메뉴 건너뛰기




Volumn 109, Issue 10, 2012, Pages 3790-3795

Iterative approach to computational enzyme design

Author keywords

Computational protein design; De novo enzyme design; Proton transfer

Indexed keywords

AMINO ACID; ENZYME; HG 1 PROTEIN; HG 2 ENZYME; HG 3 PROTEIN; PROTEIN; SCAFFOLD PROTEIN; UNCLASSIFIED DRUG;

EID: 84863230018     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1118082108     Document Type: Article
Times cited : (272)

References (31)
  • 4
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel JB, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329:309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1
  • 5
    • 0029920337 scopus 로고    scopus 로고
    • Protein design automation
    • Dahiyat BI, Mayo SL (1996) Protein design automation. Protein Sci 5:895-903. (Pubitemid 26139177)
    • (1996) Protein Science , vol.5 , Issue.5 , pp. 895-903
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 6
    • 0033135227 scopus 로고    scopus 로고
    • Computational protein design
    • DOI 10.1016/S0969-2126(99)80062-8
    • Street AG, Mayo SL (1999) Computational protein design. Structure 7:R105-R109. (Pubitemid 29230480)
    • (1999) Structure , vol.7 , Issue.5
    • Street, A.G.1    Mayo, S.L.2
  • 8
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • Dahiyat BI, Gordon B, Mayo SL (1997) Automated design of the surface positions of protein helices. Protein Sci 6:1333-1337. (Pubitemid 27260167)
    • (1997) Protein Science , vol.6 , Issue.6 , pp. 1333-1337
    • Dahiyat, B.I.1    Benjamin, G.D.2    Mayo, S.L.3
  • 9
    • 33746546176 scopus 로고    scopus 로고
    • Simple electrostatic model improves designed protein sequences
    • DOI 10.1110/ps.062105506
    • Zollars ES, Marshall SA, Mayo SL (2006) Simple electrostatic model improves designed protein sequences. Protein Sci 15:2014-2018. (Pubitemid 44141520)
    • (2006) Protein Science , vol.15 , Issue.8 , pp. 2014-2018
    • Zollars, E.S.1    Marshall, S.A.2    Mayo, S.L.3
  • 10
    • 79956080813 scopus 로고    scopus 로고
    • Computational design of an endo-1,4-{beta}-xylanase ligand binding site
    • Morin A, et al. (2011) Computational design of an endo-1,4-{beta}- xylanase ligand binding site. Protein Eng Des Sel 24:503-516.
    • (2011) Protein Eng des Sel , vol.24 , pp. 503-516
    • Morin, A.1
  • 12
    • 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
  • 13
    • 33947086265 scopus 로고
    • Physical organic chemistry of benzisoxazoles. II. Linearity of the Broensted free energy relation for the base-catalyzed decomposition of benzisoxazoles
    • Kemp D, Casey M (1973) Physical organic chemistry of benzisoxazoles. II. Linearity of the Broensted free energy relation for the base-catalyzed decomposition of benzisoxazoles. J Am Chem Soc 95:6670-6680.
    • (1973) J Am Chem Soc , vol.95 , pp. 6670-6680
    • Kemp, D.1    Casey, M.2
  • 14
    • 0028869408 scopus 로고
    • Large rate accelerations in antibody catalysis by strategic use of haptenic charge
    • Thorn SN, Daniels RG, Auditor MM, 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.M.3    Hilvert, D.4
  • 15
    • 0035943306 scopus 로고    scopus 로고
    • Off-the-shelf proteins that rival tailor-made antibodies as catalysts
    • Hollfelder F, Kirby AJ, Tawfik DS (2001) Off-the-shelf proteins that rival tailor-made antibodies as catalysts. J Org Chem 66:5866-5874.
    • (2001) J Org Chem , vol.66 , pp. 5866-5874
    • Hollfelder, F.1    Kirby, A.J.2    Tawfik, D.S.3
  • 16
    • 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
  • 18
    • 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
    • 0001348193 scopus 로고
    • Physical organic chemistry of benzisoxazoles. I. Mechanism of the base-catalyzed decomposition of benzisoxazoles
    • Casey M, Kemp D, Paul K, Cox D (1973) Physical organic chemistry of benzisoxazoles. I. Mechanism of the base-catalyzed decomposition of benzisoxazoles. J Org Chem 38:2294-2301.
    • (1973) J Org Chem , vol.38 , pp. 2294-2301
    • Casey, M.1    Kemp, D.2    Paul, K.3    Cox, D.4
  • 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
    • 0037016451 scopus 로고    scopus 로고
    • The hydrogen bond in the solid state
    • Steiner T (2002) The hydrogen bond in the solid state. Angew Chem Int Ed 41:48-76.
    • (2002) Angew Chem Int Ed , vol.41 , pp. 48-76
    • Steiner, T.1
  • 23
    • 70349632843 scopus 로고    scopus 로고
    • The influence of protein dynamics on the success of computational enzyme design
    • Ruscio J, Kohn J, Ball K, Head-Gordon T (2009) The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc 131:14111-14115.
    • (2009) J Am Chem Soc , vol.131 , pp. 14111-14115
    • Ruscio, J.1    Kohn, J.2    Ball, K.3    Head-Gordon, T.4
  • 24
    • 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
    • DOI 10.1016/S0022-2836(02)00378-9
    • Hennig M, Darimont BD, Jansonius JN, Kirschner K (2002) The catalytic mechanism of indole-3-glycoerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product. J Mol Biol 319:757-766. (Pubitemid 34729448)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.3 , pp. 757-766
    • Hennig, M.1    Darimont, B.D.2    Jansonius, J.N.3    Kirschner, K.4
  • 25
    • 0034284955 scopus 로고    scopus 로고
    • Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion
    • Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M (2000) Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion. Science 289:1546-1550.
    • (2000) Science , vol.289 , pp. 1546-1550
    • Lang, D.1    Thoma, R.2    Henn-Sax, M.3    Sterner, R.4    Wilmanns, M.5
  • 26
    • 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
  • 27
    • 78650543850 scopus 로고    scopus 로고
    • Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries
    • Chica RA, Moore MM, Allen BD, Mayo SL (2010) Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries. Proc Natl Acad Sci USA 107:20257-20262.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 20257-20262
    • Chica, R.A.1    Moore, M.M.2    Allen, B.D.3    Mayo, S.L.4
  • 28
    • 0036643430 scopus 로고    scopus 로고
    • Fast and Accurate Side-Chain Topology and Energy Refinement (FASTER) as a new method for protein structure optimization
    • DOI 10.1002/prot.10131
    • Desmet J, Spriet J, Lasters I (2002) Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. Proteins 48:31-43. (Pubitemid 34595046)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.1 , pp. 31-43
    • Desmet, J.1    Spriet, J.2    Lasters, I.3
  • 29
    • 33745614865 scopus 로고    scopus 로고
    • Dramatic performance enhancements for the FASTER optimization algorithm
    • DOI 10.1002/jcc.20420
    • Allen BD, Mayo SL (2006) Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 27:1071-1075. (Pubitemid 43989799)
    • (2006) Journal of Computational Chemistry , vol.27 , Issue.10 , pp. 1071-1075
    • Allen, B.D.1    Mayo, S.L.2
  • 31
    • 0034625322 scopus 로고    scopus 로고
    • Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
    • Voigt CA, Gordon DB, Mayo SL (2000) Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J Mol Biol 299:789-803.
    • (2000) J Mol Biol , vol.299 , pp. 789-803
    • Voigt, C.A.1    Gordon, D.B.2    Mayo, S.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.