메뉴 건너뛰기




Volumn 19, Issue 7, 2010, Pages 1420-1431

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

Author keywords

Electron density sampling; Rotamers; Side chain ensembles; Structural polymorphism; X ray crystallography

Indexed keywords

CALMODULIN; PROTEIN;

EID: 77953977241     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.423     Document Type: Article
Times cited : (140)

References (41)
  • 1
    • 33846939583 scopus 로고    scopus 로고
    • Determination of conformationally heterogeneous states of proteins
    • DOI 10.1016/j.sbi.2007.01.002, PII S0959440X07000036, Foldinf and Binding / Protein-Nucleic Interactions
    • Vendruscolo M (2007) Determination of conformationally heterogeneous states of proteins. Curr Opin Struct Biol 17:15-20. (Pubitemid 46240813)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.1 , pp. 15-20
    • Vendruscolo, M.1
  • 3
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • DOI 10.1126/science.1130258
    • Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638-1642. (Pubitemid 44414038)
    • (2006) Science , vol.313 , Issue.5793 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wrightt, P.E.4
  • 4
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462:669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6
  • 5
    • 44849141472 scopus 로고    scopus 로고
    • Internal dynamics control activation and activity of the autoinhibited Vav DH domain
    • Li PL, Martins IRS, Amarasinghe GK, Rosen MK (2008) Internal dynamics control activation and activity of the autoinhibited Vav DH domain. Nat Struct Mol Biol 15:613-618.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 613-618
    • Li, P.L.1    Martins, I.R.S.2    Amarasinghe, G.K.3    Rosen, M.K.4
  • 6
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203-207.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 7
    • 33645834303 scopus 로고    scopus 로고
    • Review - New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier A, Kay LE (2006) Review - new tools provide new insights in NMR studies of protein dynamics. Science 312:224-228.
    • (2006) Science , vol.312 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 9
    • 0029585945 scopus 로고
    • Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive
    • Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW (1995) Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. Protein Eng 8:1017-1022.
    • (1995) Protein Eng , vol.8 , pp. 1017-1022
    • Zhang, X.J.1    Baase, W.A.2    Shoichet, B.K.3    Wilson, K.P.4    Matthews, B.W.5
  • 11
    • 32044434962 scopus 로고    scopus 로고
    • Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography
    • Niimura N, Arai S, Kurihara K, Chatake T, Tanaka I, Bau R (2006) Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography. Cell Mol Life Sci 63:285-300.
    • (2006) Cell Mol Life Sci , vol.63 , pp. 285-300
    • Niimura, N.1    Arai, S.2    Kurihara, K.3    Chatake, T.4    Tanaka, I.5    Bau, R.6
  • 12
    • 0026720247 scopus 로고
    • Crystalline ribonuclease a loses function below the dynamical transition at 220 K
    • Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357:423-424.
    • (1992) Nature , vol.357 , pp. 423-424
    • Rasmussen, B.F.1    Stock, A.M.2    Ringe, D.3    Petsko, G.A.4
  • 13
    • 1642588255 scopus 로고    scopus 로고
    • Structures of mismatch replication errors observed in a DNA polymerase
    • Johnson SJ, Beese LS (2004) Structures of mismatch replication errors observed in a DNA polymerase. Cell 116:803-816.
    • (2004) Cell , vol.116 , pp. 803-816
    • Johnson, S.J.1    Beese, L.S.2
  • 14
    • 0018793861 scopus 로고
    • Temperature-dependent X-ray-diffraction as a probe of protein structural dynamics
    • Frauenfelder H, Petsko GA, Tsernoglou D (1979) Temperature-dependent X-ray-diffraction as a probe of protein structural dynamics. Nature 280:558-563.
    • (1979) Nature , vol.280 , pp. 558-563
    • Frauenfelder, H.1    Petsko, G.A.2    Tsernoglou, D.3
  • 16
    • 0030841588 scopus 로고    scopus 로고
    • Refinement and reliability of macromolecular models based on X-ray diffraction data
    • San Diego: Academic Press
    • Jensen LH (1997) Refinement and reliability of macromolecular models based on X-ray diffraction data. Methods in enzymology: Macromolecular crystallography, Part B, Vol. 277. San Diego: Academic Press, pp 353-366.
    • (1997) Methods in Enzymology: Macromolecular Crystallography, Part B , vol.277 , pp. 353-366
    • Jensen, L.H.1
  • 18
    • 0023053635 scopus 로고
    • Effect of anisotropy and anharmonicity on protein crystallographic refinement - An evaluation by moleculardynamics
    • Kuriyan J, Petsko GA, Levy RM, Karplus M (1986) Effect of anisotropy and anharmonicity on protein crystallographic refinement - an evaluation by moleculardynamics. J Mol Biol 190:227-254.
    • (1986) J Mol Biol , vol.190 , pp. 227-254
    • Kuriyan, J.1    Petsko, G.A.2    Levy, R.M.3    Karplus, M.4
  • 19
    • 32044456003 scopus 로고    scopus 로고
    • The backrub motion: How protein backbone shrugs when a sidechain dances
    • Davis IW, Arendall WB, Richardson DC, Richardson JS (2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14:265-274.
    • (2006) Structure , vol.14 , pp. 265-274
    • Davis, I.W.1    Arendall, W.B.2    Richardson, D.C.3    Richardson, J.S.4
  • 20
    • 33846011887 scopus 로고    scopus 로고
    • Statistical and conformational analysis of the electron density of protein side chains
    • Shapovalov MV, Dunbrack RL (2007) Statistical and conformational analysis of the electron density of protein side chains. Proteins 66:279-303.
    • (2007) Proteins , vol.66 , pp. 279-303
    • Shapovalov, M.V.1    Dunbrack, R.L.2
  • 22
    • 34548387498 scopus 로고    scopus 로고
    • Ensemble refinement of protein crystal structures: Validation and application
    • Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN (2007) Ensemble refinement of protein crystal structures: validation and application. Structure 15:1040-1052.
    • (2007) Structure , vol.15 , pp. 1040-1052
    • Levin, E.J.1    Kondrashov, D.A.2    Wesenberg, G.E.3    Phillips, G.N.4
  • 23
    • 70349603852 scopus 로고    scopus 로고
    • Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    • van den Bedem H, Dhanik A, Latombe JC, Deacon AM (2009) Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. Acta Cryst D65: 1107-1117.
    • (2009) Acta Cryst , vol.D65 , pp. 1107-1117
    • Van Den Bedem, H.1    Dhanik, A.2    Latombe, J.C.3    Deacon, A.M.4
  • 25
    • 0035118738 scopus 로고    scopus 로고
    • Conformational disorder of proteins assessed by real-space molecular dynamics refinement
    • Chen Z, Chapman MS (2001) Conformational disorder of proteins assessed by real-space molecular dynamics refinement. Biophys J 80:1466-1472.
    • (2001) Biophys J , vol.80 , pp. 1466-1472
    • Chen, Z.1    Chapman, M.S.2
  • 26
    • 0038853525 scopus 로고    scopus 로고
    • Crystal structures of myoglobin-ligand complexes at near-atomic resolution
    • Vojtechovsky J, Chu K, Berendzen J, Sweet RM, Schlichting I (1999) Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Biophys J 77:2153-2174.
    • (1999) Biophys J , vol.77 , pp. 2153-2174
    • Vojtechovsky, J.1    Chu, K.2    Berendzen, J.3    Sweet, R.M.4    Schlichting, I.5
  • 27
    • 0001408294 scopus 로고    scopus 로고
    • Computation of Bhat's OMIT maps with different coefficients
    • Vellieux FMD, Dijkstra BW (1997) Computation of Bhat's OMIT maps with different coefficients. J Appl Cryst 30:396-399.
    • (1997) J Appl Cryst , vol.30 , pp. 396-399
    • Vellieux, F.M.D.1    Dijkstra, B.W.2
  • 28
    • 0018115846 scopus 로고
    • Conformation of amino-acid side-chains in proteins
    • Janin J, Wodak S, Levitt M, Maigret B (1978) Conformation of amino-acid side-chains in proteins. J Mol Biol 125:357-386.
    • (1978) J Mol Biol , vol.125 , pp. 357-386
    • Janin, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 29
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM (1987) Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 31
    • 34748819551 scopus 로고    scopus 로고
    • Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids
    • Sales M, Plecs JJ, Holton JM, Alber T (2007) Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Protein Sci 16: 2224-2232.
    • (2007) Protein Sci , vol.16 , pp. 2224-2232
    • Sales, M.1    Plecs, J.J.2    Holton, J.M.3    Alber, T.4
  • 32
    • 0034257929 scopus 로고    scopus 로고
    • The 1.0 angstrom crystal structure of Ca2+-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
    • Wilson MA, Brunger AT (2000) The 1.0 angstrom crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J Mol Biol 301:1237-1256.
    • (2000) J Mol Biol , vol.301 , pp. 1237-1256
    • Wilson, M.A.1    Brunger, A.T.2
  • 34
    • 0002638463 scopus 로고
    • Heat-capacity and entropy changes in processes involving proteins
    • Sturtevant JM (1977) Heat-capacity and entropy changes in processes involving proteins. Proc Natl Acad Sci USA 74:2236-2240.
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 2236-2240
    • Sturtevant, J.M.1
  • 35
    • 67650677848 scopus 로고    scopus 로고
    • Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions
    • DuBay KH, Geissler PL (2009) Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions. J Mol Biol 391:484-497.
    • (2009) J Mol Biol , vol.391 , pp. 484-497
    • Dubay, K.H.1    Geissler, P.L.2
  • 36
    • 9944263528 scopus 로고    scopus 로고
    • Searching for new allosteric sites in enzymes
    • Hardy JA, Wells JA (2004) Searching for new allosteric sites in enzymes. Curr Opin Struct Biol 14:706-715.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 706-715
    • Hardy, J.A.1    Wells, J.A.2
  • 37
    • 0028103275 scopus 로고
    • The Ccp4 suite - Programs for protein crystallography
    • Bailey S (1994) The Ccp4 suite - programs for protein crystallography. Acta Cryst D50:760-763.
    • (1994) Acta Cryst , vol.D50 , pp. 760-763
    • Bailey, S.1
  • 39
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Cryst D60:2126-2132.
    • (2004) Acta Cryst , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.