. , vol.361 , pp. 390-398
    • Gervasio, F.L.1    Parrinello, M.2    Ceccarelli, M.3    Klein, M.L.4
  • 47
    • 84890921104 scopus 로고    scopus 로고
    • Charge transfer and polarization for chloride ions bound in ClC transport proteins: Natural bond orbital and energy decomposition analyses
    • Church, J.; Pezeshki, S.; Davis, C.; Lin, H. Charge transfer and polarization for chloride ions bound in ClC transport proteins: Natural bond orbital and energy decomposition analyses J. Phys. Chem. B 2013, 117, 16029-16043
    • (2013) J. Phys. Chem. B , vol.117 , pp. 16029-16043
    • Church, J.1    Pezeshki, S.2    Davis, C.3    Lin, H.4
  • 51
    • 84988129057 scopus 로고
    • Optimization of parameters for semiempirical methods I. Method
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods I. Method J. Comput. Chem. 1989, 10, 209-220
    • (1989) J. Comput. Chem. , vol.10 , pp. 209-220
    • Stewart, J.J.P.1
  • 52
    • 84988073214 scopus 로고
    • Optimization of parameters for semiempirical methods II. Applications
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods II. Applications J. Comput. Chem. 1989, 10, 221-264
    • (1989) J. Comput. Chem. , vol.10 , pp. 221-264
    • Stewart, J.J.P.1
  • 53
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé, S. A molecular dynamics method for simulations in the canonical ensemble Mol. Phys. 1982, 52, 255-268
    • (1982) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 54
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 55
    • 84909602966 scopus 로고    scopus 로고
    • Version 1.4.0.CO; University of Minnesota: Minneapolis
    • Lin, H.; Zhang, Y.; Pezeshki, S.; Truhlar, D. G. QMMM, Version 1.4.0.CO; University of Minnesota: Minneapolis, 2014.
    • (2014) QMMM
    • Lin, H.1    Zhang, Y.2    Pezeshki, S.3    Truhlar, D.G.4
  • 56
    • 34247531772 scopus 로고    scopus 로고
    • Version 5.1; Washington University: St. Louis, MO
    • Ponder, J. W. TINKER, Version 5.1; Washington University: St. Louis, MO, 2010.
    • (2010) TINKER
    • Ponder, J.W.1
  • 57
    • 84874829967 scopus 로고    scopus 로고
    • Version 7.0; Max-Planck-Institut für Kohlenforschung: Müheim an der Ruhr, Germany
    • Thiel, W. MNDO2005, Version 7.0; Max-Planck-Institut für Kohlenforschung: Müheim an der Ruhr, Germany, 2005.
    • (2005) MNDO2005
    • Thiel, W.1


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