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Volumn 110, Issue 4, 2013, Pages 1197-1202

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT;

EID: 84872837570     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1221231110     Document Type: Article
Times cited : (87)

References (51)
  • 1
    • 33745032291 scopus 로고    scopus 로고
    • Water mediation in protein folding and molecular recognition
    • Levy Y, Onuchic JN (2006) Water mediation in protein folding and molecular recognition. Annu Rev Biophys Biomol Struct 35:389-415.
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 389-415
    • Levy, Y.1    Onuchic, J.N.2
  • 2
    • 84872859789 scopus 로고    scopus 로고
    • Molecular recognition and ligand association
    • Baron R, McCammon JA (2013) Molecular recognition and ligand association. Annu Rev Phys Chem 64:151-175.
    • (2013) Annu Rev Phys Chem , vol.64 , pp. 151-175
    • Baron, R.1    McCammon, J.A.2
  • 3
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • Chandler D (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437(7059):640-647.
    • (2005) Nature , vol.437 , Issue.7059 , pp. 640-647
    • Chandler, D.1
  • 4
    • 67449084506 scopus 로고    scopus 로고
    • Dewetting and hydrophobic interaction in physical and biological systems
    • Berne BJ, Weeks JD, Zhou R (2009) Dewetting and hydrophobic interaction in physical and biological systems. Annu Rev Phys Chem 60:85-103.
    • (2009) Annu Rev Phys Chem , vol.60 , pp. 85-103
    • Berne, B.J.1    Weeks, J.D.2    Zhou, R.3
  • 5
    • 43049122273 scopus 로고    scopus 로고
    • Water in nonpolar confinement: From nanotubes to proteins and beyond
    • Rasaiah JC, Garde S, Hummer G (2008) Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu Rev Phys Chem 59:713-740.
    • (2008) Annu Rev Phys Chem , vol.59 , pp. 713-740
    • Rasaiah, J.C.1    Garde, S.2    Hummer, G.3
  • 6
    • 79959486658 scopus 로고    scopus 로고
    • Hydrophobicity of proteins and interfaces: Insights from density fluctuations
    • Jamadagni SN, Godawat R, Garde S (2011) Hydrophobicity of proteins and interfaces: Insights from density fluctuations. Annu Rev Chem Biomol Eng 2:147-171.
    • (2011) Annu Rev Chem Biomol Eng , vol.2 , pp. 147-171
    • Jamadagni, S.N.1    Godawat, R.2    Garde, S.3
  • 7
    • 84857761874 scopus 로고    scopus 로고
    • Sitting at the edge: How biomolecules use hydrophobicity to tune their interactions and function
    • Patel AJ, et al. (2012) Sitting at the edge: How biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B 116(8):2498-2503.
    • (2012) J Phys Chem B , vol.116 , Issue.8 , pp. 2498-2503
    • Patel, A.J.1
  • 8
    • 77953502244 scopus 로고    scopus 로고
    • Dewetting transitions in protein cavities
    • Young T, et al. (2010) Dewetting transitions in protein cavities. Proteins 78(8): 1856-1869.
    • (2010) Proteins , vol.78 , Issue.8 , pp. 1856-1869
    • Young, T.1
  • 9
    • 33846524439 scopus 로고    scopus 로고
    • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    • Young T, Abel R, Kim B, Berne BJ, Friesner RA (2007) Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci USA 104(3):808-813.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.3 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 10
    • 79952161696 scopus 로고    scopus 로고
    • Ligand binding to protein-binding pockets with wet and dry regions
    • Wang L, Berne BJ, Friesner RA (2011) Ligand binding to protein-binding pockets with wet and dry regions. Proc Natl Acad Sci USA 108(4):1326-1330.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.4 , pp. 1326-1330
    • Wang, L.1    Berne, B.J.2    Friesner, R.A.3
  • 11
    • 80455129248 scopus 로고    scopus 로고
    • Computational probe of cavitation events in protein systems
    • Wang J, Kudesia S, Bratko D, Luzar A (2011) Computational probe of cavitation events in protein systems. Phys Chem Chem Phys 13(44):19902-19910.
    • (2011) Phys Chem Chem Phys , vol.13 , Issue.44 , pp. 19902-19910
    • Wang, J.1    Kudesia, S.2    Bratko, D.3    Luzar, A.4
  • 12
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a protein hydrophobic cavity by nmr
    • Ernst JA, Clubb RT, Zhou HX, Gronenborn AM, Clore GM (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267(5205):1813-1817.
    • (1995) Science , vol.267 , Issue.5205 , pp. 1813-1817
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 15
    • 33749994956 scopus 로고    scopus 로고
    • Water properties inside nanoscopic hydrophobic pocket studied by computer simulations
    • Setny P, Geller M (2006) Water properties inside nanoscopic hydrophobic pocket studied by computer simulations. J Chem Phys 125(14):144717-144723.
    • (2006) J Chem Phys , vol.125 , Issue.14 , pp. 144717-144723
    • Setny, P.1    Geller, M.2
  • 16
    • 70350751573 scopus 로고    scopus 로고
    • Dewetting-controlled binding of ligands to hydrophobic pockets
    • Setny P, et al. (2009) Dewetting-controlled binding of ligands to hydrophobic pockets. Phys Rev Lett 103(18):187801-187804.
    • (2009) Phys Rev Lett , vol.103 , Issue.18 , pp. 187801-187804
    • Setny, P.1
  • 17
    • 77956583186 scopus 로고    scopus 로고
    • How can hydrophobic association be enthalpy driven?
    • Setny P, Baron R, McCammon JA (2010) How can hydrophobic association be enthalpy driven? J Chem Theory Comput 6(9):2866-2871.
    • (2010) J Chem Theory Comput , vol.6 , Issue.9 , pp. 2866-2871
    • Setny, P.1    Baron, R.2    McCammon, J.A.3
  • 18
    • 77956075440 scopus 로고    scopus 로고
    • Water in cavity-ligand recognition
    • Baron R, Setny P, McCammon JA (2010) Water in cavity-ligand recognition. J Am Chem Soc 132(34):12091-12097.
    • (2010) J Am Chem Soc , vol.132 , Issue.34 , pp. 12091-12097
    • Baron, R.1    Setny, P.2    McCammon, J.A.3
  • 19
    • 84870006566 scopus 로고    scopus 로고
    • Water structure, dynamics, and spectral signatures: Changes upon model cavity-ligand recognition
    • Baron R, Setny P, Paesani F (2012) Water structure, dynamics, and spectral signatures: Changes upon model cavity-ligand recognition. J Phys Chem B 116(46):13774-13780.
    • (2012) J Phys Chem B , vol.116 , Issue.46 , pp. 13774-13780
    • Baron, R.1    Setny, P.2    Paesani, F.3
  • 20
    • 78049348054 scopus 로고    scopus 로고
    • Molecular binding: Under water's influence
    • Hummer G (2010) Molecular binding: Under water's influence. Nat Chem 2(11): 906-907.
    • (2010) Nat Chem , vol.2 , Issue.11 , pp. 906-907
    • Hummer, G.1
  • 21
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352-1360.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 22
    • 0031010107 scopus 로고    scopus 로고
    • The kinetics of protein-protein recognition
    • Janin J (1997) The kinetics of protein-protein recognition. Proteins 28(2):153-161.
    • (1997) Proteins , vol.28 , Issue.2 , pp. 153-161
    • Janin, J.1
  • 23
    • 0034049350 scopus 로고    scopus 로고
    • Kinetics of desolvation-mediated protein-protein binding
    • Camacho CJ, Kimura SR, DeLisi C, Vajda S (2000) Kinetics of desolvation-mediated protein-protein binding. Biophys J 78(3):1094-1105.
    • (2000) Biophys J , vol.78 , Issue.3 , pp. 1094-1105
    • Camacho, C.J.1    Kimura, S.R.2    DeLisi, C.3    Vajda, S.4
  • 24
    • 33845493850 scopus 로고    scopus 로고
    • Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization?
    • Michel J, Verdonk ML, Essex JW (2006) Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization? J Med Chem 49(25): 7427-7439.
    • (2006) J Med Chem , vol.49 , Issue.25 , pp. 7427-7439
    • Michel, J.1    Verdonk, M.L.2    Essex, J.W.3
  • 25
    • 0002278835 scopus 로고
    • First passage time problems in chemical physics
    • Weiss GH (1966) First passage time problems in chemical physics. Adv Chem Phys 13: 1-18.
    • (1966) Adv Chem Phys , vol.13 , pp. 1-18
    • Weiss, G.H.1
  • 26
    • 0347193736 scopus 로고
    • Reaction-rate theory: Fifty years after kramers
    • Hänggi P, Talkner P, Borkovec M (1990) Reaction-rate theory: Fifty years after Kramers. Rev Mod Phys 62:251-341.
    • (1990) Rev Mod Phys , vol.62 , pp. 251-341
    • Hänggi, P.1    Talkner, P.2    Borkovec, M.3
  • 27
    • 23244438863 scopus 로고    scopus 로고
    • Position-dependent diffusion coefficients and free energies from bayesian analysis of equilibrium and replica molecular dynamics simulations
    • Hummer G (2005) Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J Phys 7:1-14.
    • (2005) New J Phys , vol.7 , pp. 1-14
    • Hummer, G.1
  • 28
    • 77954192001 scopus 로고    scopus 로고
    • How the diffusivity profile reduces the arbitrariness of protein folding energies
    • Hinczewski M, von Hansen Y, Dzubiella J, Netz RR (2010) How the diffusivity profile reduces the arbitrariness of protein folding energies. J Chem Phys 132(24):245103.
    • (2010) J Chem Phys , vol.132 , Issue.24 , pp. 245103
    • Hinczewski, M.1    Von Hansen, Y.2    Dzubiella, J.3    Netz, R.R.4
  • 29
    • 81155152245 scopus 로고    scopus 로고
    • Water dynamics at interfaces and solutes: Disentangling free energy and diffusivity contributions
    • Sedlmeier F, von Hansen Y, Mengyu L, Horinek D, Netz RR (2011) Water dynamics at interfaces and solutes: disentangling free energy and diffusivity contributions. J Stat Phys 145:240-252.
    • (2011) J Stat Phys , vol.145 , pp. 240-252
    • Sedlmeier, F.1    Von Hansen, Y.2    Mengyu, L.3    Horinek, D.4    Netz, R.R.5
  • 30
    • 0034321137 scopus 로고    scopus 로고
    • Transition path sampling of cavitation between molecular scale hydrophobic surfaces
    • Bolhuis PG, Chandler D (2000) Transition path sampling of cavitation between molecular scale hydrophobic surfaces. J Chem Phys 113:8154-8160.
    • (2000) J Chem Phys , vol.113 , pp. 8154-8160
    • Bolhuis, P.G.1    Chandler, D.2
  • 31
    • 0034301107 scopus 로고    scopus 로고
    • Dynamics of capillary evaporation. Ii. Free energy barriers
    • Leung K, Luzar A (2000) Dynamics of capillary evaporation. II. Free energy barriers. J Chem Phys 113:5845-5852.
    • (2000) J Chem Phys , vol.113 , pp. 5845-5852
    • Leung, K.1    Luzar, A.2
  • 32
    • 0037435840 scopus 로고    scopus 로고
    • Dynamics of capillary drying in water
    • Leung K, Luzar A, Bratko D (2003) Dynamics of capillary drying in water. Phys Rev Lett 90(6):065502-065505.
    • (2003) Phys Rev Lett , vol.90 , Issue.6 , pp. 065502-065505
    • Leung, K.1    Luzar, A.2    Bratko, D.3
  • 33
    • 77952938759 scopus 로고    scopus 로고
    • Liquid-vapor oscillations of water nanoconfined between hydrophobic disks: Thermodynamics and kinetics
    • Xu L, Molinero V (2010) Liquid-vapor oscillations of water nanoconfined between hydrophobic disks: Thermodynamics and kinetics. J Phys Chem B 114(21):7320-7328.
    • (2010) J Phys Chem B , vol.114 , Issue.21 , pp. 7320-7328
    • Xu, L.1    Molinero, V.2
  • 34
    • 84863398744 scopus 로고    scopus 로고
    • Evaporation rate of water in hydrophobic confinement
    • Sharma S, Debenedetti PG (2012) Evaporation rate of water in hydrophobic confinement. Proc Natl Acad Sci USA 109(12):4365-4370.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.12 , pp. 4365-4370
    • Sharma, S.1    Debenedetti, P.G.2
  • 35
    • 84862945185 scopus 로고    scopus 로고
    • Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes
    • Morrone JA, Li J, Berne BJ (2012) Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes. J Phys Chem B 116(1): 378-389.
    • (2012) J Phys Chem B , vol.116 , Issue.1 , pp. 378-389
    • Morrone, J.A.1    Li, J.2    Berne, B.J.3
  • 36
    • 84866597924 scopus 로고    scopus 로고
    • Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?
    • Li J, Morrone JA, Berne BJ (2012) Are hydrodynamic interactions important in the kinetics of hydrophobic collapse? J Phys Chem B 116(37):11537-11544.
    • (2012) J Phys Chem B , vol.116 , Issue.37 , pp. 11537-11544
    • Li, J.1    Morrone, J.A.2    Berne, B.J.3
  • 37
    • 33847327575 scopus 로고
    • The fluctuation-dissipation theorem
    • Kubo R (1966) The fluctuation-dissipation theorem. Rep Prog Phys 29:255-285.
    • (1966) Rep Prog Phys , vol.29 , pp. 255-285
    • Kubo, R.1
  • 38
    • 36449000642 scopus 로고
    • A theory for the activated barrier crossing rate constant in systems influenced by space and time dependent friction
    • Haynes GR, Voth GA, Pollack E (1994) A theory for the activated barrier crossing rate constant in systems influenced by space and time dependent friction. J Chem Phys 101:7811-7822.
    • (1994) J Chem Phys , vol.101 , pp. 7811-7822
    • Haynes, G.R.1    Voth, G.A.2    Pollack, E.3
  • 40
    • 5644247351 scopus 로고
    • Frequency-dependent friction and reaction rates
    • Grote RF, van der Zwan G, Hynes JT (1984) Frequency-dependent friction and reaction rates. J Phys Chem 88:4676-4684.
    • (1984) J Phys Chem , vol.88 , pp. 4676-4684
    • Grote, R.F.1    Van Der Zwan, G.2    Hynes, J.T.3
  • 42
    • 0000458906 scopus 로고
    • Calculation of dynamic friction on intramolecular degrees of freedom
    • Straub JE, Borkovec M, Berne BJ (1987) Calculation of dynamic friction on intramolecular degrees of freedom. J Chem Phys 91:4885-4998.
    • (1987) J Chem Phys , vol.91 , pp. 4885-4998
    • Straub, J.E.1    Borkovec, M.2    Berne, B.J.3
  • 43
    • 0040825751 scopus 로고
    • Spatial dependence of time dependent friction for pair diffusion in a simple fluid
    • Straub JE, Berne BJ, Roux B (1990) Spatial dependence of time dependent friction for pair diffusion in a simple fluid. J Chem Phys 93:6804-6812.
    • (1990) J Chem Phys , vol.93 , pp. 6804-6812
    • Straub, J.E.1    Berne, B.J.2    Roux, B.3
  • 44
    • 0042492919 scopus 로고
    • Fokker-planck equation for nonlinear stochastic dynamics in the presence of space and time dependent friction
    • Pollack E, Berezhkovskii AM (1993) Fokker-Planck equation for nonlinear stochastic dynamics in the presence of space and time dependent friction. J Chem Phys 99: 1344-1346.
    • (1993) J Chem Phys , vol.99 , pp. 1344-1346
    • Pollack, E.1    Berezhkovskii, A.M.2
  • 45
    • 0000901098 scopus 로고
    • Stochastically gated diffusioninfluenced reactions
    • Szabo A, Shoup D, Northrup S, McCammon J (1982) Stochastically gated diffusioninfluenced reactions. J Chem Phys 77:4484-4493.
    • (1982) J Chem Phys , vol.77 , pp. 4484-4493
    • Szabo, A.1    Shoup, D.2    Northrup, S.3    McCammon, J.4
  • 46
    • 80054978058 scopus 로고    scopus 로고
    • Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites
    • Barreda JL, Zhou HX (2011) Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites. J Chem Phys 135(14):145101-145115.
    • (2011) J Chem Phys , vol.135 , Issue.14 , pp. 145101-145115
    • Barreda, J.L.1    Zhou, H.X.2
  • 47
    • 0021515659 scopus 로고
    • Optimized intermolecular potential functions for liquid hydrocarbons
    • Jorgensen WL, Madura JD, Swenson CJ (1984) Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc 106:6638-6646.
    • (1984) J Am Chem Soc , vol.106 , pp. 6638-6646
    • Jorgensen, W.L.1    Madura, J.D.2    Swenson, C.J.3
  • 49
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • Nose S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81:511-519.
    • (1984) J Chem Phys , vol.81 , pp. 511-519
    • Nose, S.1
  • 50
    • 84986512474 scopus 로고
    • Charmm - A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks BR, et al. (1983) CHARMM - A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
    • (1983) J Comput Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1


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