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Volumn 106, Issue 44, 2009, Pages 18491-18496

Computational design of ligand binding is not a solved problem

Author keywords

Arabinose binding protein; Biosensor; Glucose binding protein; Ribose binding protein; Serotonin receptor

Indexed keywords

ARABINOSE; SEROTONIN RECEPTOR;

EID: 73249124179     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0907950106     Document Type: Article
Times cited : (81)

References (32)
  • 1
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368.
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1
  • 2
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger LL, et al. (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190.
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1
  • 3
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon DN, Mayo SL (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98:14274-14279.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 4
    • 4143131151 scopus 로고    scopus 로고
    • De novo design of catalytic proteins
    • Kaplan J, DeGrado WF (2004) De novo design of catalytic proteins. Proc Natl Acad Sci USA 101:11566-11570.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11566-11570
    • Kaplan, J.1    DeGrado, W.F.2
  • 5
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Jiang L, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
    • (2008) Science , vol.319 , pp. 1387-1391
    • Jiang, L.1
  • 6
    • 43449098518 scopus 로고    scopus 로고
    • Kemp elimination catalysts by computational enzyme design
    • Röthlisberger D, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-195.
    • (2008) Nature , vol.453 , pp. 190-195
    • Röthlisberger, D.1
  • 7
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman
    • Allert M, et al. (2004) Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 101:7907-7912.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7907-7912
    • Allert, M.1
  • 8
    • 0024375861 scopus 로고
    • Substrate specificity and affinity of a protein modulated by bound water molecules
    • Quiocho FA, et al. (1989) Substrate specificity and affinity of a protein modulated by bound water molecules. Nature 340:404-407.
    • (1989) Nature , vol.340 , pp. 404-407
    • Quiocho, F.A.1
  • 9
    • 60849115875 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in a thermophilic ribose-binding protein
    • Cuneo MJ, et al. (2008) Ligand-induced conformational changes in a thermophilic ribose-binding protein. BMC Struct Biol 8:50.
    • (2008) BMC Struct Biol , vol.8 , pp. 50
    • Cuneo, M.J.1
  • 10
    • 0032511137 scopus 로고    scopus 로고
    • Multiple open forms of ribose-binding protein trace the path of its conformational change
    • Bjorkman AJ, Mowbray SL (1998) Multiple open forms of ribose-binding protein trace the path of its conformational change. J Mol Biol 279:651-664.
    • (1998) J Mol Biol , vol.279 , pp. 651-664
    • Bjorkman, A.J.1    Mowbray, S.L.2
  • 11
    • 0037134514 scopus 로고    scopus 로고
    • Hinge-bending motion of D-allose-binding protein from Escherichia coli: Three open conformations
    • Magnusson U, et al. (2002) Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations. J Biol Chem 277:14077-14084.
    • (2002) J Biol Chem , vol.277 , pp. 14077-14084
    • Magnusson, U.1
  • 12
    • 28444469196 scopus 로고    scopus 로고
    • Structural studies of an engineered zinc biosensor reveal an unanticipated mode of zinc binding
    • Telmer PG, Shilton BH (2005) Structural studies of an engineered zinc biosensor reveal an unanticipated mode of zinc binding. J Mol Biol 354:829-840.
    • (2005) J Mol Biol , vol.354 , pp. 829-840
    • Telmer, P.G.1    Shilton, B.H.2
  • 13
    • 0035942160 scopus 로고    scopus 로고
    • Conversion of a maltose receptor into a zinc biosensor by computational design
    • Marvin JS, Hellinga HW (2001) Conversion of a maltose receptor into a zinc biosensor by computational design. Proc Natl Acad Sci USA 98:4955-4960.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4955-4960
    • Marvin, J.S.1    Hellinga, H.W.2
  • 14
    • 33847282451 scopus 로고    scopus 로고
    • Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy
    • Vercillo NC, et al. (2007) Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy. Protein Sci 16:362-368.
    • (2007) Protein Sci , vol.16 , pp. 362-368
    • Vercillo, N.C.1
  • 15
    • 10744232637 scopus 로고    scopus 로고
    • Structural and thermal stability characterization of Escherichia coli D-galactose/D-glucose-binding protein
    • D'Auria S, et al. (2004) Structural and thermal stability characterization of Escherichia coli D-galactose/D-glucose-binding protein. Biotechnol Prog 20:330-337.
    • (2004) Biotechnol Prog , vol.20 , pp. 330-337
    • D'Auria, S.1
  • 16
    • 0027095923 scopus 로고
    • Escherichia coli K12 arabinose-binding protein mutants with altered transport properties
    • Kehres DG, Hogg RW (1992) Escherichia coli K12 arabinose-binding protein mutants with altered transport properties. Protein Sci 1:1652-1660.
    • (1992) Protein Sci , vol.1 , pp. 1652-1660
    • Kehres, D.G.1    Hogg, R.W.2
  • 17
    • 0016200993 scopus 로고
    • Purification and properties of a ribose-binding protein from Escherichia coli
    • Willis RC, Furlong CE (1974) Purification and properties of a ribose-binding protein from Escherichia coli. J Biol Chem 249:6926-6929.
    • (1974) J Biol Chem , vol.249 , pp. 6926-6929
    • Willis, R.C.1    Furlong, C.E.2
  • 18
    • 0024237631 scopus 로고
    • Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein
    • Vyas NK, et al. (1988) Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242:1290-1295.
    • (1988) Science , vol.242 , pp. 1290-1295
    • Vyas, N.K.1
  • 19
    • 0036838307 scopus 로고    scopus 로고
    • Construction of a fluorescent biosensor family
    • de Lorimier RM, et al. (2002) Construction of a fluorescent biosensor family. Protein Sci 11:2655-2675.
    • (2002) Protein Sci , vol.11 , pp. 2655-2675
    • de Lorimier, R.M.1
  • 20
    • 0242331659 scopus 로고    scopus 로고
    • The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
    • Millet O, et al. (2003) The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc Natl Acad Sci USA 100:12700-12705.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12700-12705
    • Millet, O.1
  • 21
    • 44949229094 scopus 로고    scopus 로고
    • Design of protein-ligand binding based on the molecular-mechanics energy model
    • Boas FE, Harbury PB (2008) Design of protein-ligand binding based on the molecular-mechanics energy model. J Mol Biol 380:415-424.
    • (2008) J Mol Biol , vol.380 , pp. 415-424
    • Boas, F.E.1    Harbury, P.B.2
  • 22
    • 0030612833 scopus 로고    scopus 로고
    • Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
    • Pervushin K, et al. (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94:12366-12371.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 12366-12371
    • Pervushin, K.1
  • 23
    • 0029400480 scopus 로고
    • NMRPipe: Amultidimensional spectral processing system based on UNIX pipes
    • Delaglio F, et al. (1995) NMRPipe: Amultidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293.
    • (1995) J Biomol NMR , vol.6 , pp. 277-293
    • Delaglio, F.1
  • 24
    • 4644259437 scopus 로고    scopus 로고
    • Using NMRView to visualize and analyze the NMR spectra of macromolecules
    • Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313-352.
    • (2004) Methods Mol Biol , vol.278 , pp. 313-352
    • Johnson, B.A.1
  • 25
    • 85027632383 scopus 로고
    • Automatic-indexing of rotation diffraction patterns
    • Kabsch W (1988) Automatic-indexing of rotation diffraction patterns. J Appl Crystallogr 21:67-71.
    • (1988) J Appl Crystallogr , vol.21 , pp. 67-71
    • Kabsch, W.1
  • 26
    • 23844546311 scopus 로고    scopus 로고
    • Likelihood-enhanced fast translation functions
    • McCoy AJ, et al. (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 61:458-464.
    • (2005) Acta Crystallogr D Biol Crystallogr , vol.61 , pp. 458-464
    • McCoy, A.J.1
  • 27
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov GN, et al. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240-255.
    • (1997) Acta Crystallogr D Biol Crystallogr , vol.53 , pp. 240-255
    • Murshudov, G.N.1
  • 28
  • 29
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
    • (2007) Nucleic Acids Res , vol.35
    • Davis, I.W.1
  • 30
    • 0344186399 scopus 로고    scopus 로고
    • Errors in protein structures
    • Hooft RW, et al. (1996) Errors in protein structures. Nature 381:272.
    • (1996) Nature , vol.381 , pp. 272
    • Hooft, R.W.1
  • 31
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change:new results on citrate synthase and T4 lysozyme
    • Hayward S, Berendsen HJ (1998) Systematic analysis of domain motions in proteins from conformational change:new results on citrate synthase and T4 lysozyme. Proteins 30:144-154.
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.2
  • 32
    • 33749641136 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System
    • Palo Alto, CA
    • DeLano WL (2002) The PyMOL Molecular Graphics System. DeLano Scientific (Palo Alto, CA).
    • (2002) DeLano Scientific
    • DeLano, W.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.