메뉴 건너뛰기




Volumn 1179, Issue , 2014, Pages 261-278

Probabilistic methods in directed evolution: Library size, mutation rate, and diversity

Author keywords

Computational tools; Directed evolution; DNA shuffling; Error prone PCR; Library generation; Probabilistic modeling; Saturation mutagenesis; Staggered extension process

Indexed keywords

OLIGONUCLEOTIDE; PROTEIN VARIANT;

EID: 84925884241     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1053-3_18     Document Type: Review
Times cited : (11)

References (47)
  • 1
    • 0029670577 scopus 로고    scopus 로고
    • Directed evolution of a para-nitrobenzyl esterase for aqueousorganic solvents
    • Moore JC, Arnold FH (1996) Directed evolution of a para-nitrobenzyl esterase for aqueousorganic solvents. Nat Biotechnol 14(4):458
    • (1996) Nat Biotechnol , vol.14 , Issue.4 , pp. 458
    • Moore, J.C.1    Arnold, F.H.2
  • 3
    • 0032491867 scopus 로고    scopus 로고
    • Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution
    • Reetz MT, Zonta A, Schimossek K, Jaeger K-E, Liebeton K (1997) Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. Angew Chem Int Ed 36(24):2830-2832
    • (1997) Angew Chem Int Ed , vol.36 , Issue.24 , pp. 2830-2832
    • Reetz, M.T.1    Zonta, A.2    Schimossek, K.3    Jaeger, K.-E.4    Liebeton, K.5
  • 4
    • 0034718615 scopus 로고    scopus 로고
    • Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity
    • Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 97(20): 10701-10705
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.20 , pp. 10701-10705
    • Boder, E.T.1    Midelfort, K.S.2    Wittrup, K.D.3
  • 5
    • 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. Biomol Eng 22(4):105-112
    • (2005) Biomol Eng , vol.22 , Issue.4 , pp. 105-112
    • Patrick, W.M.1    Firth, A.E.2
  • 7
    • 84863280525 scopus 로고    scopus 로고
    • Construction of "smallintelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers
    • Tang L, Gao H, Zhu X, Wang X, Zhou M, Jiang R (2012) Construction of "smallintelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers. Biotechniques 52(3):149-158
    • (2012) Biotechniques , vol.52 , Issue.3 , pp. 149-158
    • Tang, L.1    Gao, H.2    Zhu, X.3    Wang, X.4    Zhou, M.5    Jiang, R.6
  • 9
  • 10
    • 0032004789 scopus 로고    scopus 로고
    • Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides
    • Jensen LJ, Andersen KV, Svendsen A, Kretzschmar T (1998) Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides. Nucleic Acids Res 26(3):697-702
    • (1998) Nucleic Acids Res , vol.26 , Issue.3 , pp. 697-702
    • Jensen, L.J.1    Andersen, K.V.2    Svendsen, A.3    Kretzschmar, T.4
  • 11
    • 0033055901 scopus 로고    scopus 로고
    • Combinatorial codons: A computer program to approximate amino acid probabilities with biased nucleotide usage
    • Wolf E, Kim PS (1999) Combinatorial codons: a computer program to approximate amino acid probabilities with biased nucleotide usage. Protein Sci 8(3):680-688
    • (1999) Protein Sci , vol.8 , Issue.3 , pp. 680-688
    • Wolf, E.1    Kim, P.S.2
  • 12
    • 2542563521 scopus 로고    scopus 로고
    • Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution
    • Neylon C (2004) Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res 32(4):1448-1459
    • (2004) Nucleic Acids Res , vol.32 , Issue.4 , pp. 1448-1459
    • Neylon, C.1
  • 13
    • 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(11):1797-1804
    • (2008) Chembiochem , vol.9 , Issue.11 , pp. 1797-1804
    • Reetz, M.T.1    Kahakeaw, D.2    Lohmer, R.3
  • 15
    • 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 Eng 16(6): 451-457
    • (2003) Protein Eng , vol.16 , Issue.6 , pp. 451-457
    • Patrick, W.M.1    Firth, A.E.2    Blackburn, J.M.3
  • 16
    • 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. Biomol Eng 22(1-3):57-61
    • (2005) Biomol Eng , vol.22 , Issue.1-3 , pp. 57-61
    • Bosley, A.D.1    Ostermeier, M.2
  • 17
    • 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 Res 36(suppl 2):W281-W285
    • (2008) Nucleic Acids Res , vol.36 , Issue.SUPPL. 2
    • Firth, A.E.1    Patrick, W.M.2
  • 18
    • 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. Appl Environ Microbiol 78(1):258-262
    • (2012) Appl Environ Microbiol , vol.78 , Issue.1 , pp. 258-262
    • Nov, Y.1
  • 19
    • 23944462537 scopus 로고    scopus 로고
    • Statistics of protein library construction
    • Firth AE, Patrick WM (2005) Statistics of protein library construction. Bioinformatics 21(15):3314-3315
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3314-3315
    • Firth, A.E.1    Patrick, W.M.2
  • 20
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • Reetz MT, Carballeira JD (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2(4):891-903
    • (2007) Nat Protoc , vol.2 , Issue.4 , pp. 891-903
    • Reetz, M.T.1    Carballeira, J.D.2
  • 21
    • 67649970532 scopus 로고    scopus 로고
    • Calculating complexity of large randomized libraries
    • Kong Y (2009) Calculating complexity of large randomized libraries. J Theor Biol 259(3): 641-645
    • (2009) J Theor Biol , vol.259 , Issue.3 , pp. 641-645
    • Kong, Y.1
  • 23
    • 0036997797 scopus 로고    scopus 로고
    • Mutation-replication statistics of polymerase chain reactions
    • Piau D (2004) Mutation-replication statistics of polymerase chain reactions. J Comput Biol 9(6):831-847
    • (2004) J Comput Biol , vol.9 , Issue.6 , pp. 831-847
    • Piau, D.1
  • 24
    • 0029258483 scopus 로고
    • The polymerase chain reaction and branching processes
    • Sun F (1995) The polymerase chain reaction and branching processes. J Comput Biol 2(1): 63-86
    • (1995) J Comput Biol , vol.2 , Issue.1 , pp. 63-86
    • Sun, F.1
  • 25
    • 0034100229 scopus 로고    scopus 로고
    • Estimation of the mutation rate during errorprone polymerase chain reaction
    • Wang D, Zhao C, Cheng R, Sun F (2000) Estimation of the mutation rate during errorprone polymerase chain reaction. J Comput Biol 7(1-2):143-158
    • (2000) J Comput Biol , vol.7 , Issue.1-2 , pp. 143-158
    • Wang, D.1    Zhao, C.2    Cheng, R.3    Sun, F.4
  • 26
    • 0029258947 scopus 로고
    • Modeling the polymerase chain reaction
    • Weiss G, von Haeseler A (1995) Modeling the polymerase chain reaction. J Comput Biol 2(1):49-61
    • (1995) J Comput Biol , vol.2 , Issue.1 , pp. 49-61
    • Weiss, G.1    Von Haeseler, A.2
  • 27
    • 0034617906 scopus 로고    scopus 로고
    • Modeling DNA mutation and recombination for directed evolution experiments
    • Moore GL, Maranas CD (2000) Modeling DNA mutation and recombination for directed evolution experiments. J Theor Biol 205(3): 483-503
    • (2000) J Theor Biol , vol.205 , Issue.3 , pp. 483-503
    • Moore, G.L.1    Maranas, C.D.2
  • 28
    • 70350339292 scopus 로고    scopus 로고
    • Isolation, cloning and characterization of a tyrosinase with improved activity in organic solvents from Bacillus megaterium
    • Shuster V, Fishman A (2009) Isolation, cloning and characterization of a tyrosinase with improved activity in organic solvents from Bacillus megaterium. J Mol Microbiol Biotechnol 17(4):188-200
    • (2009) J Mol Microbiol Biotechnol , vol.17 , Issue.4 , pp. 188-200
    • Shuster, V.1    Fishman, A.2
  • 29
    • 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. J Mol Biol 350(4):806-816
    • (2005) J Mol Biol , vol.350 , Issue.4 , pp. 806-816
    • Drummond, D.A.1    Iverson, B.L.2    Georgiou, G.3    Arnold, F.H.4
  • 30
    • 21444445575 scopus 로고    scopus 로고
    • A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries
    • Volles MJ, Lansbury PT (2005) A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries. Nucleic Acids Res 33(11):3667-3677
    • (2005) Nucleic Acids Res , vol.33 , Issue.11 , pp. 3667-3677
    • Volles, M.J.1    Lansbury, P.T.2
  • 31
    • 84868216091 scopus 로고    scopus 로고
    • MAP 2.0 3D: A sequence/structure based server for protein engineering
    • Verma R, Schwaneberg U, Roccatano D (2012) MAP 2.0 3D: a sequence/structure based server for protein engineering. ACS Synth Biol 1(4):139-150
    • (2012) ACS Synth Biol , vol.1 , Issue.4 , pp. 139-150
    • Verma, R.1    Schwaneberg, U.2    Roccatano, D.3
  • 32
    • 0028110130 scopus 로고
    • DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution
    • Stemmer WP (1994) DNA shuffl ing by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A 91(22):10747-10751
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.22 , pp. 10747-10751
    • Stemmer, W.P.1
  • 33
    • 0031909113 scopus 로고    scopus 로고
    • Molecular evolution by staggered extension process (StEP) in vitro recombination
    • Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16(3):258-261
    • (1998) Nat Biotechnol , vol.16 , Issue.3 , pp. 258-261
    • Zhao, H.1    Giver, L.2    Shao, Z.3    Affholter, J.A.4    Arnold, F.H.5
  • 34
    • 0031587291 scopus 로고    scopus 로고
    • Strategies for the in vitro evolution of protein function: Enzyme evolution by random recombination of improved sequences
    • Moore JC, Jin H-M, Kuchner O, Arnold FH (1997) Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J Mol Biol 272(3):336-347
    • (1997) J Mol Biol , vol.272 , Issue.3 , pp. 336-347
    • Moore, J.C.1    Jin, H.-M.2    Kuchner, O.3    Arnold, F.H.4
  • 35
    • 0032893491 scopus 로고    scopus 로고
    • Modeling DNA shuffling
    • Sun F (1999) Modeling DNA shuffl ing. J Comput Biol 6(1):77-90
    • (1999) J Comput Biol , vol.6 , Issue.1 , pp. 77-90
    • Sun, F.1
  • 38
    • 0038799745 scopus 로고    scopus 로고
    • General method for sequence-independent site-directed chimeragenesis
    • Hiraga K, Arnold FH (2003) General method for sequence-independent site-directed chimeragenesis. J Mol Biol 330(2):287-296
    • (2003) J Mol Biol , vol.330 , Issue.2 , pp. 287-296
    • Hiraga, K.1    Arnold, F.H.2
  • 39
    • 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 Eng Des Sel 20(5):219-226
    • (2007) Protein Eng des Sel , vol.20 , Issue.5 , pp. 219-226
    • Herman, A.1    Tawfik, D.S.2
  • 40
    • 2342535792 scopus 로고    scopus 로고
    • Sequence saturation mutagenesis (SeSaM): A novel method for directed evolution
    • Wong TS, Tee KL, Hauer B, Schwaneberg U (2004) Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. Nucleic Acids Res 32(3):e26
    • (2004) Nucleic Acids Res , vol.32 , Issue.3
    • Wong, T.S.1    Tee, K.L.2    Hauer, B.3    Schwaneberg, U.4
  • 41
    • 0032518211 scopus 로고    scopus 로고
    • Modified base compositions at degenerate positions of a mutagenic oligonucleotide enhance randomness in site-saturation mutagenesis
    • Airaksinen A, Hovi T (1998) Modified base compositions at degenerate positions of a mutagenic oligonucleotide enhance randomness in site-saturation mutagenesis. Nucleic Acids Res 26(2):576-581
    • (1998) Nucleic Acids Res , vol.26 , Issue.2 , pp. 576-581
    • Airaksinen, A.1    Hovi, T.2
  • 42
    • 14844325781 scopus 로고    scopus 로고
    • Reducing mutational bias in random protein libraries
    • Vanhercke T, Ampe C, Tirry L, Denolf P (2005) Reducing mutational bias in random protein libraries. Anal Biochem 339(1):9-14
    • (2005) Anal Biochem , vol.339 , Issue.1 , pp. 9-14
    • Vanhercke, T.1    Ampe, C.2    Tirry, L.3    Denolf, P.4
  • 43
    • 34250727621 scopus 로고    scopus 로고
    • Protein library design and screening: Working out the probabilities
    • In: Arndt KM, Müller KM (eds Methods in molecular biology. Humana Press Inc., Totowa, NJ
    • Denault M, Pelletier JN (2007) Protein library design and screening: working out the probabilities. In: Arndt KM, Müller KM (eds) Protein engineering protocols, vol 352, Methods in molecular biology. Humana Press Inc., Totowa, NJ
    • (2007) Protein Engineering Protocols , vol.352
    • Denault, M.1    Pelletier, J.N.2
  • 45
    • 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. J Comput Biol 12(2):247-282
    • (2005) J Comput Biol , vol.12 , Issue.2 , pp. 247-282
    • Nov, Y.1    Wein, L.M.2
  • 46
    • 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 (2007) Enzyme improvement in the absence of structural knowledge: a novel statistical approach. ISME J 2(2):171-179
    • (2007) ISME J , vol.2 , Issue.2 , pp. 171-179
    • Barak, Y.1    Nov, Y.2    Ackerley, D.F.3    Matin, A.4
  • 47
    • 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. Appl Environ Microbiol 76(19): 6397-6403
    • (2010) Appl Environ Microbiol , vol.76 , Issue.19 , pp. 6397-6403
    • Brouk, M.1    Nov, Y.2    Fishman, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.