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Volumn 366, Issue 3, 2007, Pages 945-953

Local Encoding of Computationally Designed Enzyme Activity

Author keywords

enzyme design; isomerase; periplasmic binding proteins; protein design; triose phosphate

Indexed keywords

BACTERIAL PROTEIN; BINDING PROTEIN;

EID: 33846598755     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.12.002     Document Type: Article
Times cited : (10)

References (53)
  • 1
    • 0035543093 scopus 로고    scopus 로고
    • The depth of chemical time and the power of enzymes as catalysts
    • Wolfenden R., and Snider M.J. The depth of chemical time and the power of enzymes as catalysts. Acc. Chem. Res. 34 (2001) 938-945
    • (2001) Acc. Chem. Res. , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 2
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • Benkovic S.J., and Hammes-Schiffer S. A perspective on enzyme catalysis. Science 301 (2003) 1196-1202
    • (2003) Science , vol.301 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 3
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: analysis by modern rate theory and computer simulations
    • Garcia-Viloca M., Gao J., Karplus M., and Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 4
    • 27544501461 scopus 로고    scopus 로고
    • Understanding nature's catalytic toolkit
    • Gutteridge A., and Thornton J.M. Understanding nature's catalytic toolkit. Trends Biochem. Sci. 30 (2005) 622-629
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 622-629
    • Gutteridge, A.1    Thornton, J.M.2
  • 5
    • 14744305761 scopus 로고    scopus 로고
    • Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families
    • Torrance J.W., Bartlett G.J., Porter C.T., and Thornton J.M. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J. Mol. Biol. 347 (2005) 565-581
    • (2005) J. Mol. Biol. , vol.347 , pp. 565-581
    • Torrance, J.W.1    Bartlett, G.J.2    Porter, C.T.3    Thornton, J.M.4
  • 6
    • 0033791659 scopus 로고    scopus 로고
    • Critical analysis of antibody catalysis
    • Hilvert D. Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69 (2000) 751-793
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 751-793
    • Hilvert, D.1
  • 7
    • 0034534874 scopus 로고    scopus 로고
    • Catalytic antibodies and other biomimetic catalysts
    • Stevenson J.D., and Thomas N.R. Catalytic antibodies and other biomimetic catalysts. Nature Prod. Rep. 17 (2000) 535-577
    • (2000) Nature Prod. Rep. , vol.17 , pp. 535-577
    • Stevenson, J.D.1    Thomas, N.R.2
  • 9
    • 3042655537 scopus 로고    scopus 로고
    • Computational design of a biologically active enzyme
    • Dwyer M.A., Looger L.L., and Hellinga H.W. Computational design of a biologically active enzyme. Science 304 (2004) 1967-1971
    • (2004) Science , vol.304 , pp. 1967-1971
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 10
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon D.N., and Mayo S.L. Enzyme-like proteins by computational design. Proc. Natl Acad. Sci. USA 98 (2001) 14274-14279
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 13
    • 31544477181 scopus 로고    scopus 로고
    • Design and evolution of new catalytic activity with an existing protein scaffold
    • Park H.S., Nam S.H., Lee J.K., Yoon C.N., Mannervik B., Benkovic S.J., and Kim H.S. Design and evolution of new catalytic activity with an existing protein scaffold. Science 311 (2006) 535-538
    • (2006) Science , vol.311 , pp. 535-538
    • Park, H.S.1    Nam, S.H.2    Lee, J.K.3    Yoon, C.N.4    Mannervik, B.5    Benkovic, S.J.6    Kim, H.S.7
  • 14
    • 0030978103 scopus 로고    scopus 로고
    • Construction of a catalytically active iron superoxide dismutase by rational protein design
    • Pinto A.L., Hellinga H.W., and Caradonna J.P. Construction of a catalytically active iron superoxide dismutase by rational protein design. Proc. Natl Acad. Sci. USA 94 (1997) 5562-5567
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 5562-5567
    • Pinto, A.L.1    Hellinga, H.W.2    Caradonna, J.P.3
  • 15
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman
    • Allert M., Rizk S.S., Looger L.L., and Hellinga H.W. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc. Natl Acad. Sci. USA 101 (2004) 7907-7912
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7907-7912
    • Allert, M.1    Rizk, S.S.2    Looger, L.L.3    Hellinga, H.W.4
  • 16
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger L.L., Dwyer M.A., Smith J.J., and Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 423 (2003) 185-190
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 17
    • 0025763437 scopus 로고
    • Enzyme catalysis: not different, just better
    • Knowles J.R. Enzyme catalysis: not different, just better. Nature 350 (1991) 121-124
    • (1991) Nature , vol.350 , pp. 121-124
    • Knowles, J.R.1
  • 18
    • 0022555850 scopus 로고
    • Mutants in glucose metabolism
    • Fraenkel D.G. Mutants in glucose metabolism. Annu. Rev. Biochem. 55 (1986) 317-337
    • (1986) Annu. Rev. Biochem. , vol.55 , pp. 317-337
    • Fraenkel, D.G.1
  • 19
    • 70449257873 scopus 로고
    • The mechanism of the triosephosphate isomerase reaction
    • Rieder S.V., and Rose I.A. The mechanism of the triosephosphate isomerase reaction. J. Biol. Chem. 234 (1959) 1007-1010
    • (1959) J. Biol. Chem. , vol.234 , pp. 1007-1010
    • Rieder, S.V.1    Rose, I.A.2
  • 20
    • 0037422593 scopus 로고    scopus 로고
    • Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2 Å resolution
    • Jogl G., Rozovsky S., McDermott A.E., and Tong L. Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2 Å resolution. Proc. Natl Acad. Sci. USA 100 (2003) 50-55
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 50-55
    • Jogl, G.1    Rozovsky, S.2    McDermott, A.E.3    Tong, L.4
  • 22
    • 0028296717 scopus 로고
    • Triosephosphate isomerase requires a positively charged active site: the role of lysine-12
    • Lodi P.J., Chang L.C., Knowles J.R., and Komives E.A. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry 33 (1994) 2809-2814
    • (1994) Biochemistry , vol.33 , pp. 2809-2814
    • Lodi, P.J.1    Chang, L.C.2    Knowles, J.R.3    Komives, E.A.4
  • 23
    • 0028279839 scopus 로고
    • Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid
    • Joseph-McCarthy D., Rost L.E., Komives E.A., and Petsko G.A. Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid. Biochemistry 33 (1994) 2824-2829
    • (1994) Biochemistry , vol.33 , pp. 2824-2829
    • Joseph-McCarthy, D.1    Rost, L.E.2    Komives, E.A.3    Petsko, G.A.4
  • 24
    • 0034801822 scopus 로고    scopus 로고
    • Triosephosphate isomerase: a theoretical comparison of alternative pathways
    • Cui Q., and Karplus M. Triosephosphate isomerase: a theoretical comparison of alternative pathways. J. Am. Chem. Soc. 123 (2001) 2284-2290
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 2284-2290
    • Cui, Q.1    Karplus, M.2
  • 25
    • 1442277682 scopus 로고    scopus 로고
    • Computational modeling of the catalytic reaction in triosephosphate isomerase
    • Guallar V., Jacobson M., McDermott A., and Friesner R.A. Computational modeling of the catalytic reaction in triosephosphate isomerase. J. Mol. Biol. 337 (2004) 227-239
    • (2004) J. Mol. Biol. , vol.337 , pp. 227-239
    • Guallar, V.1    Jacobson, M.2    McDermott, A.3    Friesner, R.A.4
  • 26
    • 0026335211 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry
    • Hellinga H.W., and Richards F.M. Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. J. Mol. Biol. 222 (1991) 763-785
    • (1991) J. Mol. Biol. , vol.222 , pp. 763-785
    • Hellinga, H.W.1    Richards, F.M.2
  • 27
    • 0026321752 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin
    • Hellinga H.W., Caradonna J.P., and Richards F.M. Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J. Mol. Biol. 222 (1991) 787-803
    • (1991) J. Mol. Biol. , vol.222 , pp. 787-803
    • Hellinga, H.W.1    Caradonna, J.P.2    Richards, F.M.3
  • 28
    • 0036112438 scopus 로고    scopus 로고
    • A complete sequence of the T. tengcongensis genome
    • Bao Q., Tian Y., Li W., Xu Z., Xuan Z., Hu S., et al. A complete sequence of the T. tengcongensis genome. Genome Res. 12 (2002) 689-700
    • (2002) Genome Res. , vol.12 , pp. 689-700
    • Bao, Q.1    Tian, Y.2    Li, W.3    Xu, Z.4    Xuan, Z.5    Hu, S.6
  • 29
    • 0027112289 scopus 로고
    • 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli
    • Mowbray S.L., and Cole L.B. 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J. Mol. Biol. 225 (1992) 155-175
    • (1992) J. Mol. Biol. , vol.225 , pp. 155-175
    • Mowbray, S.L.1    Cole, L.B.2
  • 31
    • 0022423881 scopus 로고
    • Reaction of triosephosphate isomerase with L-glyceraldehyde 3-phosphate and triose 1,2-enediol 3-phosphate
    • Richard J.P. Reaction of triosephosphate isomerase with L-glyceraldehyde 3-phosphate and triose 1,2-enediol 3-phosphate. Biochemistry 24 (1985) 949-953
    • (1985) Biochemistry , vol.24 , pp. 949-953
    • Richard, J.P.1
  • 32
    • 0015951899 scopus 로고
    • An activated intermediate analogue. The use of phosphoglycolohydroxamate as a stable analogue of a transiently occurring dihydroxyacetone phosphate-derived enolate in enzymatic catalysis
    • Collins K.D. An activated intermediate analogue. The use of phosphoglycolohydroxamate as a stable analogue of a transiently occurring dihydroxyacetone phosphate-derived enolate in enzymatic catalysis. J. Biol. Chem. 249 (1974) 136-142
    • (1974) J. Biol. Chem. , vol.249 , pp. 136-142
    • Collins, K.D.1
  • 33
    • 0015394088 scopus 로고
    • pH-dependence of the triose phosphate isomerase reaction
    • Plaut B., and Knowles J.R. pH-dependence of the triose phosphate isomerase reaction. Biochem. J. 129 (1972) 311-320
    • (1972) Biochem. J. , vol.129 , pp. 311-320
    • Plaut, B.1    Knowles, J.R.2
  • 34
    • 0023705796 scopus 로고
    • Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli
    • Nickbarg E.B., and Knowles J.R. Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli. Biochemistry 27 (1988) 5939-5947
    • (1988) Biochemistry , vol.27 , pp. 5939-5947
    • Nickbarg, E.B.1    Knowles, J.R.2
  • 35
    • 0000468730 scopus 로고    scopus 로고
    • Binding energy and catalysis: the implications for transition-state analogs and catalytic antibodies
    • Mader M.M., and Bartlett P.A. Binding energy and catalysis: the implications for transition-state analogs and catalytic antibodies. Chem. Rev. 97 (1997) 1281-1302
    • (1997) Chem. Rev. , vol.97 , pp. 1281-1302
    • Mader, M.M.1    Bartlett, P.A.2
  • 36
    • 4143115810 scopus 로고    scopus 로고
    • Periplasmic binding proteins: a versatile superfamily for protein engineering
    • Dwyer M.A., and Hellinga H.W. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 14 (2004) 495-504
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 495-504
    • Dwyer, M.A.1    Hellinga, H.W.2
  • 37
    • 0242331659 scopus 로고    scopus 로고
    • The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
    • Millet O., Hudson R.P., and Kay L.E. The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc. Natl Acad. Sci. USA 100 (2003) 12700-12705
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12700-12705
    • Millet, O.1    Hudson, R.P.2    Kay, L.E.3
  • 38
    • 0034863015 scopus 로고    scopus 로고
    • Manipulation of ligand binding affinity by exploitation of conformational coupling
    • Marvin J.S., and Hellinga H.W. Manipulation of ligand binding affinity by exploitation of conformational coupling. Nature Struct. Biol. 8 (2001) 795-798
    • (2001) Nature Struct. Biol. , vol.8 , pp. 795-798
    • Marvin, J.S.1    Hellinga, H.W.2
  • 39
    • 4744369286 scopus 로고    scopus 로고
    • Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody
    • Midelfort K.S., Hernandez H.H., Lippow S.M., Tidor B., Drennan C.L., and Wittrup K.D. Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. J. Mol. Biol. 343 (2004) 685-701
    • (2004) J. Mol. Biol. , vol.343 , pp. 685-701
    • Midelfort, K.S.1    Hernandez, H.H.2    Lippow, S.M.3    Tidor, B.4    Drennan, C.L.5    Wittrup, K.D.6
  • 40
    • 0027717326 scopus 로고
    • Contribution of long-range electrostatic interactions to the stabilization of the catalytic transition state of the serine protease subtilisin BPN′
    • Jackson S.E., and Fersht A.R. Contribution of long-range electrostatic interactions to the stabilization of the catalytic transition state of the serine protease subtilisin BPN′. Biochemistry 32 (1993) 13909-13916
    • (1993) Biochemistry , vol.32 , pp. 13909-13916
    • Jackson, S.E.1    Fersht, A.R.2
  • 41
    • 0037008011 scopus 로고    scopus 로고
    • Multiple conformational changes in enzyme catalysis
    • Hammes G.G. Multiple conformational changes in enzyme catalysis. Biochemistry 41 (2002) 8221-8228
    • (2002) Biochemistry , vol.41 , pp. 8221-8228
    • Hammes, G.G.1
  • 42
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr D.D., McElheny D., Dyson H.J., and Wright P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 44
    • 0027257747 scopus 로고
    • Long-range surface charge-charge interactions in proteins. Comparison of experimental results with calculations from a theoretical method
    • Loewenthal R., Sancho J., Reinikainen T., and Fersht A.R. Long-range surface charge-charge interactions in proteins. Comparison of experimental results with calculations from a theoretical method. J. Mol. Biol. 232 (1993) 574-583
    • (1993) J. Mol. Biol. , vol.232 , pp. 574-583
    • Loewenthal, R.1    Sancho, J.2    Reinikainen, T.3    Fersht, A.R.4
  • 45
    • 0036001159 scopus 로고    scopus 로고
    • Structural basis of perturbed pKa values of catalytic groups in enzyme active sites
    • Harris T.K., and Turner G.J. Structural basis of perturbed pKa values of catalytic groups in enzyme active sites. IUBMB Life 53 (2002) 85-98
    • (2002) IUBMB Life , vol.53 , pp. 85-98
    • Harris, T.K.1    Turner, G.J.2
  • 47
  • 48
    • 0014109212 scopus 로고
    • Spectroscopic determination of tryptophan and tyrosine in proteins
    • Edelhoch H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6 (1967) 1948-1954
    • (1967) Biochemistry , vol.6 , pp. 1948-1954
    • Edelhoch, H.1
  • 49
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
    • (1976) Anal. Biochem. , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 53
    • 0016754529 scopus 로고
    • The uncatalyzed rates of enolization of dihydroxyacetone phoshate and of glyceraldehyde 3-phosphate in neutral aqueous solution. The quantitative assessment of the effectiveness of an enzyme catalyst
    • Hall A., and Knowles J.R. The uncatalyzed rates of enolization of dihydroxyacetone phoshate and of glyceraldehyde 3-phosphate in neutral aqueous solution. The quantitative assessment of the effectiveness of an enzyme catalyst. Biochemistry 14 (1975) 4348-4353
    • (1975) Biochemistry , vol.14 , pp. 4348-4353
    • Hall, A.1    Knowles, J.R.2


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