Rosenthaler L (1908) Durch Enzyme bewirkte asymmetrische Synthese. Biochem Z 14:238–253
CAS
Google Scholar
Winter G et al (1982) Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature 299:756–758
CAS
CrossRef
PubMed
Google Scholar
Wilkinson AJ et al (1983) Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation. Biochemistry 22:3581–3586
CAS
CrossRef
PubMed
Google Scholar
Estell DA, Graycar TP, Wells JA (1985) Engineering an enzyme by site-directed mutagenesis to be resistant to chemical oxidation. J Biol Chem 260:6518–6521
CAS
PubMed
Google Scholar
Gorontzy T et al (1994) Microbial degradation of explosives and related compounds. Crit Rev Microbiol 20:265–284
CAS
CrossRef
PubMed
Google Scholar
Singh BK, Walker A (2006) Microbial degradation of organophosphorus compounds. FEMS Microbiol Rev 30:428–471
CAS
CrossRef
PubMed
Google Scholar
Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Iredell J, Brown J, Tagg K (2016) Antibiotic resistance in Enterobacteriaceae: mechanisms and clinical implications. BMJ 352:h6420
CrossRef
PubMed
Google Scholar
Cadwell RC, Joyce GF (1992) Randomization of genes by PCR mutagenesis. Genome Res 2:28–33
CAS
CrossRef
Google Scholar
Firth AE, Patrick WM (2005) Statistics of protein library construction. Bioinformatics 21:3314–3315
CAS
CrossRef
PubMed
Google Scholar
Arnold FH (1990) Engineering enzymes for non-aqueous solvents. Trends Biotechnol 8:244–249
CAS
CrossRef
PubMed
Google Scholar
Dube DK et al (1991) Artificial mutants generated by the insertion of random oligonucleotides into the putative nucleoside binding site of the HSV-1 thymidine kinase gene. Biochemistry 30:11760–11767
CAS
CrossRef
PubMed
Google Scholar
Chen KQ, Arnold FH (1993) Tuning the activity of an enzyme for unusual environments–sequential random mutagenesis of subtilisin-E for catalysis in dimethylformamide. Proc Nat Acad Sci USA 90:5618–5622
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Moore JC, Arnold FH (1996) Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nat Biotechnol 14:458–467
CAS
CrossRef
PubMed
Google Scholar
Stemmer WP (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A 91:10747–10751
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Stemmer WP (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389–391
CAS
CrossRef
PubMed
Google Scholar
Zhao H, Giver L, Shao Z et al (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16:258–261
CAS
CrossRef
PubMed
Google Scholar
Müller KM, Stebel SC, Knall S et al (2005) Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution. Nucleic Acids Res 33:e117
CrossRef
PubMed
PubMed Central
Google Scholar
Crameri A, Raillard SA, Bermudez E et al (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288–291
CAS
CrossRef
PubMed
Google Scholar
Ness JE, Welch M, Giver L et al (1999) DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol 17:893–896
CAS
CrossRef
PubMed
Google Scholar
Kolkman JA, Stemmer WP (2001) Directed evolution of proteins by exon shuffling. Nat Biotechnol 19:423–428
CAS
CrossRef
PubMed
Google Scholar
Patnaik R, Louie S, Gavrilovic V et al (2002) Genome shuffling of Lactobacillus for improved acid tolerance. Nat Biotechnol 20:707–712
CAS
CrossRef
PubMed
Google Scholar
Romero PA, Arnold FA (2009) Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 10:866–876
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Patrick WM, Firth AE, Blackburn JM (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng 16:451–457
CAS
CrossRef
PubMed
Google Scholar
Acevedo-Rocha CG, Agudo R, Reetz MT (2014) Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. J Biotechnol 191:3–10
CAS
CrossRef
PubMed
Google Scholar
Martis EA, Badve RR (2011) High-throughput screening: the hits and leads of drug discovery–an overview. J Appl Pharm Sci 1:2–10
Google Scholar
Lutz S (2010) Beyond directed evolution–semi-rational protein engineering and design. Curr Opin Biotechnol 21:734–743
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Clouthier CM, Kayser MM, Reetz MT (2006) Designing new Baeyer-Villiger monooxygenases using restricted CASTing. J Org Chem 71:8431–8437
CAS
CrossRef
PubMed
Google Scholar
Reetz MT, Carballeira JD, Peyralans J et al (2006) Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chem Eur J 12:6031–6038
CAS
CrossRef
PubMed
Google Scholar
Reetz MT, Wang LW, Bocola M (2006) Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space. Angew Chem Int Ed 45:1236–1241
CAS
CrossRef
Google Scholar
Agudo R, Roiban GD, Reetz MT (2012) Achieving regio- and enantioselectivity of P450-catalyzed oxidative CH activation of small functionalized molecules by structure-guided directed evolution. ChemBioChem 13:1465–1473
CAS
CrossRef
PubMed
Google Scholar
Gumulya Y, Sanchis J, Reetz MT (2012) Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima. ChemBioChem 13:1060–1066
CAS
CrossRef
PubMed
Google Scholar
Parra LP, Agudo R, Reetz MT (2013) Directed evolution by using iterative saturation mutagenesis based on multiresidue sites. ChemBioChem 14:2301–2309
CAS
CrossRef
PubMed
Google Scholar
Kourist R, Jochens H, Bartsch S et al (2010) The α/β-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering. ChemBioChem 11:1635–1643
CAS
CrossRef
PubMed
Google Scholar
Kuipers RK, Joosten HJ, van Berkel WJ et al (2010) 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Proteins 78:2101–2113
CAS
PubMed
Google Scholar
Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with YASARA NOVA–a self-parameterizing force field. Proteins 47:393–402
CAS
CrossRef
PubMed
Google Scholar
Das R, Baker D (2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77:363–382
CAS
CrossRef
PubMed
Google Scholar
Richter F, Leaver-Fay A, Khare SD et al (2011) De novo enzyme design using Rosetta3. PLoS One 6:e19230
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Bartsch S, Wybenga GG, Jansen M et al (2013) Redesign of a phenylalanine aminomutase into a phenylalanine ammonia lyase. ChemCatChem 5:1797–1802
CAS
CrossRef
Google Scholar
Floor RJ, Wijma HJ, Colpa DI et al (2014) Computational library design for increasing haloalkane dehalogenase stability. ChemBioChem 15:1660–1672
CAS
CrossRef
PubMed
Google Scholar
Wijma HJ, Floor HJ, Jekel PA et al (2014) Computationally designed libraries for rapid enzyme stabilization. Protein Eng Des Sel 27:49–58
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Liao J, Warmuth MK, Govindarajan S et al (2007) Engineering proteinase K using machine learning and synthetic genes. BMC Biotechnol 7:16
CrossRef
PubMed
PubMed Central
Google Scholar
Ehren J, Govindarajan S, Morón B et al (2008) Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng Des Sel 21:699–707
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Midelfort KS, Kumar R, Han S et al (2013) Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin. Protein Eng Des Sel 26:25–33
CAS
CrossRef
PubMed
Google Scholar
Govindarajan S, Mannervik B, Silverman JA et al (2015) Mapping of amino acid substitutions conferring herbicide resistance in wheat glutathione transferase. ACS Synth Biol 4:221–227
CAS
CrossRef
PubMed
Google Scholar
Lutz S, Patrick WM (2004) Novel methods for directed evolution of enzymes: quality, not quantity. Curr Opin Biotechnol 15:291–297
CAS
CrossRef
PubMed
Google Scholar
Lodish H, Berk A, Zipursky SL et al (2000) Molecular cell biology, 4th edn. W. H. Freeman, New York, Section 7.1, DNA cloning with plasmid vectors. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21498/
Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557
CAS
CrossRef
PubMed
Google Scholar
Chao G, Lau WL, Hackel BJ et al (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protocols 1:755–768
CAS
CrossRef
PubMed
Google Scholar
Bratkovič T (2009) Progress in phage display: evolution of the technique and its applications. Cell Mol Life Sci 67:749–767
CrossRef
Google Scholar
Çelik E, Fischer AC, Guarino C et al (2010) A filamentous phage display system for N-linked glycoproteins. Protein Sci 19:2006–2013
CrossRef
PubMed
PubMed Central
Google Scholar
Karlsson AJ, Lim HK, Xu H et al (2012) Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins. J Mol Biol 416:94–107
CAS
CrossRef
PubMed
Google Scholar
Tawfik DS, Griffiths AD (1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16:652–656
CAS
CrossRef
PubMed
Google Scholar
Bernath K, Hai M, Mastrobattista E et al (2004) In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem 325:151–157
CAS
CrossRef
PubMed
Google Scholar
Aharoni A, Griffiths AD, Tawfik DS (2005) High-throughput screens and selections of enzyme-encoding genes. Curr Opin Chem Biol 9:210–216
CAS
CrossRef
PubMed
Google Scholar
Agresti JJ, Antipov E, Abate AR et al (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci U S A 107:4004–4009
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Fischlechner M, Shaerli Y, Mohamed MF et al (2014) Evolution of enzyme catalysts caged in biomimetic gel-shell beads. Nat Chem 6:791–796
CAS
CrossRef
PubMed
Google Scholar
Ostafe R, Prodanovic R, Nazor J et al (2014) Ultra-high-throughput screening method for the directed evolution of glucose oxidase. Chem Biol 21:414–421
CAS
CrossRef
PubMed
Google Scholar
Zinchenko A, Devenish SRA, Kintses B et al (2014) One in a million: flow cytometric sorting of single cell-lysate assays in monodisperse picolitre double emulsion droplets for directed evolution. Anal Chem 86:2526–2533
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Romero PA, Tran TM, Abate AR (2015) Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci U S A 112:7159–7164
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Bornscheuer UT, Huisman GW, Kazlauskas RJ et al (2012) Engineering the third wave of biocatalysis. Nature 485:185–194
CAS
CrossRef
PubMed
Google Scholar
Prier CK, Arnold FH (2015) Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts. J Am Chem Soc 137:13992–14006
CAS
CrossRef
PubMed
Google Scholar
Coelho PS, Brustad EM, Kannan A et al (2013) Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes. Science 339:307–310
CAS
CrossRef
PubMed
Google Scholar
Bordeaux M, Tyagi V, Fasan R (2015) Highly diastereoselective and enantioselective olefin cyclopropanation using engineered myoglobin-based catalysts. Angew Chem Int Ed 54:1744–1748
CAS
CrossRef
Google Scholar
Heinisch T, Pellizzoni M, Dürrenberger M et al (2015) Improving the catalytic performance of an artificial metalloenzyme by computational design. J Am Chem Soc 137:10414–10419
CAS
CrossRef
PubMed
Google Scholar
Srivastava P, Yang H, Ellis-Guardiola K et al (2015) Engineering a dirhodium artificial metalloenzyme for selective olefin cyclopropanation. Nat Commun 6:7789
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Althoff EA, Wang L, Jiang L et al (2012) Robust design and optimization of retroaldol enzymes. Protein Sci 21:717–726
CAS
CrossRef
PubMed
PubMed Central
Google Scholar
Giger L, Caner S, Obexer R et al (2013) Evolution of a designed retro-aldolase
leads to complete active site remodeling. Nat Chem Biol 9:494–498
Google Scholar