메뉴 건너뛰기




Volumn 105, Issue 38, 2008, Pages 14406-14411

Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme

Author keywords

Bound water; Hydrogen bonding; Protein cavity

Indexed keywords

LYSOZYME; SELENOMETHIONINE;

EID: 55749086402     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0806307105     Document Type: Article
Times cited : (35)

References (43)
  • 1
    • 0023051843 scopus 로고
    • Internal cavities and buried waters in globular proteins
    • Rashin AA, Iofin M, Honig B (1986) Internal cavities and buried waters in globular proteins. Biochemistry 25:3619-3625.
    • (1986) Biochemistry , vol.25 , pp. 3619-3625
    • Rashin, A.A.1    Iofin, M.2    Honig, B.3
  • 2
    • 0028095182 scopus 로고
    • Buried waters and internal cavities in monomeric proteins
    • Williams MA, Goodfellow JM, Thornton JM (1994) Buried waters and internal cavities in monomeric proteins. Protein Sci 3:1224-1235.
    • (1994) Protein Sci , vol.3 , pp. 1224-1235
    • Williams, M.A.1    Goodfellow, J.M.2    Thornton, J.M.3
  • 3
    • 0027918556 scopus 로고
    • Water: Now you see it, now you don't
    • Levitt M, Park BH (1993) Water: Now you see it, now you don't. Structure (London) 1:223-226.
    • (1993) Structure (London) , vol.1 , pp. 223-226
    • Levitt, M.1    Park, B.H.2
  • 5
    • 0026475084 scopus 로고
    • Does hydrophobic hydration destabilize protein native structures?
    • Muller N (1992) Does hydrophobic hydration destabilize protein native structures? Trends Biochem Sci 17:459-463.
    • (1992) Trends Biochem Sci , vol.17 , pp. 459-463
    • Muller, N.1
  • 6
    • 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
  • 7
    • 0029561720 scopus 로고
    • Use of NMR to detect water within nonpolar cavities
    • Matthews BW, Morton AG, Dahlquist FW (1995) Use of NMR to detect water within nonpolar cavities. Science 270:1847-1849.
    • (1995) Science , vol.270 , pp. 1847-1849
    • Matthews, B.W.1    Morton, A.G.2    Dahlquist, F.W.3
  • 8
    • 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
  • 9
    • 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 103:18148-18153.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 18148-18153
    • Quillin, M.L.1    Wingfield, P.T.2    Matthews, B.W.3
  • 10
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
    • Roux B, Nina M, Pomes R, Smith JC (1996) Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 71:670-681.
    • (1996) Biophys J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.C.4
  • 11
    • 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
  • 12
    • 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 (1991) A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 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
  • 13
    • 0028093141 scopus 로고
    • On the probability of finding a water molecule in a nonpolar cavity
    • Wolfenden R, Radzicka A (1994) On the probability of finding a water molecule in a nonpolar cavity. Science 265:936-937.
    • (1994) Science , vol.265 , pp. 936-937
    • Wolfenden, R.1    Radzicka, A.2
  • 14
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang L, Hermans J (1996) Hydrophilicity of cavities in proteins. Proteins 24:433-438.
    • (1996) Proteins , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 15
    • 0030038545 scopus 로고    scopus 로고
    • Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
    • Burling FT, Weis WI, Flaherty KM, Brunger AT (1996) Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271:72-77.
    • (1996) Science , vol.271 , pp. 72-77
    • Burling, F.T.1    Weis, W.I.2    Flaherty, K.M.3    Brunger, A.T.4
  • 16
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson AE, et al. (1992) Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1
  • 17
    • 0026509036 scopus 로고
    • A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
    • Eriksson AE, Baase WA, Wozniak JA, Matthews BW (1992) A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355:371-373.
    • (1992) Nature , vol.355 , pp. 371-373
    • Eriksson, A.E.1    Baase, W.A.2    Wozniak, J.A.3    Matthews, B.W.4
  • 18
    • 0029016268 scopus 로고
    • Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
    • Morton A, Baase WA, Matthews BW (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34:8564-8575.
    • (1995) Biochemistry , vol.34 , pp. 8564-8575
    • Morton, A.1    Baase, W.A.2    Matthews, B.W.3
  • 19
    • 0034730423 scopus 로고    scopus 로고
    • Size versus polarizability in protein-ligand interactions: Binding of noble gases within engineered cavities in phage T4 lysozyme
    • Quillin ML, Breyer WA, Griswold IJ, Matthews BW (2000) Size versus polarizability in protein-ligand interactions: Binding of noble gases within engineered cavities in phage T4 lysozyme. J Mol Biol 302:955-977.
    • (2000) J Mol Biol , vol.302 , pp. 955-977
    • Quillin, M.L.1    Breyer, W.A.2    Griswold, I.J.3    Matthews, B.W.4
  • 20
    • 0034680315 scopus 로고    scopus 로고
    • Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR
    • Mulder FAA,HonB, Muhandiram DR, Dahlquist FW, Kay LE (2000) Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR. Biochemistry 39:12614-12622.
    • (2000) Biochemistry , vol.39 , pp. 12614-12622
    • Mulder, F.A.A.1    Hon, B.2    Muhandiram, D.R.3    Dahlquist, F.W.4    Kay, L.E.5
  • 21
    • 0037138654 scopus 로고    scopus 로고
    • Slow internal dynamics in proteins: Application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme
    • Mulder FAA, Hon B, Mittermaier A, Dahlquist FW, Kay LE (2002) Slow internal dynamics in proteins: Application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme. J Am Chem Soc 124:1443-1451.
    • (2002) J Am Chem Soc , vol.124 , pp. 1443-1451
    • Mulder, F.A.A.1    Hon, B.2    Mittermaier, A.3    Dahlquist, F.W.4    Kay, L.E.5
  • 22
    • 23944438905 scopus 로고    scopus 로고
    • Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy
    • Desvaux H, et al. (2005) Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. J Am Chem Soc 127:11676-11683.
    • (2005) J Am Chem Soc , vol.127 , pp. 11676-11683
    • Desvaux, H.1
  • 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
  • 24
    • 33847308554 scopus 로고    scopus 로고
    • Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography
    • Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM (2007) Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. J Mol Biol 367:752-763.
    • (2007) J Mol Biol , vol.367 , pp. 752-763
    • Collins, M.D.1    Quillin, M.L.2    Hummer, G.3    Matthews, B.W.4    Gruner, S.M.5
  • 25
    • 0031893269 scopus 로고    scopus 로고
    • The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
    • Xu J, Baase WA, Baldwin E, Matthews BW (1998) The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci 7:158-177.
    • (1998) Protein Sci , vol.7 , pp. 158-177
    • Xu, J.1    Baase, W.A.2    Baldwin, E.3    Matthews, B.W.4
  • 26
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography and NMR system (CNS): A new software system for macromolecular structure determination
    • Brunger AT, et al. (1998) Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Crystallogr D 54:905-921.
    • (1998) Acta Crystallogr D , vol.54 , pp. 905-921
    • Brunger, A.T.1
  • 27
    • 0026532266 scopus 로고
    • Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
    • Hurley JH, Baase WA, Matthews BW (1992) Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J Mol Biol 224:1143-1159.
    • (1992) J Mol Biol , vol.224 , pp. 1143-1159
    • Hurley, J.H.1    Baase, W.A.2    Matthews, B.W.3
  • 28
    • 0017821233 scopus 로고
    • Structure of lysozyme from bacteriophage T4: An electron density map at 2.4 Å resolution
    • Remington SJ, et al. (1978) Structure of lysozyme from bacteriophage T4: An electron density map at 2.4 Å resolution. J Mol Biol 118:81-98.
    • (1978) J Mol Biol , vol.118 , pp. 81-98
    • Remington, S.J.1
  • 29
    • 0023104358 scopus 로고
    • Structure of bacteriophage T4 lysozyme refined at 1.7Å resolution
    • Weaver LH, Matthews BW (1987) Structure of bacteriophage T4 lysozyme refined at 1.7Å resolution. J Mol Biol 193:189-199.
    • (1987) J Mol Biol , vol.193 , pp. 189-199
    • Weaver, L.H.1    Matthews, B.W.2
  • 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
  • 33
    • 0344950364 scopus 로고    scopus 로고
    • Heat transfer from protein crystals: Implications for flash-cooling and X-ray beam heating
    • Kriminski S, Kazmierczak M, Thorne RE (2003) Heat transfer from protein crystals: Implications for flash-cooling and X-ray beam heating. Acta Crystallogr D 59:697-708.
    • (2003) Acta Crystallogr D , vol.59 , pp. 697-708
    • Kriminski, S.1    Kazmierczak, M.2    Thorne, R.E.3
  • 35
    • 0024564552 scopus 로고
    • Control of enzyme activity by an engineered disulfide bond
    • Matsumura M, Matthews BW (1989) Control of enzyme activity by an engineered disulfide bond. Science 243:792-794.
    • (1989) Science , vol.243 , pp. 792-794
    • Matsumura, M.1    Matthews, B.W.2
  • 36
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    • Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229:105-124.
    • (1993) J Mol Biol , vol.229 , pp. 105-124
    • Van Duyne, G.D.1    Standaert, R.F.2    Karplus, P.A.3    Schreiber, S.L.4    Clardy, J.5
  • 37
    • 0027394606 scopus 로고
    • Similar hydrophobic replacements of Leu 99 and Phe 153 within the core of T4 lysozyme have different structural and thermodynamic consequences
    • Eriksson AE, Baase WA, Matthews BW (1993) Similar hydrophobic replacements of Leu 99 and Phe 153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J Mol Biol 229:747-769.
    • (1993) J Mol Biol , vol.229 , pp. 747-769
    • Eriksson, A.E.1    Baase, W.A.2    Matthews, B.W.3
  • 38
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 39
    • 0038210935 scopus 로고    scopus 로고
    • Advances in direct methods for protein crystallography
    • Uson I, Sheldrick GM (1999) Advances in direct methods for protein crystallography. Curr Opin Struct Biol 9:643-648.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 643-648
    • Uson, I.1    Sheldrick, G.M.2
  • 40
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project No. 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
    • Collaborative Computational Project No. 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
  • 41
    • 0027159949 scopus 로고
    • The molecular surface package
    • Connolly ML (1993) The molecular surface package. J Mol Graphics 11:139-141.
    • (1993) J Mol Graphics , vol.11 , pp. 139-141
    • Connolly, M.L.1
  • 42
    • 0015987251 scopus 로고
    • Determination of molecular weight from protein crystals
    • Matthews BW (1974) Determination of molecular weight from protein crystals. J Mol Biol 82:513-526.
    • (1974) J Mol Biol , vol.82 , pp. 513-526
    • Matthews, B.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.