메뉴 건너뛰기




Volumn 105, Issue 17, 2008, Pages 6296-6301

A dry ligand-binding cavity in a solvated protein

Author keywords

lactoglobulin; Free energy simulation; Hydrophobic hydration; Magnetic relaxation dispersion

Indexed keywords

BETA LACTOGLOBULIN; CARBON NANOTUBE; DEUTERIUM; OXYGEN 17; WATER; APOPROTEIN; LACTOGLOBULIN; LIGAND; OXYGEN; PROTON;

EID: 44049083019     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0709844105     Document Type: Article
Times cited : (99)

References (44)
  • 1
    • 0242559057 scopus 로고    scopus 로고
    • Inhomogeneous molecular density: Reference packing densities and distribution of cavities within proteins
    • Rother K, Preissner R, Goede A, Frömmel C (2003) Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics 19:2112-2121.
    • (2003) Bioinformatics , vol.19 , pp. 2112-2121
    • Rother, K.1    Preissner, R.2    Goede, A.3    Frömmel, C.4
  • 2
    • 23044435317 scopus 로고    scopus 로고
    • Statistical and molecular dynamics studies of buried waters in globular proteins
    • Park S, Saven JG (2005) Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 60:450-463.
    • (2005) Proteins , vol.60 , pp. 450-463
    • Park, S.1    Saven, J.G.2
  • 4
    • 2142715470 scopus 로고    scopus 로고
    • Water dynamics and dewetting transitions in the small mechanosensitive channel MscS
    • Anishkin A, Sukharev S (2004) Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys J 86:2883-2895.
    • (2004) Biophys J , vol.86 , pp. 2883-2895
    • Anishkin, A.1    Sukharev, S.2
  • 5
    • 24344448662 scopus 로고    scopus 로고
    • Observation of a dewetting transition in the collapse of the melittin tetramer
    • Liu P, Huang X, Zhou R, Berne BJ (2005) Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 437:159-162.
    • (2005) Nature , vol.437 , pp. 159-162
    • Liu, P.1    Huang, X.2    Zhou, R.3    Berne, B.J.4
  • 6
    • 23944481864 scopus 로고    scopus 로고
    • Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water
    • Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SEV, Homans SW (2005) Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water. J Am Chem Soc 127:11827-11834.
    • (2005) J Am Chem Soc , vol.127 , pp. 11827-11834
    • Barratt, E.1    Bingham, R.J.2    Warner, D.J.3    Laughton, C.A.4    Phillips, S.E.V.5    Homans, S.W.6
  • 7
    • 13244260957 scopus 로고    scopus 로고
    • Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase
    • Tashiro M, Stuchebrukhov AA (2005) Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase. J Phys Chem B 109:1015-1022.
    • (2005) J Phys Chem B , vol.109 , pp. 1015-1022
    • Tashiro, M.1    Stuchebrukhov, A.A.2
  • 8
    • 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 104:808-813.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 10
    • 0035207954 scopus 로고    scopus 로고
    • The X-ray structure of a recombinant major urinary protein at 1.75 Å resolution. A comparative study of X-ray and NMR-derived structures
    • Kuser PR, Franzoni L, Ferrari E, Spisni A, Polikarpov I (2001) The X-ray structure of a recombinant major urinary protein at 1.75 Å resolution. A comparative study of X-ray and NMR-derived structures. Acta Crystallogr D 57:1863-1869.
    • (2001) Acta Crystallogr D , vol.57 , pp. 1863-1869
    • Kuser, P.R.1    Franzoni, L.2    Ferrari, E.3    Spisni, A.4    Polikarpov, I.5
  • 11
    • 1842687872 scopus 로고    scopus 로고
    • Biomolecular cryocrystallography: Structural changes during flashcooling
    • Halle B (2004) Biomolecular cryocrystallography: Structural changes during flashcooling. Proc Natl Acad Sci USA 101:4793-4798.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 4793-4798
    • Halle, B.1
  • 12
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
    • Ernst JA, Clubb RT, Zhou H-X, Gronenborn AM, Clore GM (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267:1813-1817.
    • (1995) Science , vol.267 , pp. 1813-1817
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.-X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 13
    • 0030892956 scopus 로고    scopus 로고
    • NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules
    • Otting G, Liepinsh E, Halle B, Frey U (1997) NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nat Struct Biol 4:396-404.
    • (1997) Nat Struct Biol , vol.4 , pp. 396-404
    • Otting, G.1    Liepinsh, E.2    Halle, B.3    Frey, U.4
  • 14
    • 0003233568 scopus 로고    scopus 로고
    • NMR studies of water bound to biological molecules
    • Otting G (1997) NMR studies of water bound to biological molecules. Progr NMR Spectrosc 31:259-285.
    • (1997) Progr NMR Spectrosc , vol.31 , pp. 259-285
    • Otting, G.1
  • 15
    • 0346212520 scopus 로고    scopus 로고
    • Cross-relaxation between macromolecular and solvent spins: The role of long-range dipole couplings
    • Halle B (2003) Cross-relaxation between macromolecular and solvent spins: The role of long-range dipole couplings. J Chem Phys 119:12372-12385.
    • (2003) J Chem Phys , vol.119 , pp. 12372-12385
    • Halle, B.1
  • 16
    • 0001351418 scopus 로고
    • Importance of polarization for dipolar solutes in low-dielectric media: 1,2-dichloroethane and water in cyklohexane
    • Jorgensen WL, McDonald NA, Selmi M, Rablen PR (1995) Importance of polarization for dipolar solutes in low-dielectric media: 1,2-dichloroethane and water in cyklohexane. J Am Chem Soc 117:11809-11810.
    • (1995) J Am Chem Soc , vol.117 , pp. 11809-11810
    • Jorgensen, W.L.1    McDonald, N.A.2    Selmi, M.3    Rablen, P.R.4
  • 17
    • 3042592839 scopus 로고    scopus 로고
    • Hydration free energies and entropies for water in protein interiors
    • Olano LR, Rick SW (2004) Hydration free energies and entropies for water in protein interiors. J Am Chem Soc 126:7991-8000.
    • (2004) J Am Chem Soc , vol.126 , pp. 7991-8000
    • Olano, L.R.1    Rick, S.W.2
  • 18
    • 0033524454 scopus 로고    scopus 로고
    • Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography
    • Yu B, Blaber M, Gronenborn AM, Clore GM, Caspar DLD (1999) Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography. Proc Natl Acad Sci USA 96:103-108.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 103-108
    • Yu, B.1    Blaber, M.2    Gronenborn, A.M.3    Clore, G.M.4    Caspar, D.L.D.5
  • 19
    • 33845957884 scopus 로고    scopus 로고
    • Determination of solvent content in cavities in IL-1β using experimentally phased electron density
    • Quillin ML, Wingfield PT, Matthews BW (2006) Determination of solvent content in cavities in IL-1β using experimentally phased electron density. Proc Natl Acad Sci USA 103:19749-19753.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 19749-19753
    • Quillin, M.L.1    Wingfield, P.T.2    Matthews, B.W.3
  • 21
    • 34248572405 scopus 로고    scopus 로고
    • Hydration of a hydrophobic cavity and its functional role: A simulation study of human interleukin-1β
    • Somani S, Chng C-P, Verma CS (2007) Hydration of a hydrophobic cavity and its functional role: A simulation study of human interleukin-1β. Proteins 67:868-885.
    • (2007) Proteins , vol.67 , pp. 868-885
    • Somani, S.1    Chng, C.-P.2    Verma, C.S.3
  • 22
    • 34250845103 scopus 로고    scopus 로고
    • Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion
    • Yin H, Hummer G, Rasaiah JC (2007) Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc 129:7369-7377.
    • (2007) J Am Chem Soc , vol.129 , pp. 7369-7377
    • Yin, H.1    Hummer, G.2    Rasaiah, J.C.3
  • 23
    • 28044463816 scopus 로고    scopus 로고
    • Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
    • Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM (2005) Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci USA 102:16668-16671.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 16668-16671
    • Collins, M.D.1    Hummer, G.2    Quillin, M.L.3    Matthews, B.W.4    Gruner, S.M.5
  • 25
    • 0345313659 scopus 로고    scopus 로고
    • β-Lactoglobulin binds palmitate within its central cavity
    • Wu S-Y, Pérez MD, Puyol P, Sawyer L (1999) β-Lactoglobulin binds palmitate within its central cavity. J Biol Chem 274:170-174.
    • (1999) J Biol Chem , vol.274 , pp. 170-174
    • Wu, S.-Y.1    Pérez, M.D.2    Puyol, P.3    Sawyer, L.4
  • 27
    • 0036228989 scopus 로고    scopus 로고
    • Flexibility, functionality and hydrophobicity of bovine β-lactoglobulin
    • Jameson GB, Adams JJ, Creamer LK (2002) Flexibility, functionality and hydrophobicity of bovine β-lactoglobulin. Int Dairy J 12:319-329.
    • (2002) Int Dairy J , vol.12 , pp. 319-329
    • Jameson, G.B.1    Adams, J.J.2    Creamer, L.K.3
  • 28
    • 0035829539 scopus 로고    scopus 로고
    • Water conduction through the hydrophobic channel of a carbon nanotube
    • Hummer G, Rasaiah JC, Noworyta JP (2001) Water conduction through the hydrophobic channel of a carbon nanotube. Nature 414:188-190.
    • (2001) Nature , vol.414 , pp. 188-190
    • Hummer, G.1    Rasaiah, J.C.2    Noworyta, J.P.3
  • 29
    • 0000202632 scopus 로고    scopus 로고
    • Multinuclear relaxation dispersion studies of protein hydration
    • eds. Krishna NR & Berliner LJ Kluwer Academic/Plenum, New York, pp
    • Halle B, Denisov VP, Venu K (1999) Multinuclear relaxation dispersion studies of protein hydration. In Biological Magnetic Resonance, eds. Krishna NR & Berliner LJ (Kluwer Academic/Plenum, New York), pp 419-484.
    • (1999) Biological Magnetic Resonance , pp. 419-484
    • Halle, B.1    Denisov, V.P.2    Venu, K.3
  • 30
    • 0029994817 scopus 로고    scopus 로고
    • Using buried water molecules to explore the energy landscape of proteins
    • Denisov VP, Peters J, Hörlein HD, Halle B (1996) Using buried water molecules to explore the energy landscape of proteins. Nat Struct Biol 3:505-509.
    • (1996) Nat Struct Biol , vol.3 , pp. 505-509
    • Denisov, V.P.1    Peters, J.2    Hörlein, H.D.3    Halle, B.4
  • 32
    • 10044267947 scopus 로고    scopus 로고
    • Stabilization of internal charges in a protein: Water penetration or conformational change?
    • Denisov VP, Schlessman JL, García-Moreno E. B., Halle B (2004) Stabilization of internal charges in a protein: Water penetration or conformational change? Biophys J 87:3982-3994.
    • (2004) Biophys J , vol.87 , pp. 3982-3994
    • Denisov, V.P.1    Schlessman, J.L.2    García-Moreno, E.B.3    Halle, B.4
  • 33
    • 0037115859 scopus 로고    scopus 로고
    • Filling and emptying kinetics of carbon nanotubes in water
    • Waghe A, Rasaiah JC, Hummer G (2002) Filling and emptying kinetics of carbon nanotubes in water. J Chem Phys 117:10789-10795.
    • (2002) J Chem Phys , vol.117 , pp. 10789-10795
    • Waghe, A.1    Rasaiah, J.C.2    Hummer, G.3
  • 34
    • 8344280383 scopus 로고    scopus 로고
    • Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes
    • Vaitheeswaran S, Rasaiah JC, Hummer G (2004) Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. J Chem Phys 121:7955-7965.
    • (2004) J Chem Phys , vol.121 , pp. 7955-7965
    • Vaitheeswaran, S.1    Rasaiah, J.C.2    Hummer, G.3
  • 36
    • 0027244075 scopus 로고
    • Rat intestinal fatty acid binding protein
    • Sacchettini JC, Gordon JI (1993) Rat intestinal fatty acid binding protein. J Biol Chem 268:18399-18402.
    • (1993) J Biol Chem , vol.268 , pp. 18399-18402
    • Sacchettini, J.C.1    Gordon, J.I.2
  • 37
    • 0036037132 scopus 로고    scopus 로고
    • The ligand-binding site of bovine β-lactoglobulin: Evidence for a function?
    • Kontopidis G, Holt C, Sawyer L (2002) The ligand-binding site of bovine β-lactoglobulin: Evidence for a function? J Mol Biol 318:1043-1055.
    • (2002) J Mol Biol , vol.318 , pp. 1043-1055
    • Kontopidis, G.1    Holt, C.2    Sawyer, L.3
  • 38
    • 0028076831 scopus 로고
    • Equilibrium constants for the binding of fatty acids with fatty acid-binding proteins from adipocyte, intestine, heart, and liver measured with the fluorescent probe ADIFAB
    • Richieri GV, Ogata RT, Kleinfeld AM (1994) Equilibrium constants for the binding of fatty acids with fatty acid-binding proteins from adipocyte, intestine, heart, and liver measured with the fluorescent probe ADIFAB. J Biol Chem 269:23918-23930.
    • (1994) J Biol Chem , vol.269 , pp. 23918-23930
    • Richieri, G.V.1    Ogata, R.T.2    Kleinfeld, A.M.3
  • 40
    • 0038472282 scopus 로고    scopus 로고
    • Liquid-vapor oscillations of water in hydrophobic nanopores
    • Beckstein O, Sansom MSP (2003) Liquid-vapor oscillations of water in hydrophobic nanopores. Proc Natl Acad Sci USA 100:7063-7068.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7063-7068
    • Beckstein, O.1    Sansom, M.S.P.2
  • 43
    • 0031058541 scopus 로고    scopus 로고
    • The statistical- thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical- thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72:1047-1069.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 44
    • 2942659093 scopus 로고    scopus 로고
    • Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method
    • Hamelberg D, McCammon JA (2004) Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method. J Am Chem Soc 126:7683-7689.
    • (2004) J Am Chem Soc , vol.126 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.