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Volumn 363, Issue , 2007, Pages 59-89

Protein engineering

Author keywords

Bioinformatics; Crystallization; DNA shuf fling; Error proned PCR; Limited proteolysis; Mutagenesis

Indexed keywords

DNA;

EID: 33847327522     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-209-2:59     Document Type: Article
Times cited : (4)

References (52)
  • 1
    • 0032387685 scopus 로고    scopus 로고
    • Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census
    • Gerstein, M. (1998) Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33, 518-534.
    • (1998) Proteins , vol.33 , pp. 518-534
    • Gerstein, M.1
  • 2
    • 0032411225 scopus 로고    scopus 로고
    • How representative are the known structures of the proteins in a complete genome? A comprehensive structural census
    • Gerstein, M. (1998) How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des. 3, 497-512.
    • (1998) Fold Des , vol.3 , pp. 497-512
    • Gerstein, M.1
  • 4
    • 14244271957 scopus 로고    scopus 로고
    • Parallel cloning, expression, purification and crystallization of human proteins for structural genomics
    • Ding, H. T., Ren, H., Chen, Q., et al. (2002) Parallel cloning, expression, purification and crystallization of human proteins for structural genomics. Acta Crystallogr. D Biol. Crystallogr. 58, 2102-2108.
    • (2002) Acta Crystallogr. D Biol. Crystallogr , vol.58 , pp. 2102-2108
    • Ding, H.T.1    Ren, H.2    Chen, Q.3
  • 5
    • 0029785464 scopus 로고    scopus 로고
    • Potential use of additivity of mutational effects in simplifying protein engineering
    • Skinner, M. M. and Terwilliger, T. C. (1996) Potential use of additivity of mutational effects in simplifying protein engineering. Proc. Natl. Acad. Sci. USA 93, 10,753-10,757.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93
    • Skinner, M.M.1    Terwilliger, T.C.2
  • 6
    • 0026552361 scopus 로고
    • Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence
    • Heinz, D. W., Baase, W. A., and Matthews, B. W. (1992) Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. Proc. Natl. Acad. Sci. USA 89, 3751-3755.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 3751-3755
    • Heinz, D.W.1    Baase, W.A.2    Matthews, B.W.3
  • 7
    • 0033199837 scopus 로고    scopus 로고
    • Crystal engineering: Deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus
    • Dale, G. E., Kostrewa, D., Gsell, B., Stieger, M., and D'Arcy, A. (1999) Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus. Acta Crystallogr. D Biol. Crystallogr. 55, 1626-1629.
    • (1999) Acta Crystallogr. D Biol. Crystallogr , vol.55 , pp. 1626-1629
    • Dale, G.E.1    Kostrewa, D.2    Gsell, B.3    Stieger, M.4    D'Arcy, A.5
  • 8
    • 0030470263 scopus 로고    scopus 로고
    • Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants
    • Longhi, S., Nicolas, A., Creveld, L., et al. (1996) Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants. Proteins 26, 442-458.
    • (1996) Proteins , vol.26 , pp. 442-458
    • Longhi, S.1    Nicolas, A.2    Creveld, L.3
  • 9
    • 0034664049 scopus 로고    scopus 로고
    • Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP
    • Martin, G., Keller, W., and Doublié, S. (2000) Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 19, 4193-4203.
    • (2000) EMBO J , vol.19 , pp. 4193-4203
    • Martin, G.1    Keller, W.2    Doublié, S.3
  • 10
    • 0037013858 scopus 로고    scopus 로고
    • An RNA cap (nucleoside-2'-0-)-methyltransferase in the flavivirus RNA polymerase NS5: Crystal structure and functional characterization
    • Egloff, M. P., Benarroch, D., Selisko, B., Romette, J. L., and Canard, B. (2002) An RNA cap (nucleoside-2'-0-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J. 21, 2757-2768.
    • (2002) EMBO J , vol.21 , pp. 2757-2768
    • Egloff, M.P.1    Benarroch, D.2    Selisko, B.3    Romette, J.L.4    Canard, B.5
  • 11
    • 0034816151 scopus 로고    scopus 로고
    • Random PCR-based screening for soluble domains using green fluorescent protein
    • Kawasaki, M. and Inagaki, F. (2001) Random PCR-based screening for soluble domains using green fluorescent protein. Biochem. Biophys. Res. Commun. 280, 842-844.
    • (2001) Biochem. Biophys. Res. Commun , vol.280 , pp. 842-844
    • Kawasaki, M.1    Inagaki, F.2
  • 12
    • 0034522971 scopus 로고    scopus 로고
    • BLAST Search Updater: A notification system for new database matches
    • Boone, M. and Upton, C. (2000) BLAST Search Updater: a notification system for new database matches. Bioinformatics 16, 1054-1055.
    • (2000) Bioinformatics , vol.16 , pp. 1054-1055
    • Boone, M.1    Upton, C.2
  • 14
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 11, 4673-4680.
    • (1994) Nucleic Acids Res , vol.11 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 15
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 16
    • 0029889988 scopus 로고    scopus 로고
    • PHD: Predicting one-dimensional protein structure by profilebased neural networks
    • Rost, B. (1996) PHD: predicting one-dimensional protein structure by profilebased neural networks. Meth. Enzymol. 266, 525-539.
    • (1996) Meth. Enzymol , vol.266 , pp. 525-539
    • Rost, B.1
  • 17
    • 0032961270 scopus 로고    scopus 로고
    • ESPript: Analysis of multiple sequence alignments in PostScript
    • Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305-308.
    • (1999) Bioinformatics , vol.15 , pp. 305-308
    • Gouet, P.1    Courcelle, E.2    Stuart, D.I.3    Metoz, F.4
  • 18
    • 0042622240 scopus 로고    scopus 로고
    • GlobPlot: Exploring protein sequences for globularity and disorder
    • Linding, R., Russell, R. B., Neduva, V., and Gibson, T. J. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701-3708.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3701-3708
    • Linding, R.1    Russell, R.B.2    Neduva, V.3    Gibson, T.J.4
  • 19
    • 0025129872 scopus 로고
    • Hydrophobic cluster analysis: Procedures to derive structural and functional information from 2-D-representation of protein sequences
    • Lemesle-Varloot, L., Henrissat, B., Gaboriaud, C., Bissery, V., Morgat, A., and Mornon, J. P. (1990) Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72, 555-574.
    • (1990) Biochimie , vol.72 , pp. 555-574
    • Lemesle-Varloot, L.1    Henrissat, B.2    Gaboriaud, C.3    Bissery, V.4    Morgat, A.5    Mornon, J.P.6
  • 20
    • 0242582329 scopus 로고    scopus 로고
    • Crystal structure of the measles virus phosphoprotein domain responsible for the induced folding of the C-terminal domain of the nucleoprotein
    • Johansson, K., Bourhis, J. M., Campanacci, V., Cambillau, C., Canard, B., and Longhi, S. (2003) Crystal structure of the measles virus phosphoprotein domain responsible for the induced folding of the C-terminal domain of the nucleoprotein. J. Biol. Chem. 278, 44,567-44,573.
    • (2003) J. Biol. Chem , vol.278
    • Johansson, K.1    Bourhis, J.M.2    Campanacci, V.3    Cambillau, C.4    Canard, B.5    Longhi, S.6
  • 21
    • 0037304389 scopus 로고    scopus 로고
    • Genetic screens and directed evolution for protein solubility
    • Waldo, G. S. (2003) Genetic screens and directed evolution for protein solubility. Curr. Opin. Chem. Biol. 7, 33-38.
    • (2003) Curr. Opin. Chem. Biol , vol.7 , pp. 33-38
    • Waldo, G.S.1
  • 22
    • 0021253525 scopus 로고
    • Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing
    • Henikoff, S. (1984) Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28, 351-359.
    • (1984) Gene , vol.28 , pp. 351-359
    • Henikoff, S.1
  • 24
    • 0028816556 scopus 로고
    • Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction
    • Fromant, M., Blanquet, S., and Plateau, P. (1995) Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal. Biochem. 224, 347-353.
    • (1995) Anal. Biochem , vol.224 , pp. 347-353
    • Fromant, M.1    Blanquet, S.2    Plateau, P.3
  • 25
    • 0033557326 scopus 로고    scopus 로고
    • Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus
    • Melnikov, A. and Youngman, P. J. (1999) Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus. Nucleic Acids Res. 27, 1056-1062.
    • (1999) Nucleic Acids Res , vol.27 , pp. 1056-1062
    • Melnikov, A.1    Youngman, P.J.2
  • 26
    • 0032940418 scopus 로고    scopus 로고
    • Directed evolution of a fungal peroxidase
    • Cherry, J. R., Lamsa, M. H., Schneider, P., et al. (1999) Directed evolution of a fungal peroxidase. Nat. Biotechnol. 17, 379-384.
    • (1999) Nat. Biotechnol , vol.17 , pp. 379-384
    • Cherry, J.R.1    Lamsa, M.H.2    Schneider, P.3
  • 27
    • 0030737949 scopus 로고    scopus 로고
    • Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization
    • Shafikhani, S., Siegel, R. A., Ferrari, E., and Schellenberger, V. (1997) Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. BioTechniques 23, 304-310.
    • (1997) BioTechniques , vol.23 , pp. 304-310
    • Shafikhani, S.1    Siegel, R.A.2    Ferrari, E.3    Schellenberger, V.4
  • 28
    • 0029969577 scopus 로고    scopus 로고
    • Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide
    • You, L. and Arnold, F. H. (1996) Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. Protein Eng. 9,77-83.
    • (1996) Protein Eng , vol.9 , pp. 77-83
    • You, L.1    Arnold, F.H.2
  • 29
    • 0027298218 scopus 로고
    • PCR amplification of megabase DNA with tagged random primers (T-PCR)
    • Grothues, D., Cantor, C. R., and Smith, C. L. (1993) PCR amplification of megabase DNA with tagged random primers (T-PCR). Nucleic Acids Res. 21, 1321-1322.
    • (1993) Nucleic Acids Res , vol.21 , pp. 1321-1322
    • Grothues, D.1    Cantor, C.R.2    Smith, C.L.3
  • 31
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer, W P. (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391.
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.1
  • 32
    • 0032518266 scopus 로고    scopus 로고
    • DNA shuffling of a family of genes from diverse species accelerates directed evolution
    • Crameri, A., Raillard, S. A., Bermudez, E., and Stemmer, W. P. (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291.
    • (1998) Nature , vol.391 , pp. 288-291
    • Crameri, A.1    Raillard, S.A.2    Bermudez, E.3    Stemmer, W.P.4
  • 33
    • 0029670330 scopus 로고    scopus 로고
    • Improved green fluorescent protein by molecular evolution using DNA shuffling
    • Crameri, A., Whitehorn, E. A., Tate, E., and Stemmer, W. P. (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14, 315-319.
    • (1996) Nat. Biotechnol , vol.14 , pp. 315-319
    • Crameri, A.1    Whitehorn, E.A.2    Tate, E.3    Stemmer, W.P.4
  • 36
    • 0028110130 scopus 로고
    • DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution
    • Stemmer, W. P. (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10,747-10,751.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91
    • Stemmer, W.P.1
  • 37
    • 0027537709 scopus 로고
    • Production of crystallizable cruzain, the major cysteine protease from Trypanosoma cruzi
    • Eakin, A. E., McGrath, M. E., McKerrow, J. H., Fletterick, R. J., and Craik, C. S. (1993) Production of crystallizable cruzain, the major cysteine protease from Trypanosoma cruzi. J. Biol. Chem. 268, 6115-6118.
    • (1993) J. Biol. Chem , vol.268 , pp. 6115-6118
    • Eakin, A.E.1    McGrath, M.E.2    McKerrow, J.H.3    Fletterick, R.J.4    Craik, C.S.5
  • 38
    • 0029111451 scopus 로고
    • Activation of blood coagulation factor Vila with cleaved tissue factor extracellular domain and crystallization of the active complex
    • Kirchhofer, D., Guha, A., Nemerson, Y., et al. (1995) Activation of blood coagulation factor Vila with cleaved tissue factor extracellular domain and crystallization of the active complex. Proteins 11,419-425.
    • (1995) Proteins , vol.11 , pp. 419-425
    • Kirchhofer, D.1    Guha, A.2    Nemerson, Y.3
  • 40
    • 0345276579 scopus 로고    scopus 로고
    • Three-dimensional crystallization of the Escherichia coli glycerol-3-phosphate transporter: A member of the major facilitator superfamily
    • Lemieux, M. J., Song, J., Kim, M. J., et al. (2003) Three-dimensional crystallization of the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Protein Sci. 12, 2748-2756.
    • (2003) Protein Sci , vol.12 , pp. 2748-2756
    • Lemieux, M.J.1    Song, J.2    Kim, M.J.3
  • 41
    • 0035975629 scopus 로고    scopus 로고
    • Cleavage of vesicular stomatitis virus matrix protein prevents self- association and leads to crystallization
    • Gaudier, M., Gaudin, Y., and Knossow, M. (2001) Cleavage of vesicular stomatitis virus matrix protein prevents self- association and leads to crystallization. Virology 288, 308-314.
    • (2001) Virology , vol.288 , pp. 308-314
    • Gaudier, M.1    Gaudin, Y.2    Knossow, M.3
  • 42
    • 0034651605 scopus 로고    scopus 로고
    • Crystal structure of a class I alpha 1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control
    • Vallee, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., and Howell, P. L. (2000) Crystal structure of a class I alpha 1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control. EMBO J. 19, 581-588.
    • (2000) EMBO J , vol.19 , pp. 581-588
    • Vallee, F.1    Lipari, F.2    Yip, P.3    Sleno, B.4    Herscovics, A.5    Howell, P.L.6
  • 43
    • 0036164151 scopus 로고    scopus 로고
    • Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase: Expression, purification, characterization and crystallization
    • Nachon, F., Nicolet, Y., Viguie, N., Masson, P., Fontecilla-Camps, J. C., and Lockridge, O. (2002) Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase: expression, purification, characterization and crystallization. Eur. J. Biochem. 269, 630-637.
    • (2002) Eur. J. Biochem , vol.269 , pp. 630-637
    • Nachon, F.1    Nicolet, Y.2    Viguie, N.3    Masson, P.4    Fontecilla-Camps, J.C.5    Lockridge, O.6
  • 44
    • 0035214095 scopus 로고    scopus 로고
    • Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1
    • Josephson, K., McPherson, D. T., and Walter, M. R. (2001) Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1. Acta Crystallogr. D Biol. Crystallogr. 57, 1908-1911.
    • (2001) Acta Crystallogr. D Biol. Crystallogr , vol.57 , pp. 1908-1911
    • Josephson, K.1    McPherson, D.T.2    Walter, M.R.3
  • 45
    • 0030977992 scopus 로고    scopus 로고
    • Crystal structure of the obese protein leptin-E100
    • Zhang, F., Basinski, M. B., Beals, J. M., et al. (1997) Crystal structure of the obese protein leptin-E100. Nature 387, 206-209.
    • (1997) Nature , vol.387 , pp. 206-209
    • Zhang, F.1    Basinski, M.B.2    Beals, J.M.3
  • 46
    • 0035024436 scopus 로고    scopus 로고
    • Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI
    • Longenecker, K. L., Garrard, S. M., Sheffield, P. J., and Derewenda, Z. S. (2001) Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta Crystallogr. D Biol. Crystallogr. 57, 679-688.
    • (2001) Acta Crystallogr. D Biol. Crystallogr , vol.57 , pp. 679-688
    • Longenecker, K.L.1    Garrard, S.M.2    Sheffield, P.J.3    Derewenda, Z.S.4
  • 47
    • 0033607292 scopus 로고    scopus 로고
    • Measures of residue density in protein structures
    • Baud, F. and Karlin, S. (1999) Measures of residue density in protein structures. Proc. Natl. Acad. Sci. USA 96, 12,494-12,499.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96
    • Baud, F.1    Karlin, S.2
  • 48
    • 0030877077 scopus 로고    scopus 로고
    • Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
    • Dasgupta, S., Iyer, G. H., Bryant, S. H., Lawrence, C. E., and Bell, J. A. (1997) Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 28, 494-514.
    • (1997) Proteins , vol.28 , pp. 494-514
    • Dasgupta, S.1    Iyer, G.H.2    Bryant, S.H.3    Lawrence, C.E.4    Bell, J.A.5
  • 49
    • 0036900352 scopus 로고    scopus 로고
    • The impact of Glu→Ala and Glu→Asp mutations on the crystallization properties of RhoGDI: The structure of RhoGDI at 1.3 A resolution
    • Mateja, A., Devedjiev, Y., Krowarsch, D., et al. (2002) The impact of Glu→Ala and Glu→Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 A resolution. Acta Crystallogr. D Biol. Crystallogr. 58, 1983-1991.
    • (2002) Acta Crystallogr. D Biol. Crystallogr , vol.58 , pp. 1983-1991
    • Mateja, A.1    Devedjiev, Y.2    Krowarsch, D.3
  • 50
    • 0029017919 scopus 로고
    • Catalytic domain of human immunodeficiency virus type 1 integrase: Identification of a soluble mutant by systematic replacement of hydrophobic residues
    • Jenkins, T. M., Hickman, A. B., Dyda, F., Ghirlando, R., Davies, D. R., and Craigie, R. (1995) Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues. Proc. Natl. Acad. Sci. USA 92, 6057-6061.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 6057-6061
    • Jenkins, T.M.1    Hickman, A.B.2    Dyda, F.3    Ghirlando, R.4    Davies, D.R.5    Craigie, R.6
  • 51
    • 0035810990 scopus 로고    scopus 로고
    • Crystal structure of the SarR protein from Staphylococcus aureus
    • Liu, Y., Manna, A., Li, R., et al. (2001) Crystal structure of the SarR protein from Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 98, 6877-6882.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6877-6882
    • Liu, Y.1    Manna, A.2    Li, R.3
  • 52
    • 0031824806 scopus 로고    scopus 로고
    • Center, R. J., Kobe, B., Wilson, K. A., et al. (1998) Crystallization of a trimeric human T cell leukemia virus type 1 gp21 ectodomain fragment as a chimera with maltose-binding protein. Protein Sci. 7, 1612-1619.
    • Center, R. J., Kobe, B., Wilson, K. A., et al. (1998) Crystallization of a trimeric human T cell leukemia virus type 1 gp21 ectodomain fragment as a chimera with maltose-binding protein. Protein Sci. 7, 1612-1619.


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