메뉴 건너뛰기




Volumn 8, Issue 7, 2013, Pages

Fitness Loss and Library Size Determination in Saturation Mutagenesis

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; CATALYSIS; CODON; FITNESS; LANDSCAPE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; MUTAGENESIS; NONSENSE MUTATION; PROBABILITY; PROTEIN BINDING; PROTEIN DATABASE; SATURATION MUTAGENESIS; STOP CODON; THERMOSTABILITY;

EID: 84879757049     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068069     Document Type: Article
Times cited : (10)

References (46)
  • 2
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Maynard Smith J, (1970) Natural selection and the concept of a protein space. Nature 225: 563-564.
    • (1970) Nature , vol.225 , pp. 563-564
    • Maynard Smith, J.1
  • 3
    • 0026448484 scopus 로고
    • Potential of genetic algorithms in protein folding and protein engineering simulations
    • Dandekar T, Argos P, (1992) Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Engineering 5: 637-645.
    • (1992) Protein Engineering , vol.5 , pp. 637-645
    • Dandekar, T.1    Argos, P.2
  • 4
    • 0033770580 scopus 로고    scopus 로고
    • Rational evolutionary design: the theory of in vitro protein evolution
    • Voigt CA, Kauffman S, Wang Z-G, (2001) Rational evolutionary design: the theory of in vitro protein evolution. Advances in protein chemistry 55: 79-160.
    • (2001) Advances in Protein Chemistry , vol.55 , pp. 79-160
    • Voigt, C.A.1    Kauffman, S.2    Wang, Z.-G.3
  • 5
    • 84874609920 scopus 로고    scopus 로고
    • The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering
    • Reetz MT, (2013) The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering. Angewandte Chemie 52: 2658-2666.
    • (2013) Angewandte Chemie , vol.52 , pp. 2658-2666
    • Reetz, M.T.1
  • 6
    • 54349090614 scopus 로고    scopus 로고
    • Addressing the numbers problem in directed evolution
    • Reetz MT, Kahakeaw D, Lohmer R, (2008) Addressing the numbers problem in directed evolution. ChemBioChem 9: 1797-1804.
    • (2008) ChemBioChem , vol.9 , pp. 1797-1804
    • Reetz, M.T.1    Kahakeaw, D.2    Lohmer, R.3
  • 7
    • 80051669875 scopus 로고    scopus 로고
    • Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries
    • Alcolombri U, Elias M, Tawfik DS, (2011) Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries. Journal of Molecular Biology 411: 837-853.
    • (2011) Journal of Molecular Biology , vol.411 , pp. 837-853
    • Alcolombri, U.1    Elias, M.2    Tawfik, D.S.3
  • 8
    • 34548014497 scopus 로고    scopus 로고
    • Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries
    • Herman A, Tawfik DS, (2007) Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Engineering, Design and Selection 20: 219-226.
    • (2007) Protein Engineering, Design and Selection , vol.20 , pp. 219-226
    • Herman, A.1    Tawfik, D.S.2
  • 9
    • 84874023434 scopus 로고    scopus 로고
    • Enzyme Engineering by Targeted Libraries
    • Goldsmith M, Tawfik DS, (2013) Enzyme Engineering by Targeted Libraries. Methods in Enzymology 523: 257-283.
    • (2013) Methods in Enzymology , vol.523 , pp. 257-283
    • Goldsmith, M.1    Tawfik, D.S.2
  • 10
    • 79957559287 scopus 로고    scopus 로고
    • Revisiting the lipase from Pseudomonas aeruginosa: Directed evolution of substrate acceptance and enantioselectivity using iterative saturation mutagenesis
    • Prasad S, Bocola M, Reetz MT, (2011) Revisiting the lipase from Pseudomonas aeruginosa: Directed evolution of substrate acceptance and enantioselectivity using iterative saturation mutagenesis. ChemPhysChem 12: 1550-1557.
    • (2011) ChemPhysChem , vol.12 , pp. 1550-1557
    • Prasad, S.1    Bocola, M.2    Reetz, M.T.3
  • 11
    • 67649207267 scopus 로고    scopus 로고
    • Engineering human IgG1 affinity to human neonatal Fc receptor: Impact of affinity improvement on pharmacokinetics in primates
    • Yeung YA, Leabman MK, Marvin JS, Qiu J, Adams CW, et al. (2009) Engineering human IgG1 affinity to human neonatal Fc receptor: Impact of affinity improvement on pharmacokinetics in primates. The Journal of Immunology 182: 7663-7671.
    • (2009) The Journal of Immunology , vol.182 , pp. 7663-7671
    • Yeung, Y.A.1    Leabman, M.K.2    Marvin, J.S.3    Qiu, J.4    Adams, C.W.5
  • 12
    • 41949101106 scopus 로고    scopus 로고
    • Optimizing glycosyltransferase specificity via "hot spot" saturation mutagenesis presents a catalyst for novobiocin glycorandomization
    • Williams GJ, Goff RD, Zhang C, Thorson JS, (2008) Optimizing glycosyltransferase specificity via "hot spot" saturation mutagenesis presents a catalyst for novobiocin glycorandomization. Chemistry and biology 15: 393-401.
    • (2008) Chemistry and Biology , vol.15 , pp. 393-401
    • Williams, G.J.1    Goff, R.D.2    Zhang, C.3    Thorson, J.S.4
  • 14
    • 44449109239 scopus 로고    scopus 로고
    • Improving the photostability of bright monomeric orange and red fluorescent proteins
    • Shaner NC, Lin MZ, McKeown MR, Steinbach PA, Hazelwood KL, et al. (2008) Improving the photostability of bright monomeric orange and red fluorescent proteins. Nature Methods 5: 545-551.
    • (2008) Nature Methods , vol.5 , pp. 545-551
    • Shaner, N.C.1    Lin, M.Z.2    McKeown, M.R.3    Steinbach, P.A.4    Hazelwood, K.L.5
  • 15
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • Reetz M, Carballeira J, (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nature protocols 2: 891-903.
    • (2007) Nature Protocols , vol.2 , pp. 891-903
    • Reetz, M.1    Carballeira, J.2
  • 16
    • 23944525846 scopus 로고    scopus 로고
    • Strategies and computational tools for improving randomized protein libraries
    • Patrick WM, Firth AE, (2005) Strategies and computational tools for improving randomized protein libraries. Biomolecular engineering 22: 105-112.
    • (2005) Biomolecular Engineering , vol.22 , pp. 105-112
    • Patrick, W.M.1    Firth, A.E.2
  • 18
    • 84863280525 scopus 로고    scopus 로고
    • Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers
    • Tang L, Gao H, Zhu X, Wang X, Zhou M, et al. (2012) Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers. BioTechniques 52: 149-157.
    • (2012) BioTechniques , vol.52 , pp. 149-157
    • Tang, L.1    Gao, H.2    Zhu, X.3    Wang, X.4    Zhou, M.5
  • 19
    • 84874034041 scopus 로고    scopus 로고
    • Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis
    • Kille S, Acevedo-Rocha CG, Parra LP, Zhang ZG, Opperman DJ, et al. (2013) Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synthetic Biology 2(2) 83-92.
    • (2013) ACS Synthetic Biology , vol.2 , Issue.2 , pp. 83-92
    • Kille, S.1    Acevedo-Rocha, C.G.2    Parra, L.P.3    Zhang, Z.G.4    Opperman, D.J.5
  • 20
    • 0041765676 scopus 로고    scopus 로고
    • User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries
    • Patrick WM, Firth AE, Blackburn JM, (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Engineering 16: 451-457.
    • (2003) Protein Engineering , vol.16 , pp. 451-457
    • Patrick, W.M.1    Firth, A.E.2    Blackburn, J.M.3
  • 21
    • 18044397860 scopus 로고    scopus 로고
    • Mathematical expressions useful in the construction, description and evaluation of protein libraries
    • Bosley AD, Ostermeier M, (2005) Mathematical expressions useful in the construction, description and evaluation of protein libraries. Biomolecular Engineering 22: 57-61.
    • (2005) Biomolecular Engineering , vol.22 , pp. 57-61
    • Bosley, A.D.1    Ostermeier, M.2
  • 22
    • 48449095514 scopus 로고    scopus 로고
    • GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
    • Firth AE, Patrick WM, (2008) GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Research 36: W281-W285.
    • (2008) Nucleic Acids Research , vol.36
    • Firth, A.E.1    Patrick, W.M.2
  • 23
    • 84855716024 scopus 로고    scopus 로고
    • When second best is good enough: Another probabilistic look at saturation mutagenesis
    • Nov Y, (2012) When second best is good enough: Another probabilistic look at saturation mutagenesis. Applied and Environmental Microbiology 78: 258-262.
    • (2012) Applied and Environmental Microbiology , vol.78 , pp. 258-262
    • Nov, Y.1
  • 24
    • 0024803111 scopus 로고
    • The NK model of rugged fitness landscapes and its application to maturation of the immune response
    • Kauffman SA, Weinberger ED, (1989) The NK model of rugged fitness landscapes and its application to maturation of the immune response. Journal of Theoretical Biology 141: 211-245.
    • (1989) Journal of Theoretical Biology , vol.141 , pp. 211-245
    • Kauffman, S.A.1    Weinberger, E.D.2
  • 25
    • 0034280643 scopus 로고    scopus 로고
    • Adaptive walks by the fittest among finite random mutants on a Mt. Fuji-type fitness landscape - II. Effects of small non-additivity
    • Aita T, Husimi Y, (2000) Adaptive walks by the fittest among finite random mutants on a Mt. Fuji-type fitness landscape - II. Effects of small non-additivity. Journal of Mathematical Biology 41: 207-231.
    • (2000) Journal of Mathematical Biology , vol.41 , pp. 207-231
    • Aita, T.1    Husimi, Y.2
  • 26
    • 15944369582 scopus 로고    scopus 로고
    • Modeling and analysis of protein design under resource constraints
    • Nov Y, Wein LM, (2005) Modeling and analysis of protein design under resource constraints. Journal of Computational Biology 12: 247-282.
    • (2005) Journal of Computational Biology , vol.12 , pp. 247-282
    • Nov, Y.1    Wein, L.M.2
  • 28
    • 38949210848 scopus 로고    scopus 로고
    • Enzyme improvement in the absence of structural knowledge: a novel statistical approach
    • Barak Y, Nov Y, Ackerley DF, Matin A, (2008) Enzyme improvement in the absence of structural knowledge: a novel statistical approach. The ISME Journal 2: 171-179.
    • (2008) The ISME Journal , vol.2 , pp. 171-179
    • Barak, Y.1    Nov, Y.2    Ackerley, D.F.3    Matin, A.4
  • 29
    • 78049263384 scopus 로고    scopus 로고
    • Improving biocatalyst performance by integrating statistical methods into protein engineering
    • Brouk M, Nov Y, Fishman A, (2010) Improving biocatalyst performance by integrating statistical methods into protein engineering. Applied and Environmental Microbiology 76: 6397-6403.
    • (2010) Applied and Environmental Microbiology , vol.76 , pp. 6397-6403
    • Brouk, M.1    Nov, Y.2    Fishman, A.3
  • 31
    • 55849148481 scopus 로고    scopus 로고
    • Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions
    • Reetz M, Wu S (2008) Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chemical Communications: 5499-5501.
    • (2008) Chemical Communications , pp. 5499-5501
    • Reetz, M.1    Wu, S.2
  • 32
    • 0030483509 scopus 로고    scopus 로고
    • Directed evolution: Creating biocatalysts for the future
    • Arnold FH, (1996) Directed evolution: Creating biocatalysts for the future. Chemical Engineering Science 51: 5091-5102.
    • (1996) Chemical Engineering Science , vol.51 , pp. 5091-5102
    • Arnold, F.H.1
  • 33
    • 0030620273 scopus 로고    scopus 로고
    • Evolution of high mutation rates in experimental populations of E. coli
    • Sniegowski PD, Gerrish PJ, Lenski RE, (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387: 703-705.
    • (1997) Nature , vol.387 , pp. 703-705
    • Sniegowski, P.D.1    Gerrish, P.J.2    Lenski, R.E.3
  • 34
    • 0033770580 scopus 로고    scopus 로고
    • Rational evolutionary design: the theory of in vitro protein evolution
    • Voigt CA, Kauffman S, Wang ZG, (2001) Rational evolutionary design: the theory of in vitro protein evolution. Advances in Protein Chemistry 55: 79-160.
    • (2001) Advances in Protein Chemistry , vol.55 , pp. 79-160
    • Voigt, C.A.1    Kauffman, S.2    Wang, Z.G.3
  • 35
    • 20544449855 scopus 로고    scopus 로고
    • Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins
    • Drummond DA, Iverson BL, Georgiou G, Arnold FH, (2005) Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins. Journal of Molecular Biology 350: 806-816.
    • (2005) Journal of Molecular Biology , vol.350 , pp. 806-816
    • Drummond, D.A.1    Iverson, B.L.2    Georgiou, G.3    Arnold, F.H.4
  • 36
    • 67849130559 scopus 로고    scopus 로고
    • HotSpot wizard: a web server for identification of hot spots in protein engineering
    • Pavelka A, Chovancova E, Damborsky J, (2009) HotSpot wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Research 37: W376-W383.
    • (2009) Nucleic Acids Research , vol.37
    • Pavelka, A.1    Chovancova, E.2    Damborsky, J.3
  • 37
    • 0029785464 scopus 로고    scopus 로고
    • Potential use of additivity of mutational effects in simplifying protein engineering
    • Skinner MM, Terwilliger TC, (1996) Potential use of additivity of mutational effects in simplifying protein engineering. Proceedings of the National Academy of Sciences 93: 10753-10757.
    • (1996) Proceedings of the National Academy of Sciences , vol.93 , pp. 10753-10757
    • Skinner, M.M.1    Terwilliger, T.C.2
  • 38
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in proteindna interactions: how good an approximation is it?
    • Benos PV, Bulyk ML, Stormo GD, (2002) Additivity in proteindna interactions: how good an approximation is it? Nucleic Acids Research 30: 4442-4451.
    • (2002) Nucleic Acids Research , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 40
    • 84944485006 scopus 로고
    • The one-sided barrier problem for Gaussian noise
    • Slepian D, (1962) The one-sided barrier problem for Gaussian noise. Bell System Technical Journal 41: 463-501.
    • (1962) Bell System Technical Journal , vol.41 , pp. 463-501
    • Slepian, D.1
  • 44
    • 79957782720 scopus 로고    scopus 로고
    • A pH-based high-throughput screening of sucrose-utilizing transglucosidases for the development of enzymatic glucosylation tools
    • Champion E, Moulis C, Morel S, Mulard LA, Monsan P, et al. (2010) A pH-based high-throughput screening of sucrose-utilizing transglucosidases for the development of enzymatic glucosylation tools. ChemCatChem 2: 969-975.
    • (2010) ChemCatChem , vol.2 , pp. 969-975
    • Champion, E.1    Moulis, C.2    Morel, S.3    Mulard, L.A.4    Monsan, P.5
  • 45
    • 78349313517 scopus 로고    scopus 로고
    • Beyond directed evolution - semi-rational protein engineering and design
    • Lutz S, (2010) Beyond directed evolution - semi-rational protein engineering and design. Current Opinion in Biotechnology 21: 734-743.
    • (2010) Current Opinion in Biotechnology , vol.21 , pp. 734-743
    • Lutz, S.1
  • 46
    • 84868611622 scopus 로고    scopus 로고
    • Principles for designing ideal protein structures
    • Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, et al. (2012) Principles for designing ideal protein structures. Nature 491: 222-227.
    • (2012) Nature , vol.491 , pp. 222-227
    • Koga, N.1    Tatsumi-Koga, R.2    Liu, G.3    Xiao, R.4    Acton, T.B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.