메뉴 건너뛰기




Volumn 9, Issue 8, 2013, Pages 494-498

Evolution of a designed retro-aldolase leads to complete active site remodeling

Author keywords

[No Author keywords available]

Indexed keywords

FRUCTOSE BISPHOSPHATE ALDOLASE; LYSINE; SCHIFF BASE;

EID: 84880920662     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1276     Document Type: Article
Times cited : (209)

References (41)
  • 1
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon, D.N. & Mayo, S.L. Enzyme-like proteins by computational design. Proc. Natl. Acad. Sci. USA 98, 14274-14279 (2001
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 2
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387-1391 (2008
    • (2008) Science , vol.319 , pp. 1387-1391
    • Jiang, L.1
  • 3
    • 43449098518 scopus 로고    scopus 로고
    • Kemp elimination catalysts by computational enzyme design
    • Röthlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190-195 (2008
    • (2008) Nature , vol.453 , pp. 190-195
    • Röthlisberger, D.1
  • 4
    • 84863230018 scopus 로고    scopus 로고
    • Iterative approach to computational enzyme design
    • Privett, H.K. et al. Iterative approach to computational enzyme design. Proc. Natl. Acad. Sci. USA 109, 3790-3795 (2012
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 3790-3795
    • Privett, H.K.1
  • 5
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel, J.B. et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329, 309-313 (2010
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1
  • 7
    • 84860115640 scopus 로고    scopus 로고
    • Robust design and optimization of retroaldol enzymes
    • Althoff, E.A. et al. Robust design and optimization of retroaldol enzymes. Protein Sci. 21, 717-726 (2012
    • (2012) Protein Sci , vol.21 , pp. 717-726
    • Althoff, E.A.1
  • 8
    • 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. 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
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 10358-10363
    • Khersonsky, O.1
  • 9
    • 0029444684 scopus 로고
    • Class I aldolases: Substrate specificity, mechanism, inhibitors and structural aspects
    • Gefflaut, T., Blonski, C., Perie, J. & Willson, M.l. Class I aldolases: Substrate specificity, mechanism, inhibitors and structural aspects. Prog. Biophys. Mol. Biol. 63, 301-340 (1995
    • (1995) Prog. Biophys. Mol. Biol , vol.63 , pp. 301-340
    • Gefflaut, T.1    Blonski, C.2    Perie, J.3    Willson, M.L.4
  • 10
    • 77950437360 scopus 로고    scopus 로고
    • Origins of catalysis by computationally designed retroaldolase enzymes
    • Lassila, J.K., Baker, D. & Herschlag, D. Origins of catalysis by computationally designed retroaldolase enzymes. Proc. Natl. Acad. Sci. USA 107, 4937-4942 (2010
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 4937-4942
    • Lassila, J.K.1    Baker, D.2    Herschlag, D.3
  • 11
    • 84855858058 scopus 로고    scopus 로고
    • Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design
    • Wang, L. et al. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. J. Mol. Biol. 415, 615-625 (2012
    • (2012) J. Mol. Biol , vol.415 , pp. 615-625
    • Wang, L.1
  • 13
    • 0026023382 scopus 로고
    • Polyamino-β-cyclodextrin as a model of aldolase
    • Tagaki, W. & Yamamoto, H. Polyamino-β-cyclodextrin as a model of aldolase. Tetrahedr. Lett. 32, 1207-1208 (1991
    • (1991) Tetrahedr. Lett , vol.32 , pp. 1207-1208
    • Tagaki, W.1    Yamamoto, H.2
  • 14
    • 18844456318 scopus 로고    scopus 로고
    • Development of small designer aldolase enzymes: Catalytic activity, folding, and substrate specificity
    • Tanaka, F., Fuller, R. & Barbas, C.F. III. Development of small designer aldolase enzymes: Catalytic activity, folding, and substrate specificity. Biochemistry 44, 7583-7592 (2005
    • (2005) Biochemistry , vol.44 , pp. 7583-7592
    • Tanaka, F.1    Fuller, R.2    Barbas III, C.F.3
  • 17
    • 0035148643 scopus 로고    scopus 로고
    • Directed evolution of a new catalytic site in 2-keto-3-deoxy-6- phosphogluconate aldolase from Escherichia coli
    • Wymer, N. et al. Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli. Structure 9, 1-9 (2001
    • (2001) Structure , vol.9 , pp. 1-9
    • Wymer, N.1
  • 18
    • 0035850820 scopus 로고    scopus 로고
    • Observation of covalent intermediates in an enzyme mechanism at atomic resolution
    • Heine, A. et al. Observation of covalent intermediates in an enzyme mechanism at atomic resolution. Science 294, 369-374 (2001
    • (2001) Science , vol.294 , pp. 369-374
    • Heine, A.1
  • 19
    • 0002694056 scopus 로고
    • A method For random mutagenesis of a defined DNA segment using a modified polymerase chain reaction
    • Leung, D.W., Chen, E. & Goeddel, D.V. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1, 11-15 (1989
    • (1989) Technique , vol.1 , pp. 11-15
    • Leung, D.W.1    Chen, E.2    Goeddel, D.V.3
  • 20
    • 0028110130 scopus 로고
    • DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution
    • Stemmer, W.P. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10747-10751 (1994
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10747-10751
    • Stemmer, W.P.1
  • 21
    • 0031457319 scopus 로고    scopus 로고
    • Immune versus natural selection: Antibody aldolases with enzymic rates but broader scope
    • Barbas, C.F. et al. Immune versus natural selection: Antibody aldolases with enzymic rates but broader scope. Science 278, 2085-2092 (1997
    • (1997) Science , vol.278 , pp. 2085-2092
    • Barbas, C.F.1
  • 22
    • 0037032455 scopus 로고    scopus 로고
    • Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance
    • Esposito, G. et al. Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance. FEBS Lett. 531, 152-156 (2002
    • (2002) FEBS Lett , vol.531 , pp. 152-156
    • Esposito, G.1
  • 23
    • 84865405490 scopus 로고    scopus 로고
    • Comparison of designed and randomly generated catalysts for simple chemical reactions
    • Kipnis, Y. & Baker, D. Comparison of designed and randomly generated catalysts for simple chemical reactions. Protein Sci. 21, 1388-1395 (2012
    • (2012) Protein Sci , vol.21 , pp. 1388-1395
    • Kipnis, Y.1    Baker, D.2
  • 24
    • 66349123522 scopus 로고    scopus 로고
    • Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase
    • St-Jean, M., Blonski, C. & Sygusch, J. Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase. Biochemistry 48, 4528-4537 (2009
    • (2009) Biochemistry , vol.48 , pp. 4528-4537
    • St-Jean, M.1    Blonski, C.2    Sygusch, J.3
  • 25
    • 0028606741 scopus 로고
    • Antibody-antigen interactions: New structures and new conformational changes
    • Wilson, I.A. & Stanfield, R.L. Antibody-antigen interactions: New structures and new conformational changes. Curr. Opin. Struct. Biol. 4, 857-867 (1994
    • (1994) Curr. Opin. Struct. Biol , vol.4 , pp. 857-867
    • Wilson, I.A.1    Stanfield, R.L.2
  • 26
    • 1542408991 scopus 로고    scopus 로고
    • Structural mechanism for affinity maturation of an anti-lysozyme antibody
    • Cauerhff, A., Goldbaum, F.A. & Braden, B.C. Structural mechanism for affinity maturation of an anti-lysozyme antibody. Proc. Natl. Acad. Sci. USA 101, 3539-3544 (2004
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 3539-3544
    • Cauerhff, A.1    Goldbaum, F.A.2    Braden, B.C.3
  • 27
    • 70349632843 scopus 로고    scopus 로고
    • The influence of protein dynamics on the success of computational enzyme design
    • Ruscio, J.Z., Kohn, J.E., Ball, K.A. & Head-Gordon, T. The influence of protein dynamics on the success of computational enzyme design. J. Am. Chem. Soc. 131, 14111-14115 (2009
    • (2009) J. Am. Chem. Soc , vol.131 , pp. 14111-14115
    • Ruscio, J.Z.1    Kohn, J.E.2    Ball, K.A.3    Head-Gordon, T.4
  • 28
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki, N. & Tawfik, D.S. Protein dynamism and evolvability. Science 324, 203-207 (2009
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 29
    • 0030667789 scopus 로고    scopus 로고
    • Understanding enzyme superfamilies Chemistry as the fundamental determinant in the evolution of new catalytic activities
    • Babbitt, P.C. & Gerlt, J.A. Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272, 30591-30594 (1997
    • (1997) J. Biol. Chem , vol.272 , pp. 30591-30594
    • Babbitt, P.C.1    Gerlt, J.A.2
  • 30
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364-1368 (2003
    • (2003) Science , vol.302 , pp. 1364-1368
    • Kuhlman, B.1
  • 31
    • 33751525692 scopus 로고    scopus 로고
    • New algorithms and an in silico benchmark for computational enzyme design
    • Zanghellini, A. et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 15, 2785-2794 (2006
    • (2006) Protein Sci , vol.15 , pp. 2785-2794
    • Zanghellini, A.1
  • 32
    • 2542563521 scopus 로고    scopus 로고
    • Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution
    • Neylon, C. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution. Nucleic Acids Res. 32, 1448-1459 (2004
    • (2004) Nucleic Acids Res , vol.32 , pp. 1448-1459
    • Neylon, C.1
  • 33
    • 0024520745 scopus 로고
    • Site-directed mutagenesis by overlap extension using the polymerase chain-reaction
    • Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K. & Pease, L.R. Site-directed mutagenesis by overlap extension using the polymerase chain-reaction. Gene 77, 51-59 (1989
    • (1989) Gene , vol.77 , pp. 51-59
    • Ho, S.N.1    Hunt, H.D.2    Horton, R.M.3    Pullen, J.K.4    Pease, L.R.5
  • 35
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007
    • (2007) J. Appl. Crystallogr , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 36
    • 0036308014 scopus 로고    scopus 로고
    • The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product
    • Hennig, M., Darimont, B.D., Jansonius, J.N. & Kirschner, K. The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product. J. Mol. Biol. 319, 757-766 (2002
    • (2002) J. Mol. Biol , vol.319 , pp. 757-766
    • Hennig, M.1    Darimont, B.D.2    Jansonius, J.N.3    Kirschner, K.4
  • 37
    • 11844301261 scopus 로고    scopus 로고
    • Recent developments in the PHENIX software for automated crystallographic structure determination
    • Adams, P.D. et al. Recent developments in the PHENIX software for automated crystallographic structure determination. J. Synchotron Radiat. 11, 53-55 (2004
    • (2004) J. Synchotron Radiat , vol.11 , pp. 53-55
    • Adams, P.D.1
  • 38
  • 39
    • 84861425552 scopus 로고    scopus 로고
    • Linking crystallographic model and data quality
    • Karplus, P.A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012
    • (2012) Science , vol.336 , pp. 1030-1033
    • Karplus, P.A.1    Diederichs, K.2
  • 40
    • 0032416718 scopus 로고    scopus 로고
    • Aldol sensors for the rapid generation of tunable fluorescence by antibody catalysis
    • List, B., Barbas, C.F. III & Lerner, R.A. Aldol sensors for the rapid generation of tunable fluorescence by antibody catalysis. Proc. Natl. Acad. Sci. USA 95, 15351-15355 (1998
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 15351-15355
    • List, B.1    Barbas III, C.F.2    Lerner, R.A.3
  • 41
    • 0034604430 scopus 로고    scopus 로고
    • An efficient benchtop system for multigram-scale kinetic resolutions using aldolase antibodies
    • Turner, J.M., Bui, T., Lerner, R.A., Barbas, C.F. III & List, B. An efficient benchtop system for multigram-scale kinetic resolutions using aldolase antibodies. Chemistry 6, 2772-2774 (2000
    • (2000) Chemistry , vol.6 , pp. 2772-2774
    • Turner, J.M.1    Bui, T.2    Lerner, R.A.3    Barbas III, C.F.4    List, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.