메뉴 건너뛰기




Volumn , Issue , 2008, Pages 189-221

Methods to characterize the structure of enzyme binding sites

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME-BINDING SITES;

EID: 84969228248     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812778789_0008     Document Type: Chapter
Times cited : (14)

References (57)
  • 3
    • 84892166712 scopus 로고
    • Einfluss der configuration auf die wirkung der enzyme
    • Fischer E. (1894) Einfluss der configuration auf die wirkung der enzyme. Ber Dtsch Chem Ges 27: 2985-2993.
    • (1894) Ber Dtsch Chem Ges , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 4
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE. (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44: 98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 5
    • 0035487690 scopus 로고    scopus 로고
    • A tour of structural genomics
    • Brenner SE. (2001) A tour of structural genomics. Nature Rev 2: 801-809.
    • (2001) Nature Rev , vol.2 , pp. 801-809
    • Brenner, S.E.1
  • 7
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
    • Nayal M, Honig B. (2006) On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 63: 892-906.
    • (2006) Proteins , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 9
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski RA. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13: 323-330.
    • (1995) J Mol Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 10
    • 33646262869 scopus 로고    scopus 로고
    • Testing electrostatic complementarity in enzyme catalysis: Hydrogen bonding in the ketosteroid isomerase oxyanion hole
    • Kraut DA, Sigala PA, Pybus B, et al. (2006) Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Plos Biol 4: 501-519.
    • (2006) Plos Biol , vol.4 , pp. 501-519
    • Kraut, D.A.1    Sigala, P.A.2    Pybus, B.3
  • 11
    • 33748102999 scopus 로고    scopus 로고
    • Travel depth, a new shape descriptor for macromolecules: Application to ligand binding
    • Coleman RG, Sharp KA. (2006) Travel depth, a new shape descriptor for macromolecules: Application to ligand binding. J Mol Biol 362: 441-458.
    • (2006) J Mol Biol , vol.362 , pp. 441-458
    • Coleman, R.G.1    Sharp, K.A.2
  • 12
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge A, Thornton J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 346: 21-28.
    • (2005) J Mol Biol , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 13
    • 0034684969 scopus 로고    scopus 로고
    • Zn(2+)-mediated structure formation and compaction of the "natively unfolded" human prothymosin alpha
    • Uversky VN, Gillespie JR, Millett IS, et al. (2000) Zn(2+)-mediated structure formation and compaction of the "natively unfolded" human prothymosin alpha. Biocheml Biophys Res Commun 267: 663-668.
    • (2000) Biocheml Biophys Res Commun , vol.267 , pp. 663-668
    • Uversky, V.N.1    Gillespie, J.R.2    Millett, I.S.3
  • 14
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution-a 60-year-old hypothesis revisited
    • James LC, Tawfik DS. (2003) Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci 28: 361-368.
    • (2003) Trends Biochem Sci , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 15
    • 8444245890 scopus 로고    scopus 로고
    • Automated clustering of ensembles of alternative models in protein structure databases
    • Domingues FS, Rahnenfuhrer J, Lengauer T. (2004) Automated clustering of ensembles of alternative models in protein structure databases. Protein Eng Des Sel 17: 537-543.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 537-543
    • Domingues, F.S.1    Rahnenfuhrer, J.2    Lengauer, T.3
  • 17
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F, Pupko T, Paz I, et al. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3
  • 18
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE. (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 19
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM, Goodsell DS, Halliday RS, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662.
    • (1998) J Comput Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3
  • 20
    • 0344837306 scopus 로고    scopus 로고
    • Conservation of electrostatic properties within enzyme families and superfamilies
    • Livesay DR, Jambeck, P, Rojnuckarin, A, Subramaniam, S. (2003) Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry 42: 3464-3473.
    • (2003) Biochemistry , vol.42 , pp. 3464-3473
    • Livesay, D.R.1    Jambeck, P.2    Rojnuckarin, A.3    Subramaniam, S.4
  • 21
    • 2542557409 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    • Tsuchiya Y, Kinoshita K, Nakamura H. (2004) Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins 55: 885-894.
    • (2004) Proteins , vol.55 , pp. 885-894
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 22
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K, Furui, J, Nakamura H. (2002) Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics 2: 9-22.
    • (2002) J Struct Funct Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 23
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. (1995) Classical electrostatics in biology and chemistry. Science 268: 1144.
    • (1995) Science , vol.268 , pp. 1144
    • Honig, B.1    Nicholls, A.2
  • 24
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1: 47-59.
    • (1986) Proteins , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 25
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock AH. (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol 312: 885-896.
    • (2001) J Mol Biol , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 26
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen MJ, Clifton JG, Ringe D. (2001) THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci USA 98:12473-12478.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3
  • 27
    • 0042386537 scopus 로고    scopus 로고
    • Identification of substrate binding sites in enzymes by computational solvent mapping
    • Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S. (2003) Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol 332: 1095-1113.
    • (2003) J Mol Biol , vol.332 , pp. 1095-1113
    • Silberstein, M.1    Dennis, S.2    Brown, L.3    Kortvelyesi, T.4    Clodfelter, K.5    Vajda, S.6
  • 28
    • 0033559918 scopus 로고    scopus 로고
    • Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
    • Davis AM, Teague SJ. (1999) Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis. Angew Chem Int Ed 38: 736-749.
    • (1999) Angew Chem Int Ed , vol.38 , pp. 736-749
    • Davis, A.M.1    Teague, S.J.2
  • 30
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T, Morozov AV, Baker D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 326: 1239-1259.
    • (2003) J Mol Biol , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 31
    • 33847366247 scopus 로고    scopus 로고
    • Strong and weak hydrogen bonds in the protein-ligand interface
    • Panigrahi SK, Desiraju GR. (2007) Strong and weak hydrogen bonds in the protein-ligand interface. Proteins 67: 128-141.
    • (2007) Proteins , vol.67 , pp. 128-141
    • Panigrahi, S.K.1    Desiraju, G.R.2
  • 32
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace AC, Laskowski RA, Thornton JM. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 33
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK, Thornton JM. (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238: 777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 34
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • Laurie AT, Jackson RM. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916.
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 35
    • 0027965409 scopus 로고
    • Generation of the topa quinone cofactor in bacterial monoamine oxidase by cupric ion-dependent autooxidation of a specific tyrosyl residue
    • Matsuzaki R, Fukui T, Sato H, Ozaki Y, Tanizawa K. (1994) Generation of the topa quinone cofactor in bacterial monoamine oxidase by cupric ion-dependent autooxidation of a specific tyrosyl residue. FEBS Lett 351: 360-364.
    • (1994) FEBS Lett , vol.351 , pp. 360-364
    • Matsuzaki, R.1    Fukui, T.2    Sato, H.3    Ozaki, Y.4    Tanizawa, K.5
  • 36
    • 0031047005 scopus 로고    scopus 로고
    • Identification of an Fe(III)-dihydroxyphenylalanine site in recombinant phosphomannose isomerase from Candida albicans
    • Smith JJ, Thomson AJ, Proudfoot AE, Wells TNC. (1997) Identification of an Fe(III)-dihydroxyphenylalanine site in recombinant phosphomannose isomerase from Candida albicans. Eur J Biochem/FEBS 244: 325-333.
    • (1997) Eur J Biochem/FEBS , vol.244 , pp. 325-333
    • Smith, J.J.1    Thomson, A.J.2    Proudfoot, A.E.3    Wells, T.N.C.4
  • 37
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K, Thornton JM. (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
    • (1998) Trends Biochem Sci , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 38
    • 33751091763 scopus 로고    scopus 로고
    • Cognate ligand domain mapping for enzymes
    • Bashton M, Nobeli I, Thornton JM. (2006) Cognate ligand domain mapping for enzymes. J Mol Biol 364: 836-852.
    • (2006) J Mol Biol , vol.364 , pp. 836-852
    • Bashton, M.1    Nobeli, I.2    Thornton, J.M.3
  • 39
    • 15744375643 scopus 로고    scopus 로고
    • Three-dimensional shape searching: State-of-the-art review and future trends
    • Iyer N, Jayanti S, Lou K, Kalyanaraman Y, Ramani K. (2005) Three-dimensional shape searching: state-of-the-art review and future trends. Comput-Aided Des 37: 509-530.
    • (2005) Comput-Aided Des , vol.37 , pp. 509-530
    • Iyer, N.1    Jayanti, S.2    Lou, K.3    Kalyanaraman, Y.4    Ramani, K.5
  • 40
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucl Acids Res 32: D129-D133.
    • (2004) Nucl Acids Res , vol.32 , pp. D129-D133
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 41
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis
    • Barker JA, Thornton JM. (2003) An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 19: 1644-1649.
    • (2003) Bioinformatics , vol.19 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 42
    • 33846674048 scopus 로고    scopus 로고
    • Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family
    • Najmanovich RJ, Allali-Hassani A, Morris RJ, et al. (2007) Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. Bioinformatics 23: e104-e109.
    • (2007) Bioinformatics , vol.23 , pp. e104-e109
    • Najmanovich, R.J.1    Allali-Hassani, A.2    Morris, R.J.3
  • 43
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S, Kuhn D, Klebe G. (2002) A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323:387-406.
    • (2002) J Mol Biol , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 44
    • 0031776823 scopus 로고    scopus 로고
    • Molecular shape comparisons in searches for active sites and functional similarity
    • Rosen M, Lin SL, Wolfson H, Nussinov R. (1998) Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng 11: 263-277.
    • (1998) Protein Eng , vol.11 , pp. 263-277
    • Rosen, M.1    Lin, S.L.2    Wolfson, H.3    Nussinov, R.4
  • 45
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
    • Fetrow JS, Skolnick J. (1998) Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 281: 949-968.
    • (1998) J Mol Biol , vol.281 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 46
    • 0042890523 scopus 로고    scopus 로고
    • Inferring functional relationships of proteins from local sequence and spatial surface patterns
    • Binkowski TA, Adamian L, Liang J. (2003) Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol 332:505-526.
    • (2003) J Mol Biol , vol.332 , pp. 505-526
    • Binkowski, T.A.1    Adamian, L.2    Liang, J.3
  • 47
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed Atlas of Surface Topography of proteins
    • Binkowski TA, Naghibzadeh S, Liang J. (2003) CASTp: computed Atlas of Surface Topography of proteins. Nucl Acids Res 31: 3352-3355.
    • (2003) Nucl Acids Res , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1    Naghibzadeh, S.2    Liang, J.3
  • 48
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • Jain AN. (2006) Scoring functions for protein-ligand docking. Curr Protein Peptide Sci 7: 407-420.
    • (2006) Curr Protein Peptide Sci , vol.7 , pp. 407-420
    • Jain, A.N.1
  • 49
    • 0036510961 scopus 로고    scopus 로고
    • Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design
    • Sotriffer C, Klebe G. (2002) Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmacology 57: 243-251.
    • (2002) Farmacology , vol.57 , pp. 243-251
    • Sotriffer, C.1    Klebe, G.2
  • 50
    • 0029900085 scopus 로고    scopus 로고
    • Negative electrostatic surface potential of protein sites specific for anionic ligands
    • Ledvina PS, Yao N, Choudhary A, Quiocho FA. (1996) Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc Natl Acad Sci USA 93: 6786-6791.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 6786-6791
    • Ledvina, P.S.1    Yao, N.2    Choudhary, A.3    Quiocho, F.A.4
  • 51
    • 33748525883 scopus 로고    scopus 로고
    • Enzyme promiscuity: Evolutionary and mechanistic aspects
    • Khersonsky O, Roodveldt C, Tawfik DS. (2006) Enzyme promiscuity: evolutionary and mechanistic aspects. Curr Opin Chem Biol 10: 498-508.
    • (2006) Curr Opin Chem Biol , vol.10 , pp. 498-508
    • Khersonsky, O.1    Roodveldt, C.2    Tawfik, D.S.3
  • 52
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA. (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9: 646-652.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 53
    • 33745032291 scopus 로고    scopus 로고
    • Water mediation in protein folding and molecular recognition
    • Levy Y, Onuchic JN. (2006) Water mediation in protein folding and molecular recognition. Ann Rev Biophys and Biomol Struct 35: 389-415.
    • (2006) Ann Rev Biophys and Biomol Struct , vol.35 , pp. 389-415
    • Levy, Y.1    Onuchic, J.N.2
  • 55
    • 3042655537 scopus 로고    scopus 로고
    • Computational design of a biologically active enzyme
    • Dwyer MA, Looger LL, Hellinga HW. (2004) Computational design of a biologically active enzyme. Science 304: 1967-1971.
    • (2004) Science , vol.304 , pp. 1967-1971
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 56
    • 9144232912 scopus 로고    scopus 로고
    • UniProt: Rhe universal protein knowledgebase
    • Apweiler R, Bairoch A, Wu CH, et al. (2004) UniProt: Rhe universal protein knowledgebase. Nucl Acids Res 32: 115.
    • (2004) Nucl Acids Res , vol.32 , pp. 115
    • Apweiler, R.1    Bairoch, A.2    Wu, C.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.