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Volumn 6, Issue 1, 2011, Pages

Applying an empirical hydropathic forcefield in refinement may improve low-resolution protein x-ray crystal structures

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CRYSTALLOGRAPHY; DEGRADATION; ENTHALPY; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; METHODOLOGY; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; MACROMOLECULE; STANDARD;

EID: 79251577981     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015920     Document Type: Article
Times cited : (13)

References (36)
  • 1
    • 54549098184 scopus 로고    scopus 로고
    • Target flexibility: An emerging consideration in drug discovery and design
    • Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, et al. (2008) Target flexibility: an emerging consideration in drug discovery and design. J Med Chem 51: 6237-6255.
    • (2008) J Med Chem , vol.51 , pp. 6237-6255
    • Cozzini, P.1    Kellogg, G.E.2    Spyrakis, F.3    Abraham, D.J.4    Costantino, G.5
  • 3
    • 2342525085 scopus 로고    scopus 로고
    • Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography
    • DePristo MA, de Bakker PIW, Blundell TL (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure 12: 831-838.
    • (2004) Structure , vol.12 , pp. 831-838
    • Depristo, M.A.1    de Bakker, P.I.W.2    Blundell, T.L.3
  • 4
    • 13444270892 scopus 로고    scopus 로고
    • The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema
    • Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, et al. (2005) The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 33: D233-237.
    • (2005) Nucleic Acids Res , vol.33
    • Deshpande, N.1    Addess, K.J.2    Bluhm, W.F.3    Merino-Ott, J.C.4    Townsend-Merino, W.5
  • 5
    • 58849144330 scopus 로고    scopus 로고
    • Model-building strategies for lowresolution X-ray crystallographic data
    • Karmali AM, Blundell TL, Furnham N (2009) Model-building strategies for lowresolution X-ray crystallographic data. Acta Crystallogr D 65: 121-127.
    • (2009) Acta Crystallogr , vol.65 D , pp. 121-127
    • Karmali, A.M.1    Blundell, T.L.2    Furnham, N.3
  • 6
    • 0034257929 scopus 로고    scopus 로고
    • The 1.0 A ° crystal structure of Ca2+bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
    • Wilson MA, Brunger AT (2000) The 1.0 A ° 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
  • 7
    • 4644348577 scopus 로고    scopus 로고
    • Computational titration analysis of a multiprotic HIV-1 protease-ligand complex
    • Spyrakis F, Fornabaio M, Cozzini P, Mozzarelli A, Abraham DJ, et al. (2004) Computational titration analysis of a multiprotic HIV-1 protease-ligand complex. J Am Chem Soc 126: 11764-11765.
    • (2004) J Am Chem Soc , vol.126 , pp. 11764-11765
    • Spyrakis, F.1    Fornabaio, M.2    Cozzini, P.3    Mozzarelli, A.4    Abraham, D.J.5
  • 8
    • 77951623055 scopus 로고    scopus 로고
    • Super-resolution biomolecular crystallography with low-resolution data
    • Schröder GF, Levitt M, Brunger AT (2010) Super-resolution biomolecular crystallography with low-resolution data. Nature 464: 1218-1222.
    • (2010) Nature , vol.464 , pp. 1218-1222
    • Schröder, G.F.1    Levitt, M.2    Brunger, A.T.3
  • 9
    • 0026597444 scopus 로고
    • The free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger AT (1992) The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 11
    • 0343517556 scopus 로고    scopus 로고
    • Hydrophobicity. Is logPo/w more than the sum of its parts?
    • Kellogg GE, Abraham DJ (2000) Hydrophobicity. Is logPo/w more than the sum of its parts? Eur J Med Chem 35: 651-661.
    • (2000) Eur J Med Chem , vol.35 , pp. 651-661
    • Kellogg, G.E.1    Abraham, D.J.2
  • 12
    • 0001085722 scopus 로고
    • Linear free-energy relationship between partition coefficients and the aqueous solubility of organic liquids
    • Hansch C, Quinlan JE, Lawrence GL (1968) Linear free-energy relationship between partition coefficients and the aqueous solubility of organic liquids. J Org Chem 33: 347-350.
    • (1968) J Org Chem , vol.33 , pp. 347-350
    • Hansch, C.1    Quinlan, J.E.2    Lawrence, G.L.3
  • 13
    • 33645106609 scopus 로고    scopus 로고
    • Mapping the energetics of water-protein and water-ligand interactions with the natural HINT forcefield: Predictive tools for characterizing the roles of water in biomolecules
    • Amadasi A, Spyrakis F, Cozzini P, Abraham DJ, Kellogg GE, et al. (2006) Mapping the energetics of water-protein and water-ligand interactions with the natural HINT forcefield: predictive tools for characterizing the roles of water in biomolecules. J Mol Biol 358: 289-309.
    • (2006) J Mol Biol , vol.358 , pp. 289-309
    • Amadasi, A.1    Spyrakis, F.2    Cozzini, P.3    Abraham, D.J.4    Kellogg, G.E.5
  • 14
    • 0037030649 scopus 로고    scopus 로고
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water
    • Cozzini P, Fornabaio M, Marabotti A, Abraham DJ, Kellogg GE, et al. (2002) Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water. J Med Chem 45: 2469-2483.
    • (2002) J Med Chem , vol.45 , pp. 2469-2483
    • Cozzini, P.1    Fornabaio, M.2    Marabotti, A.3    Abraham, D.J.4    Kellogg, G.E.5
  • 16
    • 40749153054 scopus 로고    scopus 로고
    • Docking and hydropathic scoring of polysubstituted pyrrole compounds with antitubulin activity
    • Tripathi A, Fornabaio M, Kellogg GE, Gupton JT, Gewirtz DA, et al. (2008) Docking and hydropathic scoring of polysubstituted pyrrole compounds with antitubulin activity. Bioorg Med Chem 16: 2235-2242.
    • (2008) Bioorg Med Chem , vol.16 , pp. 2235-2242
    • Tripathi, A.1    Fornabaio, M.2    Kellogg, G.E.3    Gupton, J.T.4    Gewirtz, D.A.5
  • 17
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography & NMR system: A new software suite for macromolecular structure determination
    • Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D 54: 905-921.
    • (1998) Acta Crystallogr , vol.54 D , pp. 905-921
    • Brünger, A.T.1    Adams, P.D.2    Clore, G.M.3    Delano, W.L.4    Gros, P.5
  • 18
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh RA, Huber R (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 47: 392-400.
    • (1991) Acta Crystallogr , vol.47 A , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 19
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem , vol.102 B , pp. 3586-3616
    • Mackerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.4    Evanseck, J.D.5
  • 20
    • 0031551573 scopus 로고    scopus 로고
    • Hydropathic analysis of the noncovalent interactions between molecular subunits of structurallycharacterized hemoglobins
    • Abraham DJ, Kellogg GE, Holt JM, Ackers GK (1997) Hydropathic analysis of the noncovalent interactions between molecular subunits of structurallycharacterized hemoglobins. J Mol Biol 272: 613-632.
    • (1997) J Mol Biol , vol.272 , pp. 613-632
    • Abraham, D.J.1    Kellogg, G.E.2    Holt, J.M.3    Ackers, G.K.4
  • 21
    • 0024292833 scopus 로고
    • Aromatic Rings Act as Hydrogen Bond Acceptors
    • Levitt M, Perutz, MF (1988) Aromatic Rings Act as Hydrogen Bond Acceptors. J Mol Biol 201: 751-754.
    • (1988) J Mol Biol , vol.201 , pp. 751-754
    • Levitt, M.1    Perutz, M.F.2
  • 22
    • 0033081137 scopus 로고    scopus 로고
    • How many water molecules can be detected by protein crystallography?
    • Carugo O, Bordo D (1999) How many water molecules can be detected by protein crystallography? Acta Crystallogr D 55: 479-483.
    • (1999) Acta Crystallogr , vol.55 D , pp. 479-483
    • Carugo, O.1    Bordo, D.2
  • 23
    • 0033106268 scopus 로고    scopus 로고
    • Remarks about protein structure precision
    • Cruickshank DW (1999) Remarks about protein structure precision. Acta Crystallogr D 55: 583-601.
    • (1999) Acta Crystallogr , vol.55 D , pp. 583-601
    • Cruickshank, D.W.1
  • 24
    • 3242886389 scopus 로고    scopus 로고
    • MolProbity: Structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucl Acids Res 32: W615-619.
    • (2004) Nucl Acids Res , vol.32
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 25
    • 24044456039 scopus 로고    scopus 로고
    • Structure of the conserved cytoplasmic C-terminal domain of occludin: Identification of the ZO-1 binding surface
    • Li Y, Fanning AS, Anderson JM, Lavie A (2005) Structure of the conserved cytoplasmic C-terminal domain of occludin: identification of the ZO-1 binding surface. J Mol Biol 352: 151-164.
    • (2005) J Mol Biol , vol.352 , pp. 151-164
    • Li, Y.1    Fanning, A.S.2    Anderson, J.M.3    Lavie, A.4
  • 27
    • 12844250789 scopus 로고    scopus 로고
    • The 1.4 A ° structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins
    • Fermani S, Falini G, Ripamonti A, Polito L, Stirpe F, et al. (2005) The 1.4 A ° structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins. J Struct Biol 149: 204-212.
    • (2005) J Struct Biol , vol.149 , pp. 204-212
    • Fermani, S.1    Falini, G.2    Ripamonti, A.3    Polito, L.4    Stirpe, F.5
  • 28
    • 65949083763 scopus 로고    scopus 로고
    • Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2
    • Hennig S, Strauss HM, Vanselow K, Yildiz O, Schulze S, et al. (2009) Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2. PLoS Biol 7: e94.
    • (2009) PLoS Biol , vol.e94 , pp. 7
    • Hennig, S.1    Strauss, H.M.2    Vanselow, K.3    Yildiz, O.4    Schulze, S.5
  • 29
    • 0037022586 scopus 로고    scopus 로고
    • Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+
    • Tsuchiya D, Kunishima N, Kamiya N, Jingami H, Morikawa K (2002) Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+. Proc Natl Acad Sci U S A 99: 2660-2665.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 2660-2665
    • Tsuchiya, D.1    Kunishima, N.2    Kamiya, N.3    Jingami, H.4    Morikawa, K.5
  • 30
    • 1642401199 scopus 로고    scopus 로고
    • Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain
    • Ravelli RBG, Gigant B, Curmi PA, Jourdain I, Lachkar S, et al. (2004) Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature 428: 198-202.
    • (2004) Nature , vol.428 , pp. 198-202
    • Ravelli, R.B.G.1    Gigant, B.2    Curmi, P.A.3    Jourdain, I.4    Lachkar, S.5
  • 31
    • 0034704077 scopus 로고    scopus 로고
    • Mapping the binding site of colchicinoids on beta -tubulin. 2-Chloroacetyl-2-demethylthiocolchicine covalently reacts predominantly with cysteine 239 and secondarily with cysteine 354
    • Bai R, Covell DG, Pei XF, Ewell JB, Nguyen NY, et al. (2000) Mapping the binding site of colchicinoids on beta -tubulin. 2-Chloroacetyl-2-demethylthiocolchicine covalently reacts predominantly with cysteine 239 and secondarily with cysteine 354. J Biol Chem 275: 40443-40452.
    • (2000) J Biol Chem , vol.275 , pp. 40443-40452
    • Bai, R.1    Covell, D.G.2    Pei, X.F.3    Ewell, J.B.4    Nguyen, N.Y.5
  • 32
    • 24944515311 scopus 로고    scopus 로고
    • A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach
    • Nguyen TL, McGrath C, Hermone AR, Burnett JC, Zaharevitz DW, et al. (2005) A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach. J Med Chem 48: 6107-6116.
    • (2005) J Med Chem , vol.48 , pp. 6107-6116
    • Nguyen, T.L.1    McGrath, C.2    Hermone, A.R.3    Burnett, J.C.4    Zaharevitz, D.W.5
  • 33
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53: 240-255.
    • (1997) Acta Crystallogr , vol.53 D , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 34
    • 0035182073 scopus 로고    scopus 로고
    • Use of TLS parameters to model anisotropic displacements in macromolecular refinement
    • Winn MD, Isupov MN, Murshudov GN (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D 57: 122-133.
    • (2001) Acta Crystallogr , vol.57 D , pp. 122-133
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 35
    • 79251555997 scopus 로고    scopus 로고
    • version 1.3
    • Brunger AT; Announcing CNS, version 1.3. http://www.mail-archive.com/ ccp4bb@jiscmail.ac.uk/msg16733.html.
    • Brunger, A.T.1    Announcing, C.N.S.2
  • 36
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Anonymous
    • Anonymous (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50: 760-763.
    • (1994) Acta Crystallogr , vol.50 D , pp. 760-763


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