메뉴 건너뛰기




Volumn 7, Issue 5, 2012, Pages

A predictive model of intein insertion site for use in the engineering of molecular switches

Author keywords

[No Author keywords available]

Indexed keywords

INTEIN; BETA GLUCOSIDASE; ENDO 1,4 BETA XYLANASE; PROTEIN; XYNB XYLANASE;

EID: 84861401588     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037355     Document Type: Article
Times cited : (12)

References (54)
  • 1
    • 27744593757 scopus 로고    scopus 로고
    • The mechanism of intein-mediated protein splicing: Variations on a theme
    • Mills KV, Perler FB, (2005) The mechanism of intein-mediated protein splicing: Variations on a theme. Protein and Peptide Letters 12: 751-755.
    • (2005) Protein and Peptide Letters , vol.12 , pp. 751-755
    • Mills, K.V.1    Perler, F.B.2
  • 2
    • 0033782899 scopus 로고    scopus 로고
    • Protein splicing and related forms of protein autoprocessing
    • Paulus H, (2000) Protein splicing and related forms of protein autoprocessing. Annual Review of Biochemistry 69: 447-496.
    • (2000) Annual Review of Biochemistry , vol.69 , pp. 447-496
    • Paulus, H.1
  • 3
    • 33748551323 scopus 로고    scopus 로고
    • Protein splicing in cis and in trans
    • Saleh L, Perler FB, (2006) Protein splicing in cis and in trans. Chemical Record 6: 183-193.
    • (2006) Chemical Record , vol.6 , pp. 183-193
    • Saleh, L.1    Perler, F.B.2
  • 4
    • 3042742569 scopus 로고    scopus 로고
    • Temperature-sensitive control of protein activity by conditionally splicing inteins
    • Zeidler MP, Tan C, Bellaiche Y, Cherry S, Hader S, et al. (2004) Temperature-sensitive control of protein activity by conditionally splicing inteins. Nature Biotechnology 22: 871-876.
    • (2004) Nature Biotechnology , vol.22 , pp. 871-876
    • Zeidler, M.P.1    Tan, C.2    Bellaiche, Y.3    Cherry, S.4    Hader, S.5
  • 5
    • 41449091908 scopus 로고    scopus 로고
    • Activation of protein splicing with light in yeast
    • Tyszkiewicz AB, Muir TW, (2008) Activation of protein splicing with light in yeast. Nature Methods 5: 303-305.
    • (2008) Nature Methods , vol.5 , pp. 303-305
    • Tyszkiewicz, A.B.1    Muir, T.W.2
  • 6
    • 0037036791 scopus 로고    scopus 로고
    • Protein splicing triggered by a small molecule
    • Mootz HD, Muir TW, (2002) Protein splicing triggered by a small molecule. J Am Chem Soc 124: 9044-9045.
    • (2002) J Am Chem Soc , vol.124 , pp. 9044-9045
    • Mootz, H.D.1    Muir, T.W.2
  • 7
    • 0043237657 scopus 로고    scopus 로고
    • "The splice is right": how protein splicing is opening new doors in protein science
    • Schwartz EC, Muir TW, Tyszkiewicz AB, (2003) "The splice is right": how protein splicing is opening new doors in protein science. Chemical Communications 17: 2087-2090.
    • (2003) Chemical Communications , vol.17 , pp. 2087-2090
    • Schwartz, E.C.1    Muir, T.W.2    Tyszkiewicz, A.B.3
  • 8
    • 13244252218 scopus 로고    scopus 로고
    • Regulation of protein activity with small-molecule-controlled inteins
    • Skretas G, Wood DW, (2005) Regulation of protein activity with small-molecule-controlled inteins. Protein Science 14: 523-532.
    • (2005) Protein Science , vol.14 , pp. 523-532
    • Skretas, G.1    Wood, D.W.2
  • 9
    • 33745968727 scopus 로고    scopus 로고
    • Control of transcription factor activity and osteoblast differentiation in mammalian cells using an evolved small-molecule-dependent intein
    • Yuen CM, Rodda SJ, Vokes SA, McMahon AP, Liu DR, (2006) Control of transcription factor activity and osteoblast differentiation in mammalian cells using an evolved small-molecule-dependent intein. J Am Chem Soc 128: 8939-8946.
    • (2006) J Am Chem Soc , vol.128 , pp. 8939-8946
    • Yuen, C.M.1    Rodda, S.J.2    Vokes, S.A.3    McMahon, A.P.4    Liu, D.R.5
  • 10
    • 0036753960 scopus 로고    scopus 로고
    • Development of a positive genetic selection system for inhibition of protein splicing using mycobacterial inteins in Escherichia coli DNA gyrase subunit A
    • Adam E, Perler FB, (2002) Development of a positive genetic selection system for inhibition of protein splicing using mycobacterial inteins in Escherichia coli DNA gyrase subunit A. J Mol Microbiol Biotechnol 4: 479-487.
    • (2002) J Mol Microbiol Biotechnol , vol.4 , pp. 479-487
    • Adam, E.1    Perler, F.B.2
  • 11
    • 17744415288 scopus 로고    scopus 로고
    • Single-column purification of free recombinant proteins using a self-cleavable affinity tag derived from a protein splicing element
    • Chong S, Mersha FB, Comb DG, Scott ME, Landry D, et al. (1997) Single-column purification of free recombinant proteins using a self-cleavable affinity tag derived from a protein splicing element. Gene 192: 271-281.
    • (1997) Gene , vol.192 , pp. 271-281
    • Chong, S.1    Mersha, F.B.2    Comb, D.G.3    Scott, M.E.4    Landry, D.5
  • 12
    • 0032562685 scopus 로고    scopus 로고
    • Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein
    • Chong SR, Williams KS, Wotkowicz C, Xu MQ, (1998) Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. Journal of Biological Chemistry 273: 10567-10577.
    • (1998) Journal of Biological Chemistry , vol.273 , pp. 10567-10577
    • Chong, S.R.1    Williams, K.S.2    Wotkowicz, C.3    Xu, M.Q.4
  • 13
    • 0039374819 scopus 로고    scopus 로고
    • The in vitro ligation of bacterially expressed proteins using an intein from Methanobacterium thermoautotrophicum
    • Evans TC Jr, Benner J, Xu MQ, (1999) The in vitro ligation of bacterially expressed proteins using an intein from Methanobacterium thermoautotrophicum. J Biol Chem 274: 3923-3926.
    • (1999) J Biol Chem , vol.274 , pp. 3923-3926
    • Evans Jr., T.C.1    Benner, J.2    Xu, M.Q.3
  • 14
    • 0033614484 scopus 로고    scopus 로고
    • Characterization of a self-splicing mini-intein and its conversion into autocatalytic N- and C-terminal cleavage elements: facile production of protein building blocks for protein ligation
    • Mathys S, Evans TC, Chute IC, Wu H, Chong SR, et al. (1999) Characterization of a self-splicing mini-intein and its conversion into autocatalytic N- and C-terminal cleavage elements: facile production of protein building blocks for protein ligation. Gene 231: 1-13.
    • (1999) Gene , vol.231 , pp. 1-13
    • Mathys, S.1    Evans, T.C.2    Chute, I.C.3    Wu, H.4    Chong, S.R.5
  • 15
    • 0032988320 scopus 로고    scopus 로고
    • Purification of proteins fused to either the amino or carboxy terminus of the Mycobacterium xenopi gyrase A intein
    • Southworth MW, Amaya K, Evans TC, Xu MQ, Perler FB, (1999) Purification of proteins fused to either the amino or carboxy terminus of the Mycobacterium xenopi gyrase A intein. Biotechniques 27: 110-114, 116, 118-120.
    • (1999) Biotechniques , vol.27
    • Southworth, M.W.1    Amaya, K.2    Evans, T.C.3    Xu, M.Q.4    Perler, F.B.5
  • 17
    • 33644912308 scopus 로고    scopus 로고
    • Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostoc punctiforme
    • Iwai H, Zuger S, Jin J, Tam PH, (2006) Highly efficient protein trans-splicing by a naturally split DnaE intein from Nostoc punctiforme. FEBS Lett 580: 1853-1858.
    • (2006) FEBS Lett , vol.580 , pp. 1853-1858
    • Iwai, H.1    Zuger, S.2    Jin, J.3    Tam, P.H.4
  • 20
    • 0037454737 scopus 로고    scopus 로고
    • In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions
    • Gangopadhyay JP, Jiang SQ, van Berkel P, Paulus H, (2003) In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions. Biochimica et Biophysica Acta-Proteins and Proteomics 1619: 193-200.
    • (2003) Biochimica Et Biophysica Acta-Proteins and Proteomics , vol.1619 , pp. 193-200
    • Gangopadhyay, J.P.1    Jiang, S.Q.2    van Berkel, P.3    Paulus, H.4
  • 21
    • 0034595699 scopus 로고    scopus 로고
    • Structural insights into the protein splicing mechanism of PI-SceI
    • Poland BW, Xu MQ, Quiocho FA, (2000) Structural insights into the protein splicing mechanism of PI-SceI. Journal of Biological Chemistry 275: 16408-16413.
    • (2000) Journal of Biological Chemistry , vol.275 , pp. 16408-16413
    • Poland, B.W.1    Xu, M.Q.2    Quiocho, F.A.3
  • 22
    • 0034665054 scopus 로고    scopus 로고
    • An alternative protein splicing mechanism for inteins lacking an N-terminal nucleophile
    • Southworth MW, Benner J, Perler FB, (2000) An alternative protein splicing mechanism for inteins lacking an N-terminal nucleophile. EMBO Journal 19: 5019-5026.
    • (2000) EMBO Journal , vol.19 , pp. 5019-5026
    • Southworth, M.W.1    Benner, J.2    Perler, F.B.3
  • 23
    • 0034518359 scopus 로고    scopus 로고
    • Optimized single-step affinity purification with a self-cleaving intein applied to human acidic fibroblast growth factor
    • Wood DW, Derbyshire V, Wu W, Chartrain M, Belfort M, et al. (2000) Optimized single-step affinity purification with a self-cleaving intein applied to human acidic fibroblast growth factor. Biotechnol Prog 16: 1055-1063.
    • (2000) Biotechnol Prog , vol.16 , pp. 1055-1063
    • Wood, D.W.1    Derbyshire, V.2    Wu, W.3    Chartrain, M.4    Belfort, M.5
  • 24
    • 80955151478 scopus 로고    scopus 로고
    • Global and grain specific accumulation of glycoside hydrolase family 10 xylanases in transgenic maize (Zea mays)
    • Gray B, Bougri O, Carlson AR, Meisner J, Pan S, et al. (2011) Global and grain specific accumulation of glycoside hydrolase family 10 xylanases in transgenic maize (Zea mays). Plant Biotechnology Journal 9: 1100-1108.
    • (2011) Plant Biotechnology Journal , vol.9 , pp. 1100-1108
    • Gray, B.1    Bougri, O.2    Carlson, A.R.3    Meisner, J.4    Pan, S.5
  • 25
    • 0032894598 scopus 로고    scopus 로고
    • InBase, the New England Biolabs Intein Database
    • Perler FB, (1999) InBase, the New England Biolabs Intein Database. Nucleic Acids Research 27: 346-347.
    • (1999) Nucleic Acids Research , vol.27 , pp. 346-347
    • Perler, F.B.1
  • 26
    • 0033963173 scopus 로고    scopus 로고
    • InBase, the Intein Database
    • Perler FB, (2000) InBase, the Intein Database. Nucleic Acids Research 28: 344-345.
    • (2000) Nucleic Acids Research , vol.28 , pp. 344-345
    • Perler, F.B.1
  • 27
    • 0036084146 scopus 로고    scopus 로고
    • InBase: The Intein Database
    • Perler FB, (2002) InBase: The Intein Database. Nucleic Acids Research 30: 383-384.
    • (2002) Nucleic Acids Research , vol.30 , pp. 383-384
    • Perler, F.B.1
  • 28
    • 0030729344 scopus 로고    scopus 로고
    • Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family
    • Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, et al. (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Research 25: 4626-4638.
    • (1997) Nucleic Acids Research , vol.25 , pp. 4626-4638
    • Dalgaard, J.Z.1    Klar, A.J.2    Moser, M.J.3    Holley, W.R.4    Chatterjee, A.5
  • 30
    • 76049084239 scopus 로고    scopus 로고
    • Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements
    • Swithers KS, Senejani AG, Fournier GP, Gogarten JP, (2009) Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements. BMC Evolutionary Biology 9.
    • (2009) BMC Evolutionary Biology , vol.9
    • Swithers, K.S.1    Senejani, A.G.2    Fournier, G.P.3    Gogarten, J.P.4
  • 31
    • 0035425040 scopus 로고    scopus 로고
    • Intein spread and extinction in evolution
    • Pietrokovski S, (2001) Intein spread and extinction in evolution. Trends in Genetics 17: 465-472.
    • (2001) Trends in Genetics , vol.17 , pp. 465-472
    • Pietrokovski, S.1
  • 32
    • 73249132200 scopus 로고    scopus 로고
    • Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer
    • Yahara K, Fukuyo M, Sasaki A, Kobayashi I, (2009) Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer. Proc Natl Acad Sci U S A 106: 18861-18866.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 18861-18866
    • Yahara, K.1    Fukuyo, M.2    Sasaki, A.3    Kobayashi, I.4
  • 34
    • 0038167128 scopus 로고    scopus 로고
    • Learning to Classify Text Using Support Vector Machines
    • The Springer International Series in Engineering and Computer Science
    • Joachims T, (2002) Learning to Classify Text Using Support Vector Machines. Methods, Theory and Algorithms Series The Springer International Series in Engineering and Computer Science.
    • (2002) Methods, Theory and Algorithms Series
    • Joachims, T.1
  • 37
    • 0036387236 scopus 로고    scopus 로고
    • Evaluation of structural and evolutionary contributions to deleterious mutation prediction
    • Saunders CT, Baker D, (2002) Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol 322: 891-901.
    • (2002) J Mol Biol , vol.322 , pp. 891-901
    • Saunders, C.T.1    Baker, D.2
  • 38
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D, (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.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 40
    • 33846658665 scopus 로고    scopus 로고
    • Inteins - A Historical Perspective
    • In: Belfort M, Derbyshire V, Stoddard BL, Woods DW, editors
    • Perler FB, (2005) Inteins- A Historical Perspective. In: Belfort M, Derbyshire V, Stoddard BL, Woods DW, editors. Homing Endonucleases and Inteins: Springer pp. 193-210.
    • (2005) Homing Endonucleases and Inteins , pp. 193-210
    • Perler, F.B.1
  • 41
    • 0035941473 scopus 로고    scopus 로고
    • Herbicide resistance from a divided EPSPS protein: the split Synechocystis DnaE intein as an in vivo affinity domain
    • Chen LX, Pradhan S, Evans TC, (2001) Herbicide resistance from a divided EPSPS protein: the split Synechocystis DnaE intein as an in vivo affinity domain. Gene 263: 39-48.
    • (2001) Gene , vol.263 , pp. 39-48
    • Chen, L.X.1    Pradhan, S.2    Evans, T.C.3
  • 42
    • 0030952831 scopus 로고    scopus 로고
    • Identification of three core regions essential for protein splicing of the yeast Vma1 protozyme. A random mutagenesis study of the entire Vma1-derived endonuclease sequence
    • Kawasaki M, Nogami S, Satow Y, Ohya Y, Anraku Y, (1997) Identification of three core regions essential for protein splicing of the yeast Vma1 protozyme. A random mutagenesis study of the entire Vma1-derived endonuclease sequence. J Biol Chem 272: 15668-15674.
    • (1997) J Biol Chem , vol.272 , pp. 15668-15674
    • Kawasaki, M.1    Nogami, S.2    Satow, Y.3    Ohya, Y.4    Anraku, Y.5
  • 43
    • 0030982430 scopus 로고    scopus 로고
    • Probing novel elements for protein splicing in the yeast Vma1 protozyme: a study of replacement mutagenesis and intragenic suppression
    • Nogami S, Satow Y, Ohya Y, Anraku Y, (1997) Probing novel elements for protein splicing in the yeast Vma1 protozyme: a study of replacement mutagenesis and intragenic suppression. Genetics 147: 73-85.
    • (1997) Genetics , vol.147 , pp. 73-85
    • Nogami, S.1    Satow, Y.2    Ohya, Y.3    Anraku, Y.4
  • 44
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-round IX
    • Moult J, Fidelis K, Kryshtafovych A, Tramontano A, (2011) Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 79 (Suppl 10): 1-5.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 45
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 48
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the Universal Protein Resource
    • The-UniProt-Consortium
    • The-UniProt-Consortium, (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-219.
    • (2011) Nucleic Acids Res , vol.39
  • 49
    • 66449084442 scopus 로고    scopus 로고
    • Infrastructure for the life sciences: design and implementation of the UniProt website
    • Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, et al. (2009) Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10: 136.
    • (2009) BMC Bioinformatics , vol.10 , pp. 136
    • Jain, E.1    Bairoch, A.2    Duvaud, S.3    Phan, I.4    Redaschi, N.5
  • 51
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T, (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 52
    • 0030053370 scopus 로고    scopus 로고
    • ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling
    • Peitsch MC, (1996) ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24: 274-279.
    • (1996) Biochem Soc Trans , vol.24 , pp. 274-279
    • Peitsch, M.C.1
  • 54
    • 41449112448 scopus 로고    scopus 로고
    • Structure prediction of domain insertion proteins from structures of individual domains
    • Berrondo M, Ostermeier M, Gray JJ, (2008) Structure prediction of domain insertion proteins from structures of individual domains. Structure 16: 513-527.
    • (2008) Structure , vol.16 , pp. 513-527
    • Berrondo, M.1    Ostermeier, M.2    Gray, J.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.