메뉴 건너뛰기




Volumn 4, Issue 5, 1997, Pages 396-404

NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOPROPANE; ETHYLENE; HYDROGEN; METHANE; WATER;

EID: 0030892956     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (103)

References (52)
  • 1
    • 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, 1813-1817 (1995).
    • (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
  • 2
    • 0029561720 scopus 로고
    • Use of NMR to detect water within nonpolar protein cavities
    • Matthews, B.W., Morton, A.G. & Dahlquist, F.W. Use of NMR to detect water within nonpolar protein cavities. Science 270, 1847-1848 (1995).
    • (1995) Science , vol.270 , pp. 1847-1848
    • Matthews, B.W.1    Morton, A.G.2    Dahlquist, F.W.3
  • 3
    • 0029561720 scopus 로고
    • Use of NMR to detect water within nonpolar protein cavities - Response
    • Ernst, J.A., Clubb, R.T., Zhou, H.X., Gronenborn, A.M. & Clore, G.M. Use of NMR to detect water within nonpolar protein cavities - response. Science 270, 1848-1849 (1995).
    • (1995) Science , vol.270 , pp. 1848-1849
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 4
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang, L. & Hermans, J. Hydrophilicity of cavities in proteins. Proteins 24, 433-438 (1996).
    • (1996) Proteins , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 5
    • 0029882171 scopus 로고    scopus 로고
    • Structural and energetic responses to cavity-creating mutations in hydrophobic cores: Observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities
    • Buckle, A.M., Cramer, P. & Fersht, A.R. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry 35, 4298-4305 (1996).
    • (1996) Biochemistry , vol.35 , pp. 4298-4305
    • Buckle, A.M.1    Cramer, P.2    Fersht, A.R.3
  • 6
    • 0013842370 scopus 로고
    • Binding of xenon to sperm whale myoglobin
    • Schoenborn, B.P,. Watson, H.C. & Kendrew, J.C. Binding of xenon to sperm whale myoglobin. Nature 207, 28-30 (1965).
    • (1965) Nature , vol.207 , pp. 28-30
    • Schoenborn, B.P.1    Watson, H.C.2    Kendrew, J.C.3
  • 7
    • 0014198467 scopus 로고
    • Binding of cyclopropane to sperm whale myoglobin
    • Schoenborn, B. P. Binding of cyclopropane to sperm whale myoglobin. Nature 214, 1120-1122 (1967).
    • (1967) Nature , vol.214 , pp. 1120-1122
    • Schoenborn, B.P.1
  • 8
    • 0014759278 scopus 로고
    • Effects of cyclopropane and xenon upon the high-resolution nuclear magnetic resonance spectrum of ferrimyoglobin cyanide
    • Shulman, R.G., Peisach, J. & Wyluda, B.J. Effects of cyclopropane and xenon upon the high-resolution nuclear magnetic resonance spectrum of ferrimyoglobin cyanide. J. Mol. Biol. 48, 517-523 (1970).
    • (1970) J. Mol. Biol. , vol.48 , pp. 517-523
    • Shulman, R.G.1    Peisach, J.2    Wyluda, B.J.3
  • 9
    • 0030965629 scopus 로고    scopus 로고
    • Organic solvents identify specific ligand binding sites on protein surfaces
    • Liepinsh, E. & Otting, G. Organic solvents identify specific ligand binding sites on protein surfaces. Nature Biotech., 5, 264-268 (1997).
    • (1997) Nature Biotech. , vol.5 , pp. 264-268
    • Liepinsh, E.1    Otting, G.2
  • 11
    • 0025162691 scopus 로고
    • Crystal structure of low humidity tetragonal lysozyme at 2.1 Å resolution. Variability in hydration shell and its structural consequences
    • Kodandapani, R. Suresh, C.G. & Vijayan, M. Crystal structure of low humidity tetragonal lysozyme at 2.1 Å resolution. Variability in hydration shell and its structural consequences. J. Biol. Chem. 265, 16126-16131 (1990).
    • (1990) J. Biol. Chem. , vol.265 , pp. 16126-16131
    • Kodandapani, R.1    Suresh, C.G.2    Vijayan, M.3
  • 12
    • 0026757625 scopus 로고
    • Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme
    • Wilson, K.P., Malcolm, B.A. & Matthews, B.W. Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J. Biol. Chem. 267, 10842-10849 (1992).
    • (1992) J. Biol. Chem. , vol.267 , pp. 10842-10849
    • Wilson, K.P.1    Malcolm, B.A.2    Matthews, B.W.3
  • 13
    • 84944813395 scopus 로고
    • Refinement of triclinic lysozyme: I. Fourier and least-squares methods
    • Hodsdon, J.M., Brown, G.M., Sieker, L.C. & Jensen, L.H. Refinement of triclinic lysozyme: I. Fourier and least-squares methods. Acta Crystallogr. B46, 54-62 (1990).
    • (1990) Acta Crystallogr. , vol.B46 , pp. 54-62
    • Hodsdon, J.M.1    Brown, G.M.2    Sieker, L.C.3    Jensen, L.H.4
  • 14
    • 84912964993 scopus 로고
    • Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares
    • Ramanadham, M., Sieker, L.C. & Jensen, L.H. Refinement of triclinic lysozyme: II. the method of stereochemically restrained least squares. Acta Crystallogr. B46, 63-69 (1990).
    • (1990) Acta Crystallogr. , vol.B46 , pp. 63-69
    • Ramanadham, M.1    Sieker, L.C.2    Jensen, L.H.3
  • 15
    • 0023644307 scopus 로고
    • Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres
    • Kundrot, C.E. & Richards, F.M. Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres. J. Mol. Biol. 193, 157-170 (1987).
    • (1987) J. Mol. Biol. , vol.193 , pp. 157-170
    • Kundrot, C.E.1    Richards, F.M.2
  • 16
    • 0027610433 scopus 로고
    • Comparison of radiation-induced decay and structure refinement from X-ray data collected from lysozyme crystals at low and ambient temperatures
    • Young, A.C.M., Dewan, J.C., Nave, C. & Tilton, R.F. Comparison of radiation-induced decay and structure refinement from X-ray data collected from lysozyme crystals at low and ambient temperatures. J. Appl. Crystallogr. 26, 309-319 (1993).
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 309-319
    • Young, A.C.M.1    Dewan, J.C.2    Nave, C.3    Tilton, R.F.4
  • 17
    • 0028332010 scopus 로고
    • Crystal structure of pheasant and guinea fowl egg-white lysozymes
    • Lescar, J., Souchon, H. & Alzari, P.M. Crystal structure of pheasant and guinea fowl egg-white lysozymes. Protein Sci. 3, 788-798 (1994).
    • (1994) Protein Sci. , vol.3 , pp. 788-798
    • Lescar, J.1    Souchon, H.2    Alzari, P.M.3
  • 19
    • 0028785353 scopus 로고
    • Thermal stability determinants of chicken egg-white lysozyme core mutants: Hydrophobicity, packing volume, and conserved buried water molecules
    • Shih, P., Holland, D.R. & Kirsch, J.F. Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules. Protein Sci. 4, 2050-2062 (1995).
    • (1995) Protein Sci. , vol.4 , pp. 2050-2062
    • Shih, P.1    Holland, D.R.2    Kirsch, J.F.3
  • 20
    • 0026757625 scopus 로고
    • Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme
    • Wilson, K.P., Malcolm, B.A. & Matthews, B.W. Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J. Biol. Chem. 267, 10842-10849 (1992).
    • (1992) J. Biol. Chem. , vol.267 , pp. 10842-10849
    • Wilson, K.P.1    Malcolm, B.A.2    Matthews, B.W.3
  • 21
    • 0026551529 scopus 로고
    • Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 angstroms resolution
    • Cheetham, J.C., Artymiuk, P.J. & Phillips, D.C. Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 angstroms resolution. J. Mol. Biol. 224, 613-628 (1992).
    • (1992) J. Mol. Biol. , vol.224 , pp. 613-628
    • Cheetham, J.C.1    Artymiuk, P.J.2    Phillips, D.C.3
  • 23
    • 0024284779 scopus 로고
    • 1H NMR assignments and secondary structure of hen egg white lysozyme in solution
    • 1H NMR assignments and secondary structure of hen egg white lysozyme in solution. Biochemistry 27, 122-136 (1988).
    • (1988) Biochemistry , vol.27 , pp. 122-136
    • Redfield, C.1    Dobson, C.M.2
  • 24
    • 84957316785 scopus 로고
    • Proton exchange with internal water molecules in proteins in aqueous solution
    • Otting, G., Liepinsh, E. & Wüthrich, K. Proton exchange with internal water molecules in proteins in aqueous solution. J. Am. Chem. Soc. 113, 4363-4364 (1991).
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4363-4364
    • Otting, G.1    Liepinsh, E.2    Wüthrich, K.3
  • 26
    • 0011491177 scopus 로고
    • Structure determination of a tetrasaccharide: Transient nuclear Overhauser effects in the rotating frame
    • Bothner-By, A.A., Stephens, R.L., Lee, J., Warren, C.D. & Jeanloz, R.W. Structure determination of a tetrasaccharide: transient nuclear Overhauser effects in the rotating frame. J. Am. Chem. Soc. 106, 811-813 (1984).
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 811-813
    • Bothner-By, A.A.1    Stephens, R.L.2    Lee, J.3    Warren, C.D.4    Jeanloz, R.W.5
  • 27
    • 0000857486 scopus 로고
    • Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules
    • Otting, G. & Wüthrich, K. Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. J. Am. Chem. Soc 111, 1871-1875 (1989).
    • (1989) J. Am. Chem. Soc , vol.111 , pp. 1871-1875
    • Otting, G.1    Wüthrich, K.2
  • 28
    • 0000547870 scopus 로고
    • Protein hydration by high-resolution NMR spectroscopy -implications for MR image contrast
    • Otting, G. & Liepinsh, E. Protein hydration by high-resolution NMR spectroscopy -implications for MR image contrast. Acc. Chem. Res. 28, 171-177 (1995).
    • (1995) Acc. Chem. Res. , vol.28 , pp. 171-177
    • Otting, G.1    Liepinsh, E.2
  • 29
    • 0026326956 scopus 로고
    • Protein hydration in aqueous solution
    • Otting, G., Liepinsh, E. & Wüthrich, K. Protein hydration in aqueous solution. Science 254, 974-980 (1991).
    • (1991) Science , vol.254 , pp. 974-980
    • Otting, G.1    Liepinsh, E.2    Wüthrich, K.3
  • 30
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
    • Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 4559-4570 (1982).
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 32
    • 0015895751 scopus 로고
    • Quenching of protein flourescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale
    • Lakowicz, J. R. & Weber, G. Quenching of protein flourescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale. Biochemistry 12, 4171-4179 (1973).
    • (1973) Biochemistry , vol.12 , pp. 4171-4179
    • Lakowicz, J.R.1    Weber, G.2
  • 33
    • 0021114712 scopus 로고
    • Penetration of dioxygen into proteins studied by quenching of phosphorescence and flourescence
    • Calhoun, D.B., Vanderkooi, J.M., Woodrow III, G.V. & Englander, S.W. Penetration of dioxygen into proteins studied by quenching of phosphorescence and flourescence. Biochemistry 22, 1526-1532 (1983).
    • (1983) Biochemistry , vol.22 , pp. 1526-1532
    • Calhoun, D.B.1    Vanderkooi, J.M.2    Woodrow III, G.V.3    Englander, S.W.4
  • 36
    • 0029016268 scopus 로고
    • Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
    • Morton, A., Baase, W.A. & Matthews, B.W. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34, 8564-8575 (1995).
    • (1995) Biochemistry , vol.34 , pp. 8564-8575
    • Morton, A.1    Baase, W.A.2    Matthews, B.W.3
  • 37
    • 0025735698 scopus 로고
    • What solvent best represents the site of action of inhaled anesthetics in humans, rats, and dogs?
    • Taheri, S., Halsey, M.J., Liu, J., Eger II, E.I., Koblin, D.D. & Laster, M.J. What solvent best represents the site of action of inhaled anesthetics in humans, rats, and dogs? Anesth. Analg. 72, 627-634 (1991).
    • (1991) Anesth. Analg. , vol.72 , pp. 627-634
    • Taheri, S.1    Halsey, M.J.2    Liu, J.3    Eger II, E.I.4    Koblin, D.D.5    Laster, M.J.6
  • 38
    • 0028589322 scopus 로고
    • Stereospecific dihaloalkane binding in a pH-sensitive cavity in cubic insulin crystals
    • Gursky, O., Fontano, E., Bhyravbhatla, B. & Caspar, D.L. Stereospecific dihaloalkane binding in a pH-sensitive cavity in cubic insulin crystals. Proc. Natl. Acad. Sci. USA 91, 12388-12392 (1994).
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12388-12392
    • Gursky, O.1    Fontano, E.2    Bhyravbhatla, B.3    Caspar, D.L.4
  • 39
    • 0028277541 scopus 로고
    • The specific binding site of the volatile anesthetic diiodomethane to purple membrane by X-ray diffraction
    • Nakagawa, T., Hamanaka, T., Nishimura, S., Uruga, T. & Kito, Y. The specific binding site of the volatile anesthetic diiodomethane to purple membrane by X-ray diffraction. J. Mol. Biol. 238, 297-301 (1994).
    • (1994) J. Mol. Biol. , vol.238 , pp. 297-301
    • Nakagawa, T.1    Hamanaka, T.2    Nishimura, S.3    Uruga, T.4    Kito, Y.5
  • 40
    • 0020077280 scopus 로고
    • Potencies of inhaled anesthetics and alcohol in mice selectively bred for resistance and susceptibility to nitrous oxide anesthesia
    • Koblin, D.D., Deady, J.E. & Eger, E.I. Potencies of inhaled anesthetics and alcohol in mice selectively bred for resistance and susceptibility to nitrous oxide anesthesia. Anesthesiology 56, 18-24 (1982).
    • (1982) Anesthesiology , vol.56 , pp. 18-24
    • Koblin, D.D.1    Deady, J.E.2    Eger, E.I.3
  • 42
    • 0022798602 scopus 로고
    • Atomic size packing defects in proteins
    • Connolly, M.L. Atomic size packing defects in proteins. Int. J. Peptide Prot. Res. 28, 360-363 (1986).
    • (1986) Int. J. Peptide Prot. Res. , vol.28 , pp. 360-363
    • Connolly, M.L.1
  • 43
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950 (1991).
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 45
    • 0001072647 scopus 로고
    • Selective excitation of the water signal by a Q-switched selective pulse
    • Otting, G. & Liepinsh, E. Selective excitation of the water signal by a Q-switched selective pulse. J. Magn. Reson. B 107, 192-196 (1995).
    • (1995) J. Magn. Reson. B , vol.107 , pp. 192-196
    • Otting, G.1    Liepinsh, E.2
  • 46
    • 0000240249 scopus 로고
    • Selective excitation of intense solvent signals in the presence of radiation damping
    • Otting, G. & Liepinsh, E. Selective excitation of intense solvent signals in the presence of radiation damping. J. Biomol. NMR 5, 420-426 (1995).
    • (1995) J. Biomol. NMR , vol.5 , pp. 420-426
    • Otting, G.1    Liepinsh, E.2
  • 47
    • 44949280676 scopus 로고
    • Band-selective radiofrequency pulses
    • Geen, H. & Freeman, R. Band-selective radiofrequency pulses. J. Magn. Reson. 93, 93-141 (1991).
    • (1991) J. Magn. Reson. , vol.93 , pp. 93-141
    • Geen, H.1    Freeman, R.2
  • 48
    • 0000221195 scopus 로고
    • Computer-optimized homonuclear TOCSY experiments with suppression of cross relaxation
    • Briand, J. & Ernst, R.R. Computer-optimized homonuclear TOCSY experiments with suppression of cross relaxation. Chem. Phys. Lett. 185, 276-285 (1991).
    • (1991) Chem. Phys. Lett. , vol.185 , pp. 276-285
    • Briand, J.1    Ernst, R.R.2
  • 49
    • 2942697858 scopus 로고
    • Interpretation of magnetic resonance data from water nuclei in heterogeneous systems
    • Halle, B. & Wennerström, H. Interpretation of magnetic resonance data from water nuclei in heterogeneous systems. J. Chem. Phys. 75, 1928-1943 (1981).
    • (1981) J. Chem. Phys. , vol.75 , pp. 1928-1943
    • Halle, B.1    Wennerström, H.2
  • 50
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. I. Theory and range of validity
    • Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. I. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559 (1982).
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 51
    • 0010323087 scopus 로고
    • Irreducible tensor expansion of solid spherical harmonic-type operators in quantum mechanics
    • Chiu, Y. Irreducible tensor expansion of solid spherical harmonic-type operators in quantum mechanics. J. Math. Phys. 5, 283-288 (1964).
    • (1964) J. Math. Phys. , vol.5 , pp. 283-288
    • Chiu, Y.1
  • 52
    • 0001268635 scopus 로고
    • Generalization of Laplace's expansion to arbitrary powers and functions of the distance between two points
    • Sack, R.A. Generalization of Laplace's expansion to arbitrary powers and functions of the distance between two points. J. Math. Phys. 5, 245-251 (1964).
    • (1964) J. Math. Phys. , vol.5 , pp. 245-251
    • Sack, R.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.