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Volumn 57, Issue 1, 2018, Pages 38-46

Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; BIOCHEMISTRY; DNA; DNA SEQUENCES; GENE ENCODING; LEARNING SYSTEMS; MOLECULAR BIOLOGY; PROTEINS;

EID: 85040309415     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.7b00886     Document Type: Review
Times cited : (9)

References (89)
  • 1
    • 0032404542 scopus 로고    scopus 로고
    • The game of chess and searches in protein sequence space
    • Mandecki, W. (1998) The game of chess and searches in protein sequence space Trends Biotechnol. 16, 200-202 10.1016/S0167-7799(98)01188-3
    • (1998) Trends Biotechnol. , vol.16 , pp. 200-202
    • Mandecki, W.1
  • 3
    • 84905217368 scopus 로고    scopus 로고
    • Deep mutational scanning: A new style of protein science
    • Fowler, D. M. and Fields, S. (2014) Deep mutational scanning: a new style of protein science Nat. Methods 11, 801-807 10.1038/nmeth.3027
    • (2014) Nat. Methods , vol.11 , pp. 801-807
    • Fowler, D.M.1    Fields, S.2
  • 4
    • 84996931924 scopus 로고    scopus 로고
    • Deep sequencing methods for protein engineering and design
    • Wrenbeck, E. E., Faber, M. S., and Whitehead, T. A. (2017) Deep sequencing methods for protein engineering and design Curr. Opin. Struct. Biol. 45, 36-44 10.1016/j.sbi.2016.11.001
    • (2017) Curr. Opin. Struct. Biol. , vol.45 , pp. 36-44
    • Wrenbeck, E.E.1    Faber, M.S.2    Whitehead, T.A.3
  • 5
    • 85038882559 scopus 로고    scopus 로고
    • Targeted mutagenesis: A sniper-like diversity generator in microbial engineering
    • Zheng, X., Xing, X.-H., and Zhang, C. (2017) Targeted mutagenesis: A sniper-like diversity generator in microbial engineering Synth. Syst. Biotechnol. 2, 75-86 10.1016/j.synbio.2017.07.001
    • (2017) Synth. Syst. Biotechnol. , vol.2 , pp. 75-86
    • Zheng, X.1    Xing, X.-H.2    Zhang, C.3
  • 6
    • 80051794613 scopus 로고    scopus 로고
    • Deep mutational scanning:assessing protein function on a massive scale
    • Araya, C. L. and Fowler, D. M. (2011) Deep mutational scanning:assessing protein function on a massive scale Trends Biotechnol. 29, 435-442 10.1016/j.tibtech.2011.04.003
    • (2011) Trends Biotechnol. , vol.29 , pp. 435-442
    • Araya, C.L.1    Fowler, D.M.2
  • 7
    • 83355174920 scopus 로고    scopus 로고
    • Enrich: Software for analysis of protein function by enrichment and depletion of variants
    • Fowler, D. M., Araya, C. L., Gerard, W., and Fields, S. (2011) Enrich: Software for analysis of protein function by enrichment and depletion of variants Bioinformatics 27, 3430-3431 10.1093/bioinformatics/btr577
    • (2011) Bioinformatics , vol.27 , pp. 3430-3431
    • Fowler, D.M.1    Araya, C.L.2    Gerard, W.3    Fields, S.4
  • 8
    • 84979911464 scopus 로고    scopus 로고
    • Massively parallel genetics
    • Shendure, J. and Fields, S. (2016) Massively parallel genetics Genetics 203, 617-619 10.1534/genetics.115.180562
    • (2016) Genetics , vol.203 , pp. 617-619
    • Shendure, J.1    Fields, S.2
  • 10
    • 33746363486 scopus 로고    scopus 로고
    • Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits
    • Bhattacharyya, R. P., Reményi, A., Yeh, B. J., and Lim, W. A. (2006) Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits Annu. Rev. Biochem. 75, 655-680 10.1146/annurev.biochem.75.103004.142710
    • (2006) Annu. Rev. Biochem. , vol.75 , pp. 655-680
    • Bhattacharyya, R.P.1    Reményi, A.2    Yeh, B.J.3    Lim, W.A.4
  • 11
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, E. S. et al. 2001, Initial sequencing and analysis of the human genome Nature 409, 860-921 10.1038/35057062
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 13
    • 1942425613 scopus 로고    scopus 로고
    • Domain insertions in protein structures
    • Aroul-Selvam, R., Hubbard, T., and Sasidharan, R. (2004) Domain insertions in protein structures J. Mol. Biol. 338, 633-641 10.1016/j.jmb.2004.03.039
    • (2004) J. Mol. Biol. , vol.338 , pp. 633-641
    • Aroul-Selvam, R.1    Hubbard, T.2    Sasidharan, R.3
  • 14
    • 0346500466 scopus 로고    scopus 로고
    • Creation of an Allosteric Enzyme by Domain Insertion
    • Guntas, G. and Ostermeier, M. (2004) Creation of an Allosteric Enzyme by Domain Insertion J. Mol. Biol. 336, 263-273 10.1016/j.jmb.2003.12.016
    • (2004) J. Mol. Biol. , vol.336 , pp. 263-273
    • Guntas, G.1    Ostermeier, M.2
  • 15
    • 23844465160 scopus 로고    scopus 로고
    • Directed evolution of protein switches and their application to the creation of ligand-binding proteins
    • Guntas, G., Mansell, T. J., Kim, J. R., and Ostermeier, M. (2005) Directed evolution of protein switches and their application to the creation of ligand-binding proteins Proc. Natl. Acad. Sci. U. S. A. 102, 11224-9 10.1073/pnas.0502673102
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 11224-11229
    • Guntas, G.1    Mansell, T.J.2    Kim, J.R.3    Ostermeier, M.4
  • 16
    • 71849115077 scopus 로고    scopus 로고
    • Genome engineering
    • Carr, P. A. and Church, G. M. (2009) Genome engineering Nat. Biotechnol. 27, 1151-1162 10.1038/nbt.1590
    • (2009) Nat. Biotechnol. , vol.27 , pp. 1151-1162
    • Carr, P.A.1    Church, G.M.2
  • 17
    • 84873800970 scopus 로고    scopus 로고
    • Genome-scale engineering for systems and synthetic biology
    • Esvelt, K. M. and Wang, H. H. (2013) Genome-scale engineering for systems and synthetic biology Mol. Syst. Biol. 9, 641 10.1038/msb.2012.66
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 641
    • Esvelt, K.M.1    Wang, H.H.2
  • 19
    • 77952530236 scopus 로고    scopus 로고
    • Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process
    • LeProust, E. M., Peck, B. J., Spirin, K., McCuen, H. B., Moore, B., Namsaraev, E., and Caruthers, M. H. (2010) Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process Nucleic Acids Res. 38, 2522-2540 10.1093/nar/gkq163
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2522-2540
    • LeProust, E.M.1    Peck, B.J.2    Spirin, K.3    McCuen, H.B.4    Moore, B.5    Namsaraev, E.6    Caruthers, M.H.7
  • 20
    • 84968903135 scopus 로고    scopus 로고
    • Coming of age: Ten years of next- generation sequencing technologies
    • Goodwin, S., Mcpherson, J. D., and Mccombie, W. R. (2016) Coming of age: ten years of next- generation sequencing technologies Nat. Rev. Genet. 17, 333-351 10.1038/nrg.2016.49
    • (2016) Nat. Rev. Genet. , vol.17 , pp. 333-351
    • Goodwin, S.1    McPherson, J.D.2    McCombie, W.R.3
  • 21
    • 84879627975 scopus 로고    scopus 로고
    • Next-Generation Sequencing Platforms
    • Mardis, E. R. (2013) Next-Generation Sequencing Platforms Annu. Rev. Anal. Chem. 6, 287-303 10.1146/annurev-anchem-062012-092628
    • (2013) Annu. Rev. Anal. Chem. , vol.6 , pp. 287-303
    • Mardis, E.R.1
  • 22
    • 84947299022 scopus 로고    scopus 로고
    • PacBio Sequencing and Its Applications
    • Rhoads, A. and Au, K. F. (2015) PacBio Sequencing and Its Applications Genomics, Proteomics Bioinf. 13, 278-289 10.1016/j.gpb.2015.08.002
    • (2015) Genomics, Proteomics Bioinf. , vol.13 , pp. 278-289
    • Rhoads, A.1    Au, K.F.2
  • 23
    • 85030702848 scopus 로고    scopus 로고
    • The potential impact of nanopore sequencing on human genetics
    • Loose, M. W. (2017) The potential impact of nanopore sequencing on human genetics Hum. Mol. Genet. 26, R202-R207 10.1093/hmg/ddx287
    • (2017) Hum. Mol. Genet. , vol.26 , pp. R202-R207
    • Loose, M.W.1
  • 25
    • 84871288267 scopus 로고    scopus 로고
    • PFunkel: Efficient, Expansive, User-Defined Mutagenesis
    • Firnberg, E. and Ostermeier, M. (2012) PFunkel: Efficient, Expansive, User-Defined Mutagenesis PLoS One 7, e52031 10.1371/journal.pone.0052031
    • (2012) PLoS One , vol.7 , pp. e52031
    • Firnberg, E.1    Ostermeier, M.2
  • 27
    • 0035487293 scopus 로고    scopus 로고
    • Recombineering: A powerful new tool for mouse functional genomics
    • Copeland, N. G., Jenkins, N. a., and Court, D. L. (2001) Recombineering: a powerful new tool for mouse functional genomics Nat. Rev. Genet. 2, 769-779 10.1038/35093556
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 769-779
    • Copeland, N.G.1    Jenkins, N.A.2    Court, D.L.3
  • 28
    • 85031936326 scopus 로고    scopus 로고
    • Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering
    • Higgins, S. A., Ouonkap, S. V. Y., and Savage, D. F. (2017) Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering ACS Synth. Biol. n/a 10.1021/acssynbio.7b00112
    • (2017) ACS Synth. Biol. , pp. n/a
    • Higgins, S.A.1    Ouonkap, S.V.Y.2    Savage, D.F.3
  • 30
    • 84931574824 scopus 로고    scopus 로고
    • Methods for the directed evolution of proteins
    • Packer, M. S. and Liu, D. R. (2015) Methods for the directed evolution of proteins Nat. Rev. Genet. 16, 379-394 10.1038/nrg3927
    • (2015) Nat. Rev. Genet. , vol.16 , pp. 379-394
    • Packer, M.S.1    Liu, D.R.2
  • 31
    • 0034323194 scopus 로고    scopus 로고
    • Efficient gene targeted random mutagenesis in genetically stable Escherichia coli strains
    • Fabret, C., Poncet, S., Danielsen, S., Borchert, T. V., Ehrlich, S. D., and Jannière, L. (2000) Efficient gene targeted random mutagenesis in genetically stable Escherichia coli strains Nucleic Acids Res. 28, 95e 10.1093/nar/28.21.e95
    • (2000) Nucleic Acids Res. , vol.28 , pp. 95e
    • Fabret, C.1    Poncet, S.2    Danielsen, S.3    Borchert, T.V.4    Ehrlich, S.D.5    Jannière, L.6
  • 32
    • 84877280637 scopus 로고    scopus 로고
    • Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM
    • Finney-Manchester, S. P. and Maheshri, N. (2013) Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM Nucleic Acids Res. 41, e99 10.1093/nar/gkt150
    • (2013) Nucleic Acids Res. , vol.41 , pp. e99
    • Finney-Manchester, S.P.1    Maheshri, N.2
  • 34
    • 79955534060 scopus 로고    scopus 로고
    • A system for the continuous directed evolution of biomolecules
    • Esvelt, K. M., Carlson, J. C., and Liu, D. R. (2011) A system for the continuous directed evolution of biomolecules Nature 472, 499-503 10.1038/nature09929
    • (2011) Nature , vol.472 , pp. 499-503
    • Esvelt, K.M.1    Carlson, J.C.2    Liu, D.R.3
  • 35
    • 84971006562 scopus 로고    scopus 로고
    • Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
    • Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., and Liu, D. R. (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage Nature 533, 420-424 10.1038/nature17946
    • (2016) Nature , vol.533 , pp. 420-424
    • Komor, A.C.1    Kim, Y.B.2    Packer, M.S.3    Zuris, J.A.4    Liu, D.R.5
  • 36
    • 0035378483 scopus 로고    scopus 로고
    • Circular permutation of 5-aminolevulinate synthase: Mapping the polypeptide chain to its function
    • Cheltsov, A. V., Barber, M. J., and Ferreira, G. C. (2001) Circular permutation of 5-aminolevulinate synthase: Mapping the polypeptide chain to its function J. Biol. Chem. 276, 19141-19149 10.1074/jbc.M100329200
    • (2001) J. Biol. Chem. , vol.276 , pp. 19141-19149
    • Cheltsov, A.V.1    Barber, M.J.2    Ferreira, G.C.3
  • 37
    • 25844525807 scopus 로고    scopus 로고
    • Improving the catalytic activity of Candida antarctica lipase B by circular permutation
    • Qian, Z. and Lutz, S. (2005) Improving the catalytic activity of Candida antarctica lipase B by circular permutation J. Am. Chem. Soc. 127, 13466-13467 10.1021/ja053932h
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 13466-13467
    • Qian, Z.1    Lutz, S.2
  • 38
    • 73149090616 scopus 로고    scopus 로고
    • Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor
    • Okada, S., Ota, K., and Ito, T. (2009) Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor Protein Sci. 18, 2518-2527 10.1002/pro.266
    • (2009) Protein Sci. , vol.18 , pp. 2518-2527
    • Okada, S.1    Ota, K.2    Ito, T.3
  • 40
    • 0036019341 scopus 로고    scopus 로고
    • Improving a circularly permuted TEM-1 beta-lactamase by directed evolution
    • Osuna, J., Pérez-Blancas, A., and Soberón, X. (2002) Improving a circularly permuted TEM-1 beta-lactamase by directed evolution Protein Eng., Des. Sel. 15, 463-470 10.1093/protein/15.6.463
    • (2002) Protein Eng., Des. Sel. , vol.15 , pp. 463-470
    • Osuna, J.1    Pérez-Blancas, A.2    Soberón, X.3
  • 41
    • 84982695547 scopus 로고    scopus 로고
    • Rapid construction of metabolite biosensors using domain-insertion profiling
    • Nadler, D. C., Morgan, S.-A., Flamholz, A., Kortright, K. E., and Savage, D. F. (2016) Rapid construction of metabolite biosensors using domain-insertion profiling Nat. Commun. 7, 12266 10.1038/ncomms12266
    • (2016) Nat. Commun. , vol.7 , pp. 12266
    • Nadler, D.C.1    Morgan, S.-A.2    Flamholz, A.3    Kortright, K.E.4    Savage, D.F.5
  • 42
    • 0029859408 scopus 로고    scopus 로고
    • Random circular permutation of genes and expressed polypeptide chains: Application of the method to the catalytic chains of aspartate transcarbamoylase
    • Graf, R. and Schachman, H. K. (1996) Random circular permutation of genes and expressed polypeptide chains: Application of the method to the catalytic chains of aspartate transcarbamoylase Proc. Natl. Acad. Sci. U. S. A. 93, 11591-11596 10.1073/pnas.93.21.11591
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 11591-11596
    • Graf, R.1    Schachman, H.K.2
  • 43
    • 85040306989 scopus 로고    scopus 로고
    • Transposon for protein engineering
    • Shah, V. and Kim, J. R. (2016) Transposon for protein engineering Mobile Genet. Elem. 6 e1239601 10.1080/2159256X.2016.1239601
    • (2016) Mobile Genet. Elem. , vol.6 , pp. e1239601
    • Shah, V.1    Kim, J.R.2
  • 44
    • 77955244296 scopus 로고    scopus 로고
    • Regulation of β-lactamase activity by remote binding of heme: Functional coupling of unrelated proteins through domain insertion
    • Edwards, W. R., Williams, A. J., Morris, J. L., Baldwin, A. J., Allemann, R. K., and Jones, D. D. (2010) Regulation of β-lactamase activity by remote binding of heme: Functional coupling of unrelated proteins through domain insertion Biochemistry 49, 6541-6549 10.1021/bi100793y
    • (2010) Biochemistry , vol.49 , pp. 6541-6549
    • Edwards, W.R.1    Williams, A.J.2    Morris, J.L.3    Baldwin, A.J.4    Allemann, R.K.5    Jones, D.D.6
  • 45
    • 84861382322 scopus 로고    scopus 로고
    • A transposase strategy for creating libraries of circularly permuted proteins
    • Mehta, M. M., Liu, S., and Silberg, J. J. (2012) A transposase strategy for creating libraries of circularly permuted proteins Nucleic Acids Res. 40, e71 10.1093/nar/gks060
    • (2012) Nucleic Acids Res. , vol.40 , pp. e71
    • Mehta, M.M.1    Liu, S.2    Silberg, J.J.3
  • 47
    • 84923351044 scopus 로고    scopus 로고
    • Construction of a random circular permutation library using an engineered transposon
    • Pierre, B., Shah, V., Xiao, J., and Kim, J. R. (2015) Construction of a random circular permutation library using an engineered transposon Anal. Biochem. 474, 16-24 10.1016/j.ab.2014.12.011
    • (2015) Anal. Biochem. , vol.474 , pp. 16-24
    • Pierre, B.1    Shah, V.2    Xiao, J.3    Kim, J.R.4
  • 49
    • 84902239774 scopus 로고    scopus 로고
    • Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure
    • Arpino, J. a J., Reddington, S. C., Halliwell, L. M., Rizkallah, P. J., and Jones, D. D. (2014) Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure Structure 22, 889-898 10.1016/j.str.2014.03.014
    • (2014) Structure , vol.22 , pp. 889-898
    • Arpino, J.A.J.1    Reddington, S.C.2    Halliwell, L.M.3    Rizkallah, P.J.4    Jones, D.D.5
  • 50
    • 85022056365 scopus 로고    scopus 로고
    • Extensive libraries of gene truncation variants generated by in vitro transposition
    • Morelli, A., Cabezas, Y., Mills, L. J., and Seelig, B. (2017) Extensive libraries of gene truncation variants generated by in vitro transposition Nucleic Acids Res. 45, gkx030 10.1093/nar/gkx030
    • (2017) Nucleic Acids Res. , vol.45 , pp. gkx030
    • Morelli, A.1    Cabezas, Y.2    Mills, L.J.3    Seelig, B.4
  • 51
    • 27244448322 scopus 로고    scopus 로고
    • Triplet nucleotide removal at random positions in a target gene: The tolerance of TEM-1-lactamase to an amino acid deletion
    • Jones, D. D. (2005) Triplet nucleotide removal at random positions in a target gene: The tolerance of TEM-1-lactamase to an amino acid deletion Nucleic Acids Res. 33, e80 10.1093/nar/gni077
    • (2005) Nucleic Acids Res. , vol.33 , pp. e80
    • Jones, D.D.1
  • 53
    • 84901408859 scopus 로고    scopus 로고
    • A comprehensive, high-resolution map of a Gene's fitness landscape
    • Firnberg, E., Labonte, J. W., Gray, J. J., and Ostermeier, M. (2014) A comprehensive, high-resolution map of a Gene's fitness landscape Mol. Biol. Evol. 31, 1581-1592 10.1093/molbev/msu081
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 1581-1592
    • Firnberg, E.1    Labonte, J.W.2    Gray, J.J.3    Ostermeier, M.4
  • 54
    • 85011757987 scopus 로고    scopus 로고
    • Applications of yeast surface display for protein engineering
    • Cherf, G. M. and Cochran, J. R. (2015) Applications of yeast surface display for protein engineering Methods Mol. Biol. 1319, 155-175 10.1007/978-1-4939-2748-7-8
    • (2015) Methods Mol. Biol. , vol.1319 , pp. 155-175
    • Cherf, G.M.1    Cochran, J.R.2
  • 55
    • 84957439134 scopus 로고    scopus 로고
    • Advancement and applications of peptide phage display technology in biomedical science
    • Wu, C.-H., Liu, I.-J., Lu, R.-M., and Wu, H.-C. (2016) Advancement and applications of peptide phage display technology in biomedical science J. Biomed. Sci. 23, 8 10.1186/s12929-016-0223-x
    • (2016) J. Biomed. Sci. , vol.23 , pp. 8
    • Wu, C.-H.1    Liu, I.-J.2    Lu, R.-M.3    Wu, H.-C.4
  • 56
    • 0030974119 scopus 로고    scopus 로고
    • In vitro selection and evolution of functional proteins by using ribosome display
    • Hanes, J. and Plückthun, A. (1997) In vitro selection and evolution of functional proteins by using ribosome display Proc. Natl. Acad. Sci. U. S. A. 94, 4937-42 10.1073/pnas.94.10.4937
    • (1997) Proc. Natl. Acad. Sci. U. S. A. , vol.94 , pp. 4937-4942
    • Hanes, J.1    Plückthun, A.2
  • 57
    • 85020295301 scopus 로고    scopus 로고
    • Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded
    • Wrenbeck, E. E., Azouz, L. R., and Whitehead, T. A. (2017) Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded Nat. Commun. 8, 15695 10.1038/ncomms15695
    • (2017) Nat. Commun. , vol.8 , pp. 15695
    • Wrenbeck, E.E.1    Azouz, L.R.2    Whitehead, T.A.3
  • 58
    • 85015409814 scopus 로고    scopus 로고
    • Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes
    • Hassanpour, N., Ullah, E., Yousofshahi, M., Nair, N. U., and Hassoun, S. (2017) Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes Metab. Eng. Commun. 4, 37-47 10.1016/j.meteno.2017.02.003
    • (2017) Metab. Eng. Commun. , vol.4 , pp. 37-47
    • Hassanpour, N.1    Ullah, E.2    Yousofshahi, M.3    Nair, N.U.4    Hassoun, S.5
  • 59
    • 84892184252 scopus 로고    scopus 로고
    • Directed evolution of genetic parts and circuits by compartmentalized partnered replication
    • Ellefson, J. W., Meyer, A. J., Hughes, R. a., Cannon, J. R., Brodbelt, J. S., and Ellington, A. D. (2014) Directed evolution of genetic parts and circuits by compartmentalized partnered replication Nat. Biotechnol. 32, 97-101 10.1038/nbt.2714
    • (2014) Nat. Biotechnol. , vol.32 , pp. 97-101
    • Ellefson, J.W.1    Meyer, A.J.2    Hughes, R.A.3    Cannon, J.R.4    Brodbelt, J.S.5    Ellington, A.D.6
  • 60
    • 77955042704 scopus 로고    scopus 로고
    • Fluorescence Activated Cell Sorting as a General Ultra High-throughput Screening Method for Directed Evolution of Glycosyltransferases
    • Yang, G., Rich, J. R., Gilbert, M., Wakarchuk, W. W., Feng, Y., and Withers, S. G. (2010) Fluorescence Activated Cell Sorting as a General Ultra High-throughput Screening Method for Directed Evolution of Glycosyltransferases J. Am. Chem. Soc. 132, 10570-10577 10.1021/ja104167y
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 10570-10577
    • Yang, G.1    Rich, J.R.2    Gilbert, M.3    Wakarchuk, W.W.4    Feng, Y.5    Withers, S.G.6
  • 62
    • 84959519771 scopus 로고    scopus 로고
    • Genetically encoded sensors enable real-time observation of metabolite production
    • Rogers, J. K. and Church, G. M. (2016) Genetically encoded sensors enable real-time observation of metabolite production Proc. Natl. Acad. Sci. U. S. A. 113, 2388-2393 10.1073/pnas.1600375113
    • (2016) Proc. Natl. Acad. Sci. U. S. A. , vol.113 , pp. 2388-2393
    • Rogers, J.K.1    Church, G.M.2
  • 63
    • 84884920570 scopus 로고    scopus 로고
    • Label-free high-throughput assays to screen and characterize novel lactate dehydrogenase inhibitors
    • Vanderporten, E., Frick, L., Turincio, R., Thana, P., Lamarr, W., and Liu, Y. (2013) Label-free high-throughput assays to screen and characterize novel lactate dehydrogenase inhibitors Anal. Biochem. 441, 115-122 10.1016/j.ab.2013.07.003
    • (2013) Anal. Biochem. , vol.441 , pp. 115-122
    • Vanderporten, E.1    Frick, L.2    Turincio, R.3    Thana, P.4    Lamarr, W.5    Liu, Y.6
  • 64
    • 84930274369 scopus 로고    scopus 로고
    • Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study
    • Rye, P. T. and LaMarr, W. A. (2015) Measurement of glycolysis reactants by high-throughput solid phase extraction with tandem mass spectrometry: Characterization of pyrophosphate-dependent phosphofructokinase as a case study Anal. Biochem. 482, 40-47 10.1016/j.ab.2015.03.029
    • (2015) Anal. Biochem. , vol.482 , pp. 40-47
    • Rye, P.T.1    LaMarr, W.A.2
  • 66
    • 84986254038 scopus 로고    scopus 로고
    • A statistical guide to the design of deep mutational scanning experiments
    • Matuszewski, S., Hildebrandt, M. E., Ghenu, A.-H., Jensen, J. D., and Bank, C. (2016) A statistical guide to the design of deep mutational scanning experiments Genetics 204, 77-87 10.1534/genetics.116.190462
    • (2016) Genetics , vol.204 , pp. 77-87
    • Matuszewski, S.1    Hildebrandt, M.E.2    Ghenu, A.-H.3    Jensen, J.D.4    Bank, C.5
  • 67
    • 84896731976 scopus 로고    scopus 로고
    • Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets
    • Persikov, A. V., Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B. (2014) Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets Nucleic Acids Res. 42, 1497-1508 10.1093/nar/gkt1034
    • (2014) Nucleic Acids Res. , vol.42 , pp. 1497-1508
    • Persikov, A.V.1    Rowland, E.F.2    Oakes, B.L.3    Singh, M.4    Noyes, M.B.5
  • 68
    • 0016429803 scopus 로고
    • Site-directed mutagenesis: Effect of an extracistronic mutation on the in vitro propagation of bacteriophage Qbeta RNA
    • Flavell, R. A., Sabo, D. L., Bandle, E. F., and Weissmann, C. (1975) Site-directed mutagenesis: effect of an extracistronic mutation on the in vitro propagation of bacteriophage Qbeta RNA Proc. Natl. Acad. Sci. U. S. A. 72, 367-71 10.1073/pnas.72.1.367
    • (1975) Proc. Natl. Acad. Sci. U. S. A. , vol.72 , pp. 367-371
    • Flavell, R.A.1    Sabo, D.L.2    Bandle, E.F.3    Weissmann, C.4
  • 69
    • 0024403619 scopus 로고
    • High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
    • Cunningham, B. C. and Wells, J. A. (1989) High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis Science (Washington, DC, U. S.) 244, 1081-1085 10.1126/science.2471267
    • (1989) Science (Washington, DC, U. S.) , vol.244 , pp. 1081-1085
    • Cunningham, B.C.1    Wells, J.A.2
  • 71
    • 33845864966 scopus 로고    scopus 로고
    • Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
    • Bershtein, S., Segal, M., Bekerman, R., Tokuriki, N., and Tawfik, D. S. (2006) Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein Nature 444, 929-932 10.1038/nature05385
    • (2006) Nature , vol.444 , pp. 929-932
    • Bershtein, S.1    Segal, M.2    Bekerman, R.3    Tokuriki, N.4    Tawfik, D.S.5
  • 72
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki, N. and Tawfik, D. S. (2009) Stability effects of mutations and protein evolvability Curr. Opin. Struct. Biol. 19, 596-604 10.1016/j.sbi.2009.08.003
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 73
    • 84923249936 scopus 로고    scopus 로고
    • A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain
    • Olson, C. A., Wu, N. C. W., and Sun, R. (2014) A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain Curr. Biol. 24, 2643-2651 10.1016/j.cub.2014.09.072
    • (2014) Curr. Biol. , vol.24 , pp. 2643-2651
    • Olson, C.A.1    Wu, N.C.W.2    Sun, R.3
  • 74
    • 84906217475 scopus 로고    scopus 로고
    • Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
    • Melnikov, A., Rogov, P., Wang, L., Gnirke, A., and Mikkelsen, T. S. (2014) Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes Nucleic Acids Res. 42, e112 10.1093/nar/gku511
    • (2014) Nucleic Acids Res. , vol.42 , pp. e112
    • Melnikov, A.1    Rogov, P.2    Wang, L.3    Gnirke, A.4    Mikkelsen, T.S.5
  • 75
    • 84892997887 scopus 로고    scopus 로고
    • One contact for every twelve residues allows robust and accurate topology-level protein structure modeling
    • Kim, D. E., Dimaio, F., Yu-Ruei Wang, R., Song, Y., and Baker, D. (2014) One contact for every twelve residues allows robust and accurate topology-level protein structure modeling Proteins: Struct., Funct., Genet. 82, 208-218 10.1002/prot.24374
    • (2014) Proteins: Struct., Funct., Genet. , vol.82 , pp. 208-218
    • Kim, D.E.1    Dimaio, F.2    Yu-Ruei Wang, R.3    Song, Y.4    Baker, D.5
  • 76
    • 84988443529 scopus 로고    scopus 로고
    • The coming of age of de novo protein design
    • Huang, P.-S., Boyken, S. E., and Baker, D. (2016) The coming of age of de novo protein design Nature 537, 320-7 10.1038/nature19946
    • (2016) Nature , vol.537 , pp. 320-327
    • Huang, P.-S.1    Boyken, S.E.2    Baker, D.3
  • 80
    • 84871836463 scopus 로고    scopus 로고
    • Small changes in enzyme function can lead to surprisingly large fi tness effects during adaptive evolution of antibiotic resistance
    • Walkiewicz, K., Benitez Cardenas, A. S., Sun, C., Bacorn, C., Saxer, G., and Shamoo, Y. (2012) Small changes in enzyme function can lead to surprisingly large fi tness effects during adaptive evolution of antibiotic resistance Proc. Natl. Acad. Sci. U. S. A. 109, 21408-21413 10.1073/pnas.1209335110
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 21408-21413
    • Walkiewicz, K.1    Benitez Cardenas, A.S.2    Sun, C.3    Bacorn, C.4    Saxer, G.5    Shamoo, Y.6
  • 81
    • 84885906415 scopus 로고    scopus 로고
    • Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance
    • Miller, C., Kong, J., Tran, T. T., Arias, C. A., Saxer, G., and Shamoo, Y. (2013) Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance Antimicrob. Agents Chemother. 57, 5373-5383 10.1128/AAC.01473-13
    • (2013) Antimicrob. Agents Chemother. , vol.57 , pp. 5373-5383
    • Miller, C.1    Kong, J.2    Tran, T.T.3    Arias, C.A.4    Saxer, G.5    Shamoo, Y.6
  • 83
    • 70450242805 scopus 로고    scopus 로고
    • Exploring protein fitness landscapes by directed evolution
    • Romero, P. a. and Arnold, F. H. (2009) Exploring protein fitness landscapes by directed evolution Nat. Rev. Mol. Cell Biol. 10, 866-876 10.1038/nrm2805
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 866-876
    • Romero, P.A.1    Arnold, F.H.2
  • 85
    • 84894101033 scopus 로고    scopus 로고
    • Negative selection and stringency modulation in phage-assisted continuous evolution
    • Carlson, J. C., Badran, A. H., Guggiana-Nilo, D. A., and Liu, D. R. (2014) Negative selection and stringency modulation in phage-assisted continuous evolution Nat. Chem. Biol. 10, 216-222 10.1038/nchembio.1453
    • (2014) Nat. Chem. Biol. , vol.10 , pp. 216-222
    • Carlson, J.C.1    Badran, A.H.2    Guggiana-Nilo, D.A.3    Liu, D.R.4
  • 87
    • 34948815009 scopus 로고    scopus 로고
    • A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments
    • Li, Y., Drummond, D. A., Sawayama, A. M., Snow, C. D., Bloom, J. D., and Arnold, F. H. (2007) A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments Nat. Biotechnol. 25, 1051-1056 10.1038/nbt1333
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1051-1056
    • Li, Y.1    Drummond, D.A.2    Sawayama, A.M.3    Snow, C.D.4    Bloom, J.D.5    Arnold, F.H.6
  • 88
    • 84868144216 scopus 로고    scopus 로고
    • Random Field Model Reveals Structure of the Protein Recombinational Landscape
    • Romero, P. A. and Arnold, F. H. (2012) Random Field Model Reveals Structure of the Protein Recombinational Landscape PLoS Comput. Biol. 8, e1002713 10.1371/journal.pcbi.1002713
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002713
    • Romero, P.A.1    Arnold, F.H.2


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