메뉴 건너뛰기




Volumn 109, Issue 40, 2012, Pages 16179-16183

Engineering a model protein cavity to catalyze the Kemp elimination

Author keywords

Enzyme design; Model cavity

Indexed keywords

ARTICLE; CATALYSIS; ELIMINATION REACTION; ENZYME ACTIVITY; HYDROGEN BOND; HYDROPHOBICITY; KEMP ELIMINATION; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN STABILITY; REACTION ANALYSIS; REACTION OPTIMIZATION; SUBSTITUTION REACTION;

EID: 84867093396     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1208076109     Document Type: Article
Times cited : (51)

References (41)
  • 1
    • 5644287368 scopus 로고    scopus 로고
    • Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation miningminima algorithm
    • Chang CE, Gilson MK (2004) Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation miningminima algorithm. J Am Chem Soc 126:13156-13164.
    • (2004) J Am Chem Soc , vol.126 , pp. 13156-13164
    • Chang, C.E.1    Gilson, M.K.2
  • 2
    • 0000496129 scopus 로고
    • Cyclophane chemistry - Bent and battered benzene rings
    • Cram DJ, Cram JM (1971) Cyclophane chemistry - Bent and battered benzene rings. Acc Chem Res 4:204-213.
    • (1971) Acc Chem Res , vol.4 , pp. 204-213
    • Cram, D.J.1    Cram, J.M.2
  • 3
    • 0026509036 scopus 로고
    • A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
    • Eriksson AE, Baase WA, Wozniak JA, Matthews BW (1992) A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355:371-373.
    • (1992) Nature , vol.355 , pp. 371-373
    • Eriksson, A.E.1    Baase, W.A.2    Wozniak, J.A.3    Matthews, B.W.4
  • 6
    • 70349135928 scopus 로고    scopus 로고
    • Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme
    • Liu LJ, Baase WA, Michael MM, Matthews BW (2009) Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme. Biochemistry 48:8842-8851.
    • (2009) Biochemistry , vol.48 , pp. 8842-8851
    • Liu, L.J.1    Baase, W.A.2    Michael, M.M.3    Matthews, B.W.4
  • 7
    • 56749170877 scopus 로고    scopus 로고
    • Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination
    • Alexandrova AN, Rothlisberger D, Baker D, Jorgensen WL (2008) Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J Am Chem Soc 130:15907-15915.
    • (2008) J Am Chem Soc , vol.130 , pp. 15907-15915
    • Alexandrova, A.N.1    Rothlisberger, D.2    Baker, D.3    Jorgensen, W.L.4
  • 8
    • 33847731021 scopus 로고    scopus 로고
    • Computational protein design promises to revolutionize protein engineering
    • Alvizo O, Allen BD, Mayo SL (2007) Computational protein design promises to revolutionize protein engineering. Biotechniques 42:31-39.
    • (2007) Biotechniques , vol.42 , pp. 31-39
    • Alvizo, O.1    Allen, B.D.2    Mayo, S.L.3
  • 9
    • 75449116384 scopus 로고    scopus 로고
    • Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions
    • Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142-151.
    • (2010) Acc Chem Res , vol.43 , pp. 142-151
    • Acevedo, O.1    Jorgensen, W.L.2
  • 10
    • 79953310914 scopus 로고    scopus 로고
    • Optimizing non-natural protein function with directed evolution
    • Brustad EM, Arnold FH (2011) Optimizing non-natural protein function with directed evolution. Curr Opin Chem Biol 15:201-210.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 201-210
    • Brustad, E.M.1    Arnold, F.H.2
  • 11
    • 78049316762 scopus 로고    scopus 로고
    • Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
    • Frushicheva MP, Cao J, Chu ZT, Warshel A (2010) Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc Natl Acad Sci USA 107:16869-16874.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 16869-16874
    • Frushicheva, M.P.1    Cao, J.2    Chu, Z.T.3    Warshel, A.4
  • 12
    • 79955625862 scopus 로고    scopus 로고
    • Challenges and advances in validating enzyme design proposals: The case of Kemp eliminase catalysis
    • Frushicheva MP, Cao J, Warshel A (2011) Challenges and advances in validating enzyme design proposals: The case of Kemp eliminase catalysis. Biochemistry 50:3849-3858.
    • (2011) Biochemistry , vol.50 , pp. 3849-3858
    • Frushicheva, M.P.1    Cao, J.2    Warshel, A.3
  • 13
    • 77957316716 scopus 로고    scopus 로고
    • An exciting but challenging road ahead for computational enzyme design
    • Baker D (2010) An exciting but challenging road ahead for computational enzyme design. Protein Sci 19:1817-1819.
    • (2010) Protein Sci , vol.19 , pp. 1817-1819
    • Baker, D.1
  • 14
    • 77649271939 scopus 로고    scopus 로고
    • Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series
    • Khersonsky O, et al. (2010) Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. J Mol Biol 396:1025-1042.
    • (2010) J Mol Biol , vol.396 , pp. 1025-1042
    • Khersonsky, O.1
  • 15
    • 77950437360 scopus 로고    scopus 로고
    • Origins of catalysis by computationally designed retroaldolase enzymes
    • Lassila JK, Baker D, Herschlag D (2010) Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci USA 107:4937-4942.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 4937-4942
    • Lassila, J.K.1    Baker, D.2    Herschlag, D.3
  • 16
    • 0028869408 scopus 로고
    • Large rate accelerations in antibody catalysis by strategic use of haptenic charge
    • Thorn SN, Daniels RG, Auditor MT, Hilvert D (1995) Large rate accelerations in antibody catalysis by strategic use of haptenic charge. Nature 373:228-230.
    • (1995) Nature , vol.373 , pp. 228-230
    • Thorn, S.N.1    Daniels, R.G.2    Auditor, M.T.3    Hilvert, D.4
  • 17
    • 43449098518 scopus 로고    scopus 로고
    • Kemp elimination catalysts by computational enzyme design
    • Rothlisberger D, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-194.
    • (2008) Nature , vol.453 , pp. 190-194
    • Rothlisberger, D.1
  • 18
    • 79955570791 scopus 로고    scopus 로고
    • Design of a switchable eliminase
    • Korendovych IV, et al. (2011) Design of a switchable eliminase. Proc Natl Acad Sci USA 108:6823-6827.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 6823-6827
    • Korendovych, I.V.1
  • 19
    • 17044431448 scopus 로고    scopus 로고
    • Structural origins of efficient proton abstraction from carbon by a catalytic antibody
    • Debler EW, et al. (2005) Structural origins of efficient proton abstraction from carbon by a catalytic antibody. Proc Natl Acad Sci USA 102:4984-4989.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4984-4989
    • Debler, E.W.1
  • 20
    • 84863230018 scopus 로고    scopus 로고
    • Iterative approach to computational enzyme design
    • Privett HK, et al. (2012) Iterative approach to computational enzyme design. Proc Natl Acad Sci USA 109:3790-3795.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 3790-3795
    • Privett, H.K.1
  • 21
    • 79952437832 scopus 로고    scopus 로고
    • Optimization of the in-silico-designed Kemp eliminase KE70 by computational design and directed evolution
    • Khersonsky O, et al. (2011) Optimization of the in-silico-designed Kemp eliminase KE70 by computational design and directed evolution. J Mol Biol 407:391-412.
    • (2011) J Mol Biol , vol.407 , pp. 391-412
    • Khersonsky, O.1
  • 22
    • 0001348193 scopus 로고
    • Physical organic-chemistry of benzisoxazoles. 1. Mechanism of base-catalyzed decomposition of benzisoxazoles
    • Casey ML, Kemp DS, Paul KG, Cox DD (1973) Physical organic-chemistry of benzisoxazoles. 1. Mechanism of base-catalyzed decomposition of benzisoxazoles. J Org Chem 38:2294-2301.
    • (1973) J Org Chem , vol.38 , pp. 2294-2301
    • Casey, M.L.1    Kemp, D.S.2    Paul, K.G.3    Cox, D.D.4
  • 23
    • 0029793086 scopus 로고    scopus 로고
    • Off-the-shelf proteins that rival tailor-made antibodies as catalysts
    • DOI 10.1038/383060a0
    • Hollfelder F, Kirby AJ, Tawfik DS (1996) Off-the-shelf proteins that rival tailor-made antibodies as catalysts. Nature 383:60-63. (Pubitemid 26296457)
    • (1996) Nature , vol.383 , Issue.6595 , pp. 60-63
    • Hollfelder, F.1    Kirby, A.J.2    Tawfik, D.S.3
  • 26
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • DOI 10.1093/nar/gkl282
    • Dundas J, et al. (2006) CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34:W116-W118. (Pubitemid 44529746)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Dundas, J.1    Ouyang, Z.2    Tseng, J.3    Binkowski, A.4    Turpaz, Y.5    Liang, J.6
  • 27
    • 0036121221 scopus 로고    scopus 로고
    • Structural milestones in the reaction pathway of an amide hydrolase: Substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase
    • DOI 10.1016/S0969-2126(02)00725-6, PII S0969212602007256
    • Beadle BM, Trehan I, Focia PJ, Shoichet BK (2002) Structural milestones in the reaction pathway of an amide hydrolase: Substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure 10:413-424. (Pubitemid 34230628)
    • (2002) Structure , vol.10 , Issue.3 , pp. 413-424
    • Beadle, B.M.1    Trehan, I.2    Focia, P.J.3    Shoichet, B.K.4
  • 28
    • 0036384211 scopus 로고    scopus 로고
    • Structural bases of stability-function tradeoffs in enzymes
    • Beadle BM, Shoichet BK (2002) Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 321:285-296.
    • (2002) J Mol Biol , vol.321 , pp. 285-296
    • Beadle, B.M.1    Shoichet, B.K.2
  • 30
    • 0028774340 scopus 로고
    • Stability and function - 2 constraints in the evolution of barstar and other proteins
    • Schreiber C, Buckle AM, Fersht AR (1994) Stability and function - 2 constraints in the evolution of barstar and other proteins. Structure 2:945-951.
    • (1994) Structure , vol.2 , pp. 945-951
    • Schreiber, C.1    Buckle, A.M.2    Fersht, A.R.3
  • 32
    • 0036295508 scopus 로고    scopus 로고
    • Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
    • DOI 10.1016/S0022-2836(02)00400-X
    • Wang XJ, Minasov G, Shoichet BK (2002) Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320:85-95. (Pubitemid 34722236)
    • (2002) Journal of Molecular Biology , vol.320 , Issue.1 , pp. 85-95
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 33
    • 61949243531 scopus 로고    scopus 로고
    • Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination
    • Alexandrova AN, Jorgensen WL (2009) Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination. J Phys Chem B 113:497-504.
    • (2009) J Phys Chem B , vol.113 , pp. 497-504
    • Alexandrova, A.N.1    Jorgensen, W.L.2
  • 35
    • 84863000087 scopus 로고    scopus 로고
    • Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
    • Khersonsky O, et al. (2012) Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci USA 109:10358-10363.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 10358-10363
    • Khersonsky, O.1
  • 36
    • 0024278562 scopus 로고
    • Evaluation of catalytic free-energies in genetically modified proteins
    • Warshel A, Sussman F, Hwang JK (1988) Evaluation of catalytic free-energies in genetically modified proteins. J Mol Biol 201:139-159.
    • (1988) J Mol Biol , vol.201 , pp. 139-159
    • Warshel, A.1    Sussman, F.2    Hwang, J.K.3
  • 37
    • 0000230329 scopus 로고
    • Energetics of enzyme catalysis
    • Warshel A (1978) Energetics of enzyme catalysis. Proc Natl Acad Sci USA 75:5250-5254.
    • (1978) Proc Natl Acad Sci USA , vol.75 , pp. 5250-5254
    • Warshel, A.1
  • 38
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struc Biol 19:596-604.
    • (2009) Curr Opin Struc Biol , vol.19 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 39
    • 70349832423 scopus 로고    scopus 로고
    • Following evolutionary paths to protein-protein interactions with high affinity and selectivity
    • Levin KB, et al. (2009) Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nat Struct Mol Biol 16:1049-1067.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 1049-1067
    • Levin, K.B.1
  • 40
    • 74649086461 scopus 로고    scopus 로고
    • Structural bases for stability-function tradeoffs in antibiotic resistance
    • Thomas VL, McReynolds AC, Shoichet BK (2010) Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol 396:47-59.
    • (2010) J Mol Biol , vol.396 , pp. 47-59
    • Thomas, V.L.1    McReynolds, A.C.2    Shoichet, B.K.3
  • 41
    • 0020345697 scopus 로고
    • Buffers of constant ionic-strength for studying pH-dependent processes
    • Ellis KJ, Morrison JF (1982) Buffers of constant ionic-strength for studying pH-dependent processes. Method Enzymol 87:405-426.
    • (1982) Method Enzymol , vol.87 , pp. 405-426
    • Ellis, K.J.1    Morrison, J.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.