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Volumn 24, Issue 4, 1996, Pages 433-438

Hydrophilicity of cavities in proteins

Author keywords

buried water; free energy calculation; molecular dynamics simulation; structure refinement

Indexed keywords

ARTICLE; ENTROPY; HYDROGEN BOND; HYDROPHILICITY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTITATIVE ASSAY; SIMULATION; THERMODYNAMICS;

EID: 0029937870     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F     Document Type: Article
Times cited : (339)

References (30)
  • 1
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Richards, F.M. The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82:1-14, 1974.
    • (1974) J. Mol. Biol. , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 2
    • 0028607523 scopus 로고
    • Cavities and packing at protein interfaces
    • Hubbard, S.J., Argos, P. Cavities and packing at protein interfaces. Protein Sci. 3:2194-2206, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 2194-2206
    • Hubbard, S.J.1    Argos, P.2
  • 3
    • 0023051843 scopus 로고
    • Internal cavities and buried waters in globular proteins
    • Rashin, A.A., Iofin, M., Honig, B. Internal cavities and buried waters in globular proteins. Biochemistry 25:3619-3625, 1986.
    • (1986) Biochemistry , vol.25 , pp. 3619-3625
    • Rashin, A.A.1    Iofin, M.2    Honig, B.3
  • 4
    • 0028095182 scopus 로고
    • Buried waters and internal cavities in monomeric proteins
    • Williams, M.A., Goodfellow, J.M., Thornton, J.M. Buried waters and internal cavities in monomeric proteins. Protein Sci. 3:1224-1235, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 1224-1235
    • Williams, M.A.1    Goodfellow, J.M.2    Thornton, J.M.3
  • 5
    • 0028274954 scopus 로고
    • Intramolecular cavities in globular proteins
    • Hubbard, S.J., Gross, K.-H., Argos, P. Intramolecular cavities in globular proteins. Protein Eng. 7:613-626, 1994.
    • (1994) Protein Eng. , vol.7 , pp. 613-626
    • Hubbard, S.J.1    Gross, K.-H.2    Argos, P.3
  • 6
    • 0011487604 scopus 로고
    • An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds
    • Vedani, A. An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds. J. Am. Chem. Soc. 113:5860-5862, 1991.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5860-5862
    • Vedani, A.1
  • 7
    • 0028093141 scopus 로고
    • On the probability of finding a water molecule in a hydrophobic environment
    • Wolfenden, R., Radzicka, A. On the probability of finding a water molecule in a hydrophobic environment. Science 265:936-937, 1994.
    • (1994) Science , vol.265 , pp. 936-937
    • Wolfenden, R.1    Radzicka, A.2
  • 8
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
    • Ernst, J.A., Clubb, R.T., Zhou, H.-X., Gronenborn, A.M., Clore, G.M. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267:1813-1815, 1995.
    • (1995) Science , vol.267 , pp. 1813-1815
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.-X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 10
    • 0021107965 scopus 로고
    • Solvent accessible surfaces of proteins and nucleic acids
    • Connolly, M.L. Solvent accessible surfaces of proteins and nucleic acids. Science 221:709-713, 1983.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 11
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28:849-857, 1985.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 12
    • 6944235692 scopus 로고
    • A simple analysis of noise and hysteresis in free energy simulations
    • Hermans, J. A simple analysis of noise and hysteresis in free energy simulations. J. Phys. Chem. 95:9029-9032, 1991.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9029-9032
    • Hermans, J.1
  • 13
    • 85005687495 scopus 로고
    • The free energy of xenon binding to myoglobin from molecular dynamics simulation
    • Hermans, J., Shankar, S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Israel J. Chem. 27:225-227, 1986.
    • (1986) Israel J. Chem. , vol.27 , pp. 225-227
    • Hermans, J.1    Shankar, S.2
  • 14
    • 0026189146 scopus 로고
    • A molecular dynamics study of thermodynamics and structural aspects of the hydration of cavities in proteins
    • Wade, R.C., Mazor, M.H.: McCammon, J.A., Quiocho, F.A. A molecular dynamics study of thermodynamics and structural aspects of the hydration of cavities in proteins. Biopolymers 31:919-931, 1991.
    • (1991) Biopolymers , vol.31 , pp. 919-931
    • Wade, R.C.1    Mazor, M.H.2    McCammon, J.A.3    Quiocho, F.A.4
  • 15
    • 0029160249 scopus 로고
    • Thermodynamics of water mediating protem-ligand interactions in cytochrome P45cam: A molecular dynamics study
    • Helms, V., Wade, R.C. Thermodynamics of water mediating protem-ligand interactions in cytochrome P45cam: A molecular dynamics study. Biophys. J. 69:810-824, 1995.
    • (1995) Biophys. J. , vol.69 , pp. 810-824
    • Helms, V.1    Wade, R.C.2
  • 16
    • 0001120964 scopus 로고
    • Grand canonical Monte Carlo simulation of water positions in crystal hydrates
    • Resat, H., Mezei, M. Grand canonical Monte Carlo simulation of water positions in crystal hydrates. J. Am. Chem. Soc. 116:7451-7452, 1994.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 7451-7452
    • Resat, H.1    Mezei, M.2
  • 17
    • 0026619463 scopus 로고
    • Similarities and differences between human cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 angstroms resolution
    • Ke, H. Similarities and differences between human cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 angstroms resolution. J. Mol. Biol. 228: 539-550, 1992.
    • (1992) J. Mol. Biol. , vol.228 , pp. 539-550
    • Ke, H.1
  • 18
    • 0023643147 scopus 로고
    • The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis
    • Bode, W., Papamokos, E., Musil, D. The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Eur. J. Biochem. 166:673-692, 1987.
    • (1987) Eur. J. Biochem. , vol.166 , pp. 673-692
    • Bode, W.1    Papamokos, E.2    Musil, D.3
  • 19
    • 0023729499 scopus 로고
    • Structural comparison of two serine proteinase-protein inhibitor complexes: Eglin-c-subtilisin Carlsberg and CI-2-subtilisin novo
    • McPhalen, C.A., James, M.N.G. Structural comparison of two serine proteinase-protein inhibitor complexes: Eglin-c-subtilisin Carlsberg and CI-2-subtilisin novo. Biochemistry 27:6582-6598, 1988.
    • (1988) Biochemistry , vol.27 , pp. 6582-6598
    • McPhalen, C.A.1    James, M.N.G.2
  • 22
    • 0027248959 scopus 로고
    • The structure of an interleukin-1β mutant with reduced bioactivity shows multiple subtle changes in conformation that affect protein-protein recognition
    • Camacho, N.P., Smith, B.R., Goldman, A., Schneider, B., Green, B., Young, P.R., Berman, H.M. The structure of an interleukin-1β mutant with reduced bioactivity shows multiple subtle changes in conformation that affect protein-protein recognition. Biochemistry 32:8749-8757, 1993.
    • (1993) Biochemistry , vol.32 , pp. 8749-8757
    • Camacho, N.P.1    Smith, B.R.2    Goldman, A.3    Schneider, B.4    Green, B.5    Young, P.R.6    Berman, H.M.7
  • 23
    • 0025772135 scopus 로고
    • High-resolution three-dimensional structure of interleukin 1β in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy
    • Clore, G.M., Wingfield, P.T., Gronenborn, A.M. High-resolution three-dimensional structure of interleukin 1β in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. Biochemistry 30:2315-2323, 1991.
    • (1991) Biochemistry , vol.30 , pp. 2315-2323
    • Clore, G.M.1    Wingfield, P.T.2    Gronenborn, A.M.3
  • 24
    • 0028228418 scopus 로고
    • The entropic cost of bound water in crystals and biomolecules
    • Dunitz, J.D. The entropic cost of bound water in crystals and biomolecules. Science 264:670, 1994.
    • (1994) Science , vol.264 , pp. 670
    • Dunitz, J.D.1
  • 25
    • 0024961747 scopus 로고
    • The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease
    • Tsunaaawa, S., Masaki, T., Hirose, M., Soejima, M., Sakiyama, F. The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease. J. Biol. Chem. 264:3832-3839, 1989.
    • (1989) J. Biol. Chem. , vol.264 , pp. 3832-3839
    • Tsunaaawa, S.1    Masaki, T.2    Hirose, M.3    Soejima, M.4    Sakiyama, F.5
  • 26
    • 0024447798 scopus 로고
    • Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallo-graphic data at 1.6-Å resolution
    • Swain, A.L., Kretsinger, R.H., Amma, E.L. Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallo-graphic data at 1.6-Å resolution. J. Biol. Chem. 264: 16620-16628, 1989.
    • (1989) J. Biol. Chem. , vol.264 , pp. 16620-16628
    • Swain, A.L.1    Kretsinger, R.H.2    Amma, E.L.3
  • 28
    • 0000168367 scopus 로고
    • The accuracy of refined protein structures, comparison of two independently refined models of bovine trypsin
    • Chambers, J.L., Stroud, R.M. The accuracy of refined protein structures, comparison of two independently refined models of bovine trypsin. Acta Crystallogr. B 35:1861-1874, 1979.
    • (1979) Acta Crystallogr. B , vol.35 , pp. 1861-1874
    • Chambers, J.L.1    Stroud, R.M.2
  • 29
    • 0022405087 scopus 로고
    • Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease at 1.5 angstroms resolution
    • Moult, J., Sussman, F., James, M.N.G. Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease at 1.5 angstroms resolution. J. Mol. Biol. 182:555-566, 1985.
    • (1985) J. Mol. Biol. , vol.182 , pp. 555-566
    • Moult, J.1    Sussman, F.2    James, M.N.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.