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Volumn 60, Issue 3, 2005, Pages 433-449

Molecular dynamics study of water penetration in staphylococcal nuclease

Author keywords

Hydration; Internal ionizable residues; Protein interior

Indexed keywords

GLUTAMIC ACID; LYSINE; NUCLEASE; VALINE; WATER;

EID: 21244469736     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20486     Document Type: Article
Times cited : (79)

References (62)
  • 1
    • 0015518520 scopus 로고
    • Structure of crystalline a-chymotrypsin: V. The atomic structure of tosyl-a-chymotrypsin at 2 Å resolution
    • Birktoft JJ, Blow DM. Structure of crystalline a-chymotrypsin: v. the atomic structure of tosyl-a-chymotrypsin at 2 Å resolution. J Mol Biol 1972;68:187-240.
    • (1972) J Mol Biol , vol.68 , pp. 187-240
    • Birktoft, J.J.1    Blow, D.M.2
  • 2
    • 0015895751 scopus 로고
    • Quenching of a protein fluorescence by oxygen: Detection of structural fluctuations in proteins on the nanosecond timescale
    • Lakowicz JR, Weber G. Quenching of a protein fluorescence by oxygen: detection of structural fluctuations in proteins on the nanosecond timescale. Biochemistry 1973;12:4171-4179.
    • (1973) Biochemistry , vol.12 , pp. 4171-4179
    • Lakowicz, J.R.1    Weber, G.2
  • 3
    • 0000767837 scopus 로고
    • Dynamics of a protein matrix revealed by fluorescence quenching
    • Eftink MR, Ghiron CA. Dynamics of a protein matrix revealed by fluorescence quenching. Proc Natl Acad Sci USA 1975;72:3290-3294.
    • (1975) Proc Natl Acad Sci USA , vol.72 , pp. 3290-3294
    • Eftink, M.R.1    Ghiron, C.A.2
  • 4
    • 0021107512 scopus 로고
    • Interior turns in globular proteins
    • Rose GD, Young WB. Interior turns in globular proteins. Nature 1983;304:655-657.
    • (1983) Nature , vol.304 , pp. 655-657
    • Rose, G.D.1    Young, W.B.2
  • 5
    • 0027082924 scopus 로고
    • Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications
    • Meyer E. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications. Prot Sci 1992;1:1543-1562.
    • (1992) Prot Sci , vol.1 , pp. 1543-1562
    • Meyer, E.1
  • 6
    • 0028095182 scopus 로고
    • Buried waters and internal cavities in monomeric proteins
    • Williams MA, Goodfellow JM, Thornton JM. Buried waters and internal cavities in monomeric proteins. Prot Sci 1994;3:1224-1235.
    • (1994) Prot Sci , vol.3 , pp. 1224-1235
    • Williams, M.A.1    Goodfellow, J.M.2    Thornton, J.M.3
  • 7
    • 0035937261 scopus 로고    scopus 로고
    • Core and surface mutations a ect folding kinetics, stability, and cooperativity I IL-1b: Does alteration in buried water play a role?
    • Covalt JC, Roy M, Jennings PA. Core and surface mutations a ect folding kinetics, stability, and cooperativity I IL-1b: Does alteration in buried water play a role? J Mol Biol 2001;307:657-669.
    • (2001) J Mol Biol , vol.307 , pp. 657-669
    • Covalt, J.C.1    Roy, M.2    Jennings, P.A.3
  • 8
    • 0034024888 scopus 로고    scopus 로고
    • Structural water molecules in the family of fatty acid binding proteins
    • Likic VA, Juranic N, Macura S, Prendergast FG. Structural water molecules in the family of fatty acid binding proteins. Prot Sci 2000;9:497-504.
    • (2000) Prot Sci , vol.9 , pp. 497-504
    • Likic, V.A.1    Juranic, N.2    Macura, S.3    Prendergast, F.G.4
  • 9
    • 0027068111 scopus 로고
    • Buried water in homologous serine proteases
    • Sreenivasan U, Axelsen PH. Buried water in homologous serine proteases. Biochemistry 1992;31:12785-12791.
    • (1992) Biochemistry , vol.31 , pp. 12785-12791
    • Sreenivasan, U.1    Axelsen, P.H.2
  • 10
    • 0027164289 scopus 로고
    • Designed replacement of an internal hydration water molecule in BPTI: Structural and functional implications of a glycine-to-serine mutation
    • Berndt KD, Beunink J, Schroder W, Wüthrich K. Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation. Biochemistry 1993;32:4564-4570.
    • (1993) Biochemistry , vol.32 , pp. 4564-4570
    • Berndt, K.D.1    Beunink, J.2    Schroder, W.3    Wüthrich, K.4
  • 11
    • 0030696285 scopus 로고    scopus 로고
    • Contribution of water molecules in the interior of a protein to the conformational stability
    • Takano K, Funahashi J, Yamagata Y, Fujii S, Yutani K. Contribution of water molecules in the interior of a protein to the conformational stability. J Mol Biol 1997;274:132-142.
    • (1997) J Mol Biol , vol.274 , pp. 132-142
    • Takano, K.1    Funahashi, J.2    Yamagata, Y.3    Fujii, S.4    Yutani, K.5
  • 12
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after structural collapse
    • Cheung MS, García AE, Onuchic JN. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after structural collapse. Proc Natl Acad Sci USA 2002;99: 685-690.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    García, A.E.2    Onuchic, J.N.3
  • 16
    • 0035859887 scopus 로고    scopus 로고
    • The active site dynamics of 4-chlorobenzoylcoa dehalogenase
    • Lau EY, Bruice TC. The active site dynamics of 4-chlorobenzoylcoa dehalogenase. Proc Natl Acad Sci USA 2001;98:9527-9532.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 9527-9532
    • Lau, E.Y.1    Bruice, T.C.2
  • 18
    • 0030987236 scopus 로고    scopus 로고
    • Identification of a functional water channel in cytochrome p45-enzymes
    • Oprea TI, Hummer G, García AE. Identification of a functional water channel in cytochrome p45-enzymes. Proc Natl Acad Sci USA 1997;94:2133-2138.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 2133-2138
    • Oprea, T.I.1    Hummer, G.2    García, A.E.3
  • 19
    • 0031973948 scopus 로고    scopus 로고
    • Oxygen and proton pathways in cytochrome c oxidase
    • Hofacker I, Schulten K. Oxygen and proton pathways in cytochrome c oxidase. Proteins 1998;30:100-107.
    • (1998) Proteins , vol.30 , pp. 100-107
    • Hofacker, I.1    Schulten, K.2
  • 21
    • 0028890031 scopus 로고
    • Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans
    • Iwata S, Ostermeier C, Ludwig B, Michel H. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 1995;376:660-669.
    • (1995) Nature , vol.376 , pp. 660-669
    • Iwata, S.1    Ostermeier, C.2    Ludwig, B.3    Michel, H.4
  • 22
    • 0034071764 scopus 로고    scopus 로고
    • Protein-bound water molecule counting by resolution of 1H spin-lattice relaxation mechanisms
    • Kühne S, Bryant RG. Protein-bound water molecule counting by resolution of 1H spin-lattice relaxation mechanisms. Biophys J 2000;78:2163-2169.
    • (2000) Biophys J , vol.78 , pp. 2163-2169
    • Kühne, S.1    Bryant, R.G.2
  • 23
    • 1842687872 scopus 로고    scopus 로고
    • Biomolecular cryocrystallography: Structural changes during flashcooling
    • Halle B. Biomolecular cryocrystallography: structural changes during flashcooling. Proc Natl Acad Sci USA 2004;101:4793-4798.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 4793-4798
    • Halle, B.1
  • 24
    • 0026326956 scopus 로고
    • Protein hydration in aqueous solution
    • Otting G, Liepinsh E, Wuthrich K. Protein hydration in aqueous solution. Science 1991;254:974-980.
    • (1991) Science , vol.254 , pp. 974-980
    • Otting, G.1    Liepinsh, E.2    Wuthrich, K.3
  • 25
    • 0028948786 scopus 로고
    • 17O spin relaxation dispersion
    • 17O spin relaxation dispersion. J Mol Biol 1995;245: 682-297.
    • (1995) J Mol Biol , vol.245 , pp. 682-1297
    • Denisov, V.P.1    Halle, B.2
  • 26
    • 0029081424 scopus 로고
    • Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its g36s mutant
    • Denisov VP, Halle B, Peters J, Hörlein HD. Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its g36s mutant. Biochemistry 1995;34:9046-9051.
    • (1995) Biochemistry , vol.34 , pp. 9046-9051
    • Denisov, V.P.1    Halle, B.2    Peters, J.3    Hörlein, H.D.4
  • 28
    • 0035902770 scopus 로고    scopus 로고
    • Microsecond exchange of internal water molecules in bacteriorhodopsin
    • Gottschalk M, Dencher NA, Halle B. Microsecond exchange of internal water molecules in bacteriorhodopsin. J Mol Biol 2001;311: 605-621.
    • (2001) J Mol Biol , vol.311 , pp. 605-621
    • Gottschalk, M.1    Dencher, N.A.2    Halle, B.3
  • 29
    • 0026189146 scopus 로고
    • A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
    • Wade RC, Mazor MH, McCammon JA, Quiocho FA. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 1991;31:919-931.
    • (1991) Biopolymers , vol.31 , pp. 919-931
    • Wade, R.C.1    Mazor, M.H.2    McCammon, J.A.3    Quiocho, F.A.4
  • 30
    • 0029160249 scopus 로고
    • Thermodynamics of water mediating protein-ligand interactions in cytochrome p450cam: A molecular dynamics study
    • Helms V, Wade RC. Thermodynamics of water mediating protein-ligand interactions in cytochrome p450cam: a molecular dynamics study. Biophys J 1995;69:810-824.
    • (1995) Biophys J , vol.69 , pp. 810-824
    • Helms, V.1    Wade, R.C.2
  • 31
    • 0029126354 scopus 로고
    • A comparison of neutron diffraction and molecular dynamics structures: Hydroxyl group and water molecule orientations in trypsin
    • McDowell RS, Kossiako AA. A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin. J Mol Biol 1995;250:553-570.
    • (1995) J Mol Biol , vol.250 , pp. 553-570
    • McDowell, R.S.1    Kossiako, A.A.2
  • 32
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel a molecular dynamics free energy perturbation study
    • Roux B, Nina M, Pomes R, Smith JC. Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel a molecular dynamics free energy perturbation study. Biophys J 1996;71: 670-681.
    • (1996) Biophys J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.C.4
  • 33
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang L, Hermans J. Hydrophilicity of cavities in proteins. Proteins 1996;24:433-438.
    • (1996) Proteins , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 34
    • 0034651984 scopus 로고    scopus 로고
    • Water penetration and escape in proteins
    • García AE, Hummer G. Water penetration and escape in proteins. Proteins 2000;38:261-272.
    • (2000) Proteins , vol.38 , pp. 261-272
    • García, A.E.1    Hummer, G.2
  • 35
    • 0033636839 scopus 로고    scopus 로고
    • Residence times of water molecules in the hydration sites of myoglobin
    • Makarov VA, Andrews BK, Smith PE, Pettit BM. Residence times of water molecules in the hydration sites of myoglobin. Biophys J 2000;79:2966-2974.
    • (2000) Biophys J , vol.79 , pp. 2966-2974
    • Makarov, V.A.1    Andrews, B.K.2    Smith, P.E.3    Pettit, B.M.4
  • 36
    • 0035314045 scopus 로고    scopus 로고
    • Dynamics of internal water in fatty acid binding protein: Computer simulations and comparison with experiments
    • Likic VA, Prendergast FG. Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments. Proteins 2001;43:65-72.
    • (2001) Proteins , vol.43 , pp. 65-72
    • Likic, V.A.1    Prendergast, F.G.2
  • 37
    • 0035940247 scopus 로고    scopus 로고
    • Dissecting the vibrational entropy changes on protein/ligand binding: Burial of a water molecule in bovine pancreatic trypsin inhibitor
    • Fischer S, Smith JC, Verma CS. Dissecting the vibrational entropy changes on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor. J Phys Chem B 2001;105:8050-8055.
    • (2001) J Phys Chem B , vol.105 , pp. 8050-8055
    • Fischer, S.1    Smith, J.C.2    Verma, C.S.3
  • 38
    • 0035839052 scopus 로고    scopus 로고
    • Dynamics of hydration in hen egg white lysozyme
    • Sterpone F, Ceccarelli M, Marchi M. Dynamics of hydration in hen egg white lysozyme. J Mol Biol 2001;311:409-419.
    • (2001) J Mol Biol , vol.311 , pp. 409-419
    • Sterpone, F.1    Ceccarelli, M.2    Marchi, M.3
  • 40
    • 0036306105 scopus 로고    scopus 로고
    • Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water
    • Bakowies D, van Gunsteren WF. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J Mol Biol 2002;315:713-736.
    • (2002) J Mol Biol , vol.315 , pp. 713-736
    • Bakowies, D.1    Van Gunsteren, W.F.2
  • 41
    • 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. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc 2003;126:7683-7689.
    • (2003) J Am Chem Soc , vol.126 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2
  • 42
    • 1842534583 scopus 로고    scopus 로고
    • Mhc-peptide binding is assisted by bound water molecules
    • Petrone P, García AE. Mhc-peptide binding is assisted by bound water molecules. J Mol Biol 2004;338:419-435.
    • (2004) J Mol Biol , vol.338 , pp. 419-435
    • Petrone, P.1    García, A.E.2
  • 43
    • 3042592839 scopus 로고    scopus 로고
    • Hydration free energies and entropies for water in protein interiors
    • Olano LR, Rick SW. Hydration free energies and entropies for water in protein interiors. J Am Chem Soc 2004;126:7991-8000.
    • (2004) J Am Chem Soc , vol.126 , pp. 7991-8000
    • Olano, L.R.1    Rick, S.W.2
  • 44
    • 0025879501 scopus 로고
    • In a staphylococcal nuclease mutant, the side-chain of a lysine replacing valine-66 is fully buried in the hydrophobic core
    • Stites WE, Gittis AG, Lattman EE, Shortle D. In a staphylococcal nuclease mutant, the side-chain of a lysine replacing valine-66 is fully buried in the hydrophobic core. J Mol Biol 1991;221:7-14.
    • (1991) J Mol Biol , vol.221 , pp. 7-14
    • Stites, W.E.1    Gittis, A.G.2    Lattman, E.E.3    Shortle, D.4
  • 47
    • 3342908886 scopus 로고    scopus 로고
    • X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: Insights into polarity of the protein interior
    • Nguyen DM, Reynald RL, Gittis AG, Lattman EE. X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior. J Mol Biol 2004;341:565-574.
    • (2004) J Mol Biol , vol.341 , pp. 565-574
    • Nguyen, D.M.1    Reynald, R.L.2    Gittis, A.G.3    Lattman, E.E.4
  • 48
    • 10044267947 scopus 로고    scopus 로고
    • Stabilization of internal charges in a protein: Water penetration or conformational change?
    • Denisov VP, Schlessman JL, García-Moreno EB, Halle B. Stabilization of internal charges in a protein: water penetration or conformational change? Biophys J 2004;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
  • 49
    • 0036099192 scopus 로고    scopus 로고
    • Experimental pK(a) values of buried residues: Analysis with continuum methods and role of water penetration
    • Fitch CA, Karp DA, Lee KK, States WE, Lattman EE, García-Moreno EB. Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration. Biophys J 2002;82:3289-304.
    • (2002) Biophys J , vol.82 , pp. 3289-3304
    • Fitch, C.A.1    Karp, D.A.2    Lee, K.K.3    States, W.E.4    Lattman, E.E.5    García-Moreno, E.B.6
  • 50
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric constants of proteins and how to validate electrostatic models?
    • Schutz CN, Warshel A. What are the dielectric constants of proteins and how to validate electrostatic models? Proteins 2002; 44:400-417.
    • (2002) Proteins , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 51
    • 0036228118 scopus 로고    scopus 로고
    • Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein
    • Lee KK, Fitch CA, García-Moreno EB. Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein. Protein Sci 2002;11:1004-1016.
    • (2002) Protein Sci , vol.11 , pp. 1004-1016
    • Lee, K.K.1    Fitch, C.A.2    García-Moreno, E.B.3
  • 55
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation-the Langevin piston method
    • Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation-the Langevin piston method. J Chem Phys 1995;103:4613-4621.
    • (1995) J Chem Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 56
    • 0029633186 scopus 로고
    • AMBER, a package of computerprograms for applying molecular mechanics, normal-mode analysis, moleculardynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computerprograms for applying molecular mechanics, normal-mode analysis, moleculardynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
    • (1995) Comput Phys Commun , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 59
    • 0035829539 scopus 로고    scopus 로고
    • Water conduction through the hydrophobic channel of a carbon nanotube
    • Hummer G, Rasaiah JC, Noworyta JP. Water conduction through the hydrophobic channel of a carbon nanotube. Nature 2001;414: 188-190.
    • (2001) Nature , vol.414 , pp. 188-190
    • Hummer, G.1    Rasaiah, J.C.2    Noworyta, J.P.3
  • 61
    • 0025877987 scopus 로고
    • The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution
    • Hynes TR, Fox RO. The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution. Proteins 1991;10:92-105.
    • (1991) Proteins , vol.10 , pp. 92-105
    • Hynes, T.R.1    Fox, R.O.2
  • 62
    • 0001520216 scopus 로고
    • Computation of the mean residence time of water in the hydration shells of biomolecules
    • García AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules. J Comp Chem 1993;14:1396-1406.
    • (1993) J Comp Chem , vol.14 , pp. 1396-1406
    • García, A.E.1    Stiller, L.2


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