High-Throughput Screening or Selection Methods for Evolutionary Enzyme Engineering

[1]  Manfred T Reetz,et al.  Protein engineering of stereoselective Baeyer-Villiger monooxygenases. , 2012, Chemistry.

[2]  Nicholas J Turner,et al.  Directed evolution drives the next generation of biocatalysts. , 2009, Nature chemical biology.

[3]  Philip A. Romero,et al.  Exploring protein fitness landscapes by directed evolution , 2009, Nature Reviews Molecular Cell Biology.

[4]  S. Withers,et al.  Ultrahigh‐Throughput FACS‐Based Screening for Directed Enzyme Evolution , 2009, Chembiochem : a European journal of chemical biology.

[5]  Roland Wohlgemuth,et al.  Biocatalysis--key to sustainable industrial chemistry. , 2010, Current opinion in biotechnology.

[6]  B. Katzenellenbogen,et al.  Directed Evolution of Human Estrogen Receptor Variants with Significantly Enhanced Androgen Specificity and Affinity* , 2004, Journal of Biological Chemistry.

[7]  N. Turner Agar Plate‐based Assays , 2006 .

[8]  George Georgiou,et al.  Directed Evolution of Highly Selective Proteases by Using a Novel FACS‐Based Screen that Capitalizes on the p53 Regulator MDM2 , 2012, Chembiochem : a European journal of chemical biology.

[9]  Dan S. Tawfik,et al.  Directed enzyme evolution: beyond the low-hanging fruit. , 2012, Current opinion in structural biology.

[10]  Andreas S Bommarius,et al.  Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst. , 2011, Current opinion in chemical biology.

[11]  A. Kiener,et al.  Industrial biocatalysis today and tomorrow , 2001, Nature.

[12]  D. Weitz,et al.  Droplet microfluidics for high-throughput biological assays. , 2012, Lab on a chip.

[13]  Andrew D Griffiths,et al.  A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. , 2012, Lab on a chip.

[14]  Directed co-evolution of an endoglucanase and a β-glucosidase in Escherichia coli by a novel high-throughput screening method. , 2013, Chemical communications.

[15]  Andreas Plückthun,et al.  Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display , 2000, Nature Biotechnology.

[16]  M. McLeish,et al.  Using site‐saturation mutagenesis to explore mechanism and substrate specificity in thiamin diphosphate‐dependent enzymes , 2013, The FEBS journal.

[17]  Wim J. Quax,et al.  Altering the Substrate Specificity of Cephalosporin Acylase by Directed Evolution of the β-Subunit* , 2002, The Journal of Biological Chemistry.

[18]  Yoshihiro Ito,et al.  Ribosome display selection of a metal-binding motif from an artificial peptide library. , 2008, Biotechnology and bioengineering.

[19]  V. Cornish,et al.  Chemical complementation: A reaction-independent genetic assay for enzyme catalysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[21]  Uwe Schlattner,et al.  Yeast Two-Hybrid, a Powerful Tool for Systems Biology , 2009, International journal of molecular sciences.

[22]  James C. Liao,et al.  Directed Evolution of Methanococcus jannaschii Citramalate Synthase for Biosynthesis of 1-Propanol and 1-Butanol by Escherichia coli , 2008, Applied and Environmental Microbiology.

[23]  B. Dijkstra,et al.  Directed Evolution of Bacillus subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection , 2006, Chembiochem : a European journal of chemical biology.

[24]  Martin Zacharias,et al.  A statistical analysis of random mutagenesis methods used for directed protein evolution. , 2006, Journal of molecular biology.

[25]  Roberto A Chica,et al.  Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. , 2005, Current opinion in biotechnology.

[26]  Maurizio Bettiga,et al.  Increased Ethanol Productivity in Xylose-Utilizing Saccharomyces cerevisiae via a Randomly Mutagenized Xylose Reductase , 2010, Applied and Environmental Microbiology.

[27]  Carla C. C. R. de Carvalho,et al.  Enzymatic and whole cell catalysis: finding new strategies for old processes , 2011 .

[28]  David R. Liu,et al.  Negative selection and stringency modulation in phage-assisted constinuous evolution , 2014, Nature chemical biology.

[29]  Andreas Vogel,et al.  Single-cell high-throughput screening to identify enantioselective hydrolytic enzymes. , 2008, Angewandte Chemie.

[30]  T. Pijning,et al.  Improved activity and thermostability of Bacillus pumilus lipase by directed evolution. , 2013, Journal of biotechnology.

[31]  Chi-Huey Wong,et al.  In vivo selection for the directed evolution of L-rhamnulose aldolase from L-rhamnulose-1-phosphate aldolase (RhaD). , 2007, Bioorganic & medicinal chemistry.

[32]  M. Koksharov,et al.  Thermostabilization of firefly luciferase by in vivo directed evolution. , 2011, Protein engineering, design & selection : PEDS.

[33]  C. Obinger,et al.  Directed evolution of Her2/neu-binding IgG1-Fc for improved stability and resistance to aggregation by using yeast surface display. , 2013, Protein engineering, design & selection : PEDS.

[34]  W. Dower,et al.  An in vitro polysome display system for identifying ligands from very large peptide libraries. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Bharadwaj,et al.  Droplet-based microfluidic platform for heterogeneous enzymatic assays. , 2013, Lab on a chip.

[36]  Huimin Zhao,et al.  Recent advances in biocatalyst development in the pharmaceutical industry , 2013 .

[37]  Jian Chen,et al.  Improving the Thermostability and Catalytic Efficiency of Bacillus deramificans Pullulanase by Site-Directed Mutagenesis , 2013, Applied and Environmental Microbiology.

[38]  V. Erdmann,et al.  Searching sequence space for high-affinity binding peptides using ribosome display. , 2003, Journal of molecular biology.

[39]  Courtney C Aldrich,et al.  Engineering the substrate specificity of the DhbE adenylation domain by yeast cell surface display. , 2013, Chemistry & biology.

[40]  N. Kelleher,et al.  Directed evolution of the nonribosomal peptide synthetase AdmK generates new andrimid derivatives in vivo. , 2011, Chemistry & biology.

[41]  Stefan Lutz,et al.  Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting , 2009, Nucleic acids research.

[42]  Stefan Lutz,et al.  Beyond directed evolution--semi-rational protein engineering and design. , 2010, Current opinion in biotechnology.

[43]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

[44]  Christoph A. Merten,et al.  High-throughput screening of enzymes by retroviral display using droplet-based microfluidics. , 2010, Chemistry and Biology.

[45]  Radka Snajdrova,et al.  A combination of in vivo selection and cell sorting for the identification of enantioselective biocatalysts. , 2011, Angewandte Chemie.

[46]  Richard W Roberts,et al.  Design of cyclic peptides that bind protein surfaces with antibody-like affinity. , 2007, ACS chemical biology.

[47]  W. Quax,et al.  Selection strategies for improved biocatalysts , 2007, The FEBS journal.

[48]  U. Schwaneberg,et al.  Flow Cytometer-Based High-Throughput Screening System for Accelerated Directed Evolution of P450 Monooxygenases , 2012 .

[49]  Huimin Zhao,et al.  Directed evolution of a cellodextrin transporter for improved biofuel production under anaerobic conditions in Saccharomyces cerevisiae , 2014, Biotechnology and bioengineering.

[50]  Huimin Zhao,et al.  Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins , 2013, Microbial Cell Factories.

[51]  Wim Soetaert,et al.  Creating lactose phosphorylase enzymes by directed evolution of cellobiose phosphorylase. , 2009, Protein engineering, design & selection : PEDS.

[52]  Frances H. Arnold,et al.  In Vivo Evolution of Butane Oxidation by Terminal Alkane Hydroxylases AlkB and CYP153A6 , 2008, Applied and Environmental Microbiology.

[53]  D. Schwarzer,et al.  Directed evolution of sortase A mutants with altered substrate selectivity profiles. , 2011, Journal of the American Chemical Society.

[54]  Jiong Hong,et al.  Fast identification of thermostable beta‐glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach , 2009, Biotechnology and bioengineering.

[55]  Huimin Zhao,et al.  Directed Evolution of a Thermostable Phosphite Dehydrogenase for NAD(P)H Regeneration , 2005, Applied and Environmental Microbiology.

[56]  C. Obinger,et al.  Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast , 2012, Biochimica et biophysica acta.

[57]  Baoguo Sun,et al.  Analytical method development for directed enzyme evolution research: a high throughput high-performance liquid chromatography method for analysis of ribose and ribitol and a capillary electrophoresis method for the separation of ribose enantiomers. , 2013, Journal of chromatography. A.

[58]  B. Stoddard,et al.  Computational Thermostabilization of an Enzyme , 2005, Science.

[59]  Haiquan Yang,et al.  Molecular engineering of industrial enzymes: recent advances and future prospects , 2013, Applied Microbiology and Biotechnology.

[60]  K. A. White,et al.  Directed evolution of a probe ligase with activity in the secretory pathway and application to imaging intercellular protein-protein interactions. , 2013, Biochemistry.

[61]  Joel L Sussman,et al.  Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. , 2011, Nature chemical biology.

[62]  Thomas Greiner-Stöffele,et al.  Changing the substrate specificity of P450cam towards diphenylmethane by semi-rational enzyme engineering. , 2011, Protein engineering, design & selection : PEDS.

[63]  Hening Lin,et al.  High-throughput selection for cellulase catalysts using chemical complementation. , 2008, Journal of the American Chemical Society.

[64]  Sung-Hun Nam,et al.  Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold , 2006, Science.

[65]  James A. Stapleton,et al.  Development of an In Vitro Compartmentalization Screen for High-Throughput Directed Evolution of [FeFe] Hydrogenases , 2010, PloS one.

[66]  Nikolaos E. Labrou,et al.  Random mutagenesis methods for in vitro directed enzyme evolution. , 2009 .

[67]  D. Shonnard,et al.  Improved activity and thermostability of (S)-aminotransferase by error-prone polymerase chain reaction for the production of a chiral amine , 2007 .

[68]  Huimin Zhao,et al.  Directed evolution of a highly efficient cellobiose utilizing pathway in an industrial Saccharomyces cerevisiae strain , 2013, Biotechnology and bioengineering.

[69]  Manfred T Reetz,et al.  Addressing the Numbers Problem in Directed Evolution , 2008, Chembiochem : a European journal of chemical biology.

[70]  Fabienne Courtois,et al.  Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. , 2012, Chemistry & biology.

[71]  Tjaard Pijning,et al.  A Novel Genetic Selection System for Improved Enantioselectivity of Bacillus subtilis Lipase A , 2008, Chembiochem : a European journal of chemical biology.

[72]  S. Sidhu,et al.  Two-state selection of conformation-specific antibodies , 2009, Proceedings of the National Academy of Sciences.

[73]  Jay D Keasling,et al.  Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. , 2013, ACS synthetic biology.

[74]  A. Janulaitis,et al.  Compartmentalization of destabilized enzyme-mRNA-ribosome complexes generated by ribosome display: a novel tool for the directed evolution of enzymes. , 2013, Protein engineering, design & selection : PEDS.

[75]  Andreas Plückthun,et al.  Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target , 2007, Nature Methods.

[76]  F. Arnold,et al.  Optimizing non-natural protein function with directed evolution. , 2011, Current opinion in chemical biology.

[77]  Weng Lin Tang,et al.  High-throughput method for determining the enantioselectivity of enzyme-catalyzed hydroxylations based on mass spectrometry. , 2010, Angewandte Chemie.

[78]  Artem Blagodatski,et al.  Technologies of directed protein evolution in vivo , 2011, Cellular and Molecular Life Sciences.

[79]  Son Quang Pham,et al.  Evolving P450pyr hydroxylase for highly enantioselective hydroxylation at non-activated carbon atom. , 2012, Chemical communications.

[80]  Alexander Sczyrba,et al.  High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery. , 2011, Angewandte Chemie.

[81]  Huimin Zhao,et al.  Directed evolution of estrogen receptor proteins with altered ligand-binding specificities. , 2009, Protein engineering, design & selection : PEDS.

[82]  Amir Aharoni,et al.  High-throughput screening methodology for the directed evolution of glycosyltransferases , 2006, Nature Methods.

[83]  W. Quax,et al.  Directed evolution of a glutaryl acylase into an adipyl acylase. , 2002, European journal of biochemistry.

[84]  Andrew D Griffiths,et al.  High-throughput screens and selections of enzyme-encoding genes. , 2005, Current opinion in chemical biology.

[85]  Manfred T Reetz,et al.  Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions. , 2011, Angewandte Chemie.

[86]  Huimin Zhao,et al.  Directed Enzyme Evolution and High-Throughput Screening , 2009 .

[87]  F. Martin Fifteen years of the yeast three-hybrid system: RNA-protein interactions under investigation. , 2012, Methods.

[88]  W. Suen,et al.  Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. , 2004, Protein engineering, design & selection : PEDS.

[89]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[90]  J. Oost,et al.  Reporter‐based screening and selection of enzymes , 2013, The FEBS journal.

[91]  Huimin Zhao,et al.  Directed Evolution: Past, Present and Future. , 2013, AIChE journal. American Institute of Chemical Engineers.

[92]  D. Weitz,et al.  Single-cell analysis and sorting using droplet-based microfluidics , 2013, Nature Protocols.

[93]  Bernhard Hauer,et al.  Recent progress in industrial biocatalysis. , 2011, Current opinion in chemical biology.

[94]  G. Huisman,et al.  Engineering the third wave of biocatalysis , 2012, Nature.

[95]  David R. Liu,et al.  Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes , 2007, Proceedings of the National Academy of Sciences.

[96]  E. Toone,et al.  Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate. , 2011, Bioorganic & medicinal chemistry.