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Volumn 106, Issue 23, 2009, Pages 9215-9220

Alteration of enzyme specificity by computational loop remodeling and design

Author keywords

Computational protein design; Loop modeling

Indexed keywords

GUANINE DEAMINASE;

EID: 67249107701     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0811070106     Document Type: Article
Times cited : (113)

References (44)
  • 1
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • DOI 10.1126/science.278.5335.82
    • Dahiyat BI, Mayo SL (1997) De novo protein design: Fully automated sequence selection. Science 278:82-87. (Pubitemid 27446279)
    • (1997) Science , vol.278 , Issue.5335 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 2
    • 0345306764 scopus 로고    scopus 로고
    • Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
    • DOI 10.1126/science.1089427
    • Kuhlman B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368. (Pubitemid 37452172)
    • (2003) Science , vol.302 , Issue.5649 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5    Baker, D.6
  • 3
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • DOI 10.1038/nature01556
    • Looger LL, et al. (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190. (Pubitemid 36569543)
    • (2003) Nature , vol.423 , Issue.6936 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 8
    • 0023911111 scopus 로고
    • Reshaping human antibodies for therapy
    • DOI 10.1038/332323a0
    • Riechmann L, et al. (1988) Reshaping human antibodies for therapy. Nature 332:323-327. (Pubitemid 18091075)
    • (1988) Nature , vol.332 , Issue.6162 , pp. 323-327
    • Riechmann, L.1    Clark, M.2    Waldmann, H.3    Winter, G.4
  • 9
    • 0026520387 scopus 로고
    • Converting trypsin to chymotrypsin: The role of surface loops
    • Hedstrom L, et al. (1992) Converting trypsin to chymotrypsin: The role of surface loops. Science 255:1249-1253.
    • (1992) Science , vol.255 , pp. 1249-1253
    • Hedstrom, L.1
  • 12
    • 0024609784 scopus 로고
    • New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures
    • Mazur AK, Abagyan RA (1989) New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. J Biomol Struct Dyn 6:815-832.
    • (1989) J Biomol Struct Dyn , vol.6 , pp. 815-832
    • Mazur, A.K.1    Abagyan, R.A.2
  • 13
    • 33751118503 scopus 로고    scopus 로고
    • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    • DOI 10.1002/prot.21133
    • Bradley P, Baker D (2006) Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65:922-929. (Pubitemid 44772890)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.4 , pp. 922-929
    • Bradley, P.1    Baker, D.2
  • 16
    • 0028795530 scopus 로고
    • Transfer of the HSV-tk gene into donor peripheral blood lymphocytes for in vivo modulation of donor anti-tumor immunity after allogeneic bone marrow transplantation
    • Bordignon C, et al. (1995) Transfer of the HSV-tk gene into donor peripheral blood lymphocytes for in vivo modulation of donor anti-tumor immunity after allogeneic bone marrow transplantation. Hum Gene Ther 6:813-819.
    • (1995) Hum Gene Ther , vol.6 , pp. 813-819
    • Bordignon, C.1
  • 17
    • 0032505705 scopus 로고    scopus 로고
    • Herpes simplex virus thymidine kinase gene transfer for controlled graft-versus-host disease and graft-versus-leukemia: Clinical follow-up and improved new vectors
    • Verzeletti S, et al. (1998) Herpes simplex virus thymidine kinase gene transfer for controlled graft-versus-host disease and graft-versus-leukemia: Clinical follow-up and improved new vectors. Hum Gene Ther 9:2243-2251. (Pubitemid 28498010)
    • (1998) Human Gene Therapy , vol.9 , Issue.15 , pp. 2243-2251
    • Verzeletti, S.1    Bonini, C.2    Marktel, S.3    Nobili, N.4    Ciceri, F.5    Traversari, C.6    Bordignon, C.7
  • 18
    • 34347262648 scopus 로고    scopus 로고
    • Can graft-versus-leukemia reactivity be dissociated from graft-versus-host disease?
    • Sprangers B, et al. (2007) Can graft-versus-leukemia reactivity be dissociated from graft-versus-host disease? Front Biosci 12:4568-4594.
    • (2007) Front Biosci , vol.12 , pp. 4568-4594
    • Sprangers, B.1
  • 19
    • 0033869563 scopus 로고    scopus 로고
    • Flucytosine: A review of its pharmacology, clinical indications, pharmacokinetics, toxicity and drug interactions
    • Vermes A, et al. (2000) Flucytosine: A review of its pharmacology, clinical indications, pharmacokinetics, toxicity and drug interactions. J Antimicrob Chemother 46:171-179. (Pubitemid 30639285)
    • (2000) Journal of Antimicrobial Chemotherapy , vol.46 , Issue.2 , pp. 171-179
    • Vermes, A.1    Guchelaar, H.-J.2    Dankert, J.3
  • 20
    • 0038387494 scopus 로고    scopus 로고
    • 5-Fluorouracil: Mechanisms of action and clinical strategies
    • DOI 10.1038/nrc1074
    • Longley DB, et al. (2003) 5-fluorouracil: Mechanisms of action and clinical strategies. Nat Rev Cancer 3:330-338. (Pubitemid 37328853)
    • (2003) Nature Reviews Cancer , vol.3 , Issue.5 , pp. 330-338
    • Longley, D.B.1    Harkin, D.P.2    Johnston, P.G.3
  • 24
    • 33846114132 scopus 로고    scopus 로고
    • BRENDA, AMENDA and FRENDA: The enzyme information system in 2007
    • Barthelmes J, et al. (2007) BRENDA, AMENDA and FRENDA: The enzyme information system in 2007. Nucleic Acids Res 35 (Database issue):D511-D514.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Barthelmes, J.1
  • 27
    • 0036776761 scopus 로고    scopus 로고
    • Purification, substrate range, and metal center of AtzC: The N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism
    • DOI 10.1128/JB.184.19.5376-5384.2002
    • Shapir N, et al. (2002) Purification, substrate range, and metal center of AtzC: The N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. J Bacteriol 184:5376-5384. (Pubitemid 35024384)
    • (2002) Journal of Bacteriology , vol.184 , Issue.19 , pp. 5376-5384
    • Shapir, N.1    Osborne, J.P.2    Johnson, G.3    Sadowsky, M.J.4    Wackett, L.P.5
  • 28
    • 0043133654 scopus 로고    scopus 로고
    • The 1.14 A crystal structure of yeast cytosine deaminase: Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy
    • DOI 10.1016/S0969-2126(03)00153-9
    • Ireton GC, et al. (2003) The 1.14 A crystal structure of yeast cytosine deaminase: Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy. Structure (London) 11:961-972. (Pubitemid 36966785)
    • (2003) Structure , vol.11 , Issue.8 , pp. 961-972
    • Ireton, G.C.1    Black, M.E.2    Stoddard, B.L.3
  • 29
    • 0033583291 scopus 로고    scopus 로고
    • Cloning and characterization of human guanine deaminase: Purification and partial amino acid sequence of the mouse protein
    • Yuan G, et al. (1999) Cloning and characterization of human guanine deaminase. Purification and partial amino acid sequence of the mouse protein. J Biol Chem 274:8175-8180. (Pubitemid 129518217)
    • (1999) Journal of Biological Chemistry , vol.274 , Issue.12 , pp. 8175-8180
    • Yuan, G.1    Bin, J.C.2    McKay, D.J.3    Snyder, F.F.4
  • 30
    • 0027849641 scopus 로고
    • Are there limits to enzyme-inhibitor binding discrimination? Inferences from the behavior of nucleoside deaminases
    • Wolfenden R (1993) Are there limits to enzyme-inhibitor binding discrimination? Inferences from the behavior of nucleoside deaminases. Pharmacol Ther 60:235-244. (Pubitemid 24117377)
    • (1993) Pharmacology and Therapeutics , vol.60 , Issue.2 , pp. 235-244
    • Wolfenden, R.1
  • 31
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with Rosetta
    • Das R, Baker D (2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77:363-382.
    • (2008) Annu Rev Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 33
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • DOI 10.1006/jmbi.1997.0959
    • Simons KT, et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209-225. (Pubitemid 27192690)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 34
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • DOI 10.1110/ps.0242703
    • Canutescu AA, Dunbrack RL, Jr (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci 12:963-972. (Pubitemid 36505431)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 38
    • 0025888264 scopus 로고
    • Efficient site-directed mutagenesis using uracil-containing DNA
    • Kunkel TA, et al. (1991) Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol 204:125-139.
    • (1991) Methods Enzymol , vol.204 , pp. 125-139
    • Kunkel, T.A.1
  • 39
    • 14844294424 scopus 로고    scopus 로고
    • Protein production by auto-induction in high density shaking cultures
    • Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207-234.
    • (2005) Protein Expr Purif , vol.41 , pp. 207-234
    • Studier, F.W.1
  • 41
    • 0003791868 scopus 로고    scopus 로고
    • Otwinowski Z, Minor W, eds Academic, New York
    • Otwinowski Z, Minor W, eds (1997) in Methods in Enzymology (Academic, New York).
    • (1997) Methods in Enzymology
  • 42
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • DOI 10.1107/S0907444994003112
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763. (Pubitemid 2143461)
    • (1994) Acta Crystallographica Section D: Biological Crystallography , vol.50 , Issue.5 , pp. 760-763
  • 44
    • 66349133914 scopus 로고    scopus 로고
    • Motif-directed flexible backbone design of functional interactions
    • in press
    • Havranek JJ, Baker D (2009) Motif-directed flexible backbone design of functional interactions. Protein Sci, in press.
    • (2009) Protein Sci
    • Havranek, J.J.1    Baker, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.