Genomes and Genes
directed molecular evolution
Summary: The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
Publications262 found, 100 shown here
- Fitness effects of fixed beneficial mutations in microbial populationsDaniel E Rozen
Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
Curr Biol 12:1040-5. 2002..Here, we confirm this prediction-both empirically and theoretically-by showing that fitness effects of fixed beneficial mutations follow a distribution whose mode is positive...
- Directed evolution of adeno-associated virus to an infectious respiratory virusKatherine J D A Excoffon
Department of Internal Medicine, University of Iowa, 440 EMRB, Iowa City, IA 52241, USA
Proc Natl Acad Sci U S A 106:3865-70. 2009..Thus, under appropriate selective pressures, viruses can evolve to be more infectious than observed in nature, a finding that holds significant implications for designing vectors for gene therapy and for understanding emerging pathogens...
- In the light of directed evolution: pathways of adaptive protein evolutionJesse D Bloom
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
Proc Natl Acad Sci U S A 106:9995-10000. 2009..These lessons about the coupling between adaptive and neutral protein evolution in the laboratory offer insight into the evolution of proteins in nature...
- HIV-1 proviral DNA excision using an evolved recombinaseIndrani Sarkar
Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D 01307 Dresden, Germany
Science 316:1912-5. 2007..Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses...
- Directed evolution of adeno-associated virus yields enhanced gene delivery vectorsNarendra Maheshri
The Department of Chemical Engineering and The Helen Wills Neuroscience Institute, The University of California, Berkeley, California 94720 1462, USA
Nat Biotechnol 24:198-204. 2006..This approach, which can be extended to additional gene delivery challenges and serotypes, directs viral evolution to generate 'designer' gene delivery vectors with specified, enhanced properties...
- Microbial carboxyl esterases: classification, properties and application in biocatalysisUwe T Bornscheuer
Institute for Chemistry and Biochemistry, Department of Technical Chemistry and Biotechnology, Greifswald University, Soldmannstr 16, Greifswald, Germany
FEMS Microbiol Rev 26:73-81. 2002..Special emphasis is given on their application in organic synthesis for the resolution of racemates and prostereogenic compounds. In addition, recent results for altering their properties by directed evolution are presented...
- Engineering platforms for directed evolution of Laccase from Pycnoporus cinnabarinusS Camarero
Department of Biocatalysis, Institute of Catalysis, Madrid, Spain
Appl Environ Microbiol 78:1370-84. 2012..Furthermore, some mutations arising in the evolved preproleader highlighted its potential for heterologous expression of fungal laccases in yeast (S. cerevisiae)...
- Exceptional convergent evolution in a virusJ J Bull
Department of Zoology, Institute of Cellular and Molecular Biology, University of Texas, Austin 78712, USA
Genetics 147:1497-507. 1997..Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed...
- Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufactureChristopher K Savile
Codexis, Incorporated, 200 Penobscot Drive, Redwood City, CA 94063, USA
Science 329:305-9. 2010..This work underscores the maturation of biocatalysis to enable efficient, economical, and environmentally benign processes for the manufacture of pharmaceuticals...
- Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymesManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
Nat Protoc 2:891-903. 2007..The pronounced increase in thermostability of the lipase from Bacillus subtilis (Lip A) as a result of applying ISM is illustrated here...
- Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLsShuyun Dong
Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
Nat Protoc 5:561-73. 2010..In this study, we describe a generic protocol for the directed molecular evolution of designer receptors exclusively activated by designer drugs (DREADDs)...
- Novel methods for directed evolution of enzymes: quality, not quantityStefan Lutz
Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
Curr Opin Biotechnol 15:291-7. 2004In the past decade methods of directed molecular evolution have proven revolutionary in protein engineering...
- Kemp elimination catalysts by computational enzyme designDaniela Röthlisberger
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 453:190-5. 2008..These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future...
- Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolutionIlja Bontjer
Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Meibergdreef 15 K3 105, 1105 AZ Amsterdam, The Netherlands
J Virol 83:368-83. 2009..In general, virus evolution may provide a powerful tool to optimize Env vaccine antigens...
- Directed molecular evolution to design advanced red fluorescent proteinsFedor V Subach
Department of Anatomy and Structural Biology, and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
Nat Methods 8:1019-26. 2011..We consider advances in library design by mutagenesis, protein expression systems and instrumentation for high-throughput screening that should yield improved fluorescent proteins for advanced imaging applications...
- Directed evolution of sulfotransferases and paraoxonases by ancestral librariesUria Alcolombri
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
J Mol Biol 411:837-53. 2011....
- Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolutionIlja Bontjer
Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
J Biol Chem 285:36456-70. 2010..These evolved ΔV1V2 trimers could be useful reagents for immunogenicity and structural studies...
- A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolutionAli Fallah-Araghi
Institut de Science et d Ingénierie Supramoléculaires ISIS, Universite de Strasbourg, CNRS UMR 7006, Strasbourg, France
Lab Chip 12:882-91. 2012..Compared to screening using microtiter plate-based systems, the volume and cost of PCR and IVTT reagents are reduced by almost 10(5)-fold, allowing the screening of 10(6) genes using only 150 μL of reagents...
- Robust design and optimization of retroaldol enzymesEric A Althoff
Department of Biochemistry, University of Washington and HHMI, Seattle, Washington 98195, USA
Protein Sci 21:717-26. 2012..Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited...
- Blood tolerant laccase by directed evolutionDiana M Mate
Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
Chem Biol 20:223-31. 2013..This proof of concept that laccases can be adapted to function in extreme conditions opens an array of opportunities for implantable nanobiodevices, chemical syntheses, and detoxification...
- De novo enzymes by computational designHajo Kries
Laboratory of Organic Chemistry, ETH Zurich, Zurich CH 8093, Switzerland
Curr Opin Chem Biol 17:221-8. 2013..Analysis of their evolutionary trajectories provides valuable feedback for the design algorithms and can enhance our understanding of natural protein evolution...
- Fitness landscape transformation through a single amino acid change in the rho terminatorPeter L Freddolino
Joint Centers for Systems Biology, Columbia University, New York, New York, United States of America
PLoS Genet 8:e1002744. 2012....
- Exploiting models of molecular evolution to efficiently direct protein engineeringMegan F Cole
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
J Mol Evol 72:193-203. 2011..We anticipate that the REAP approach will be used in the future to facilitate the engineering of biopolymers with expanded functions and will thus have a significant impact on the developing field of 'evolutionary synthetic biology'...
- Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coliTingjian Chen
Department of Chemical Engineering, Tsinghua University, Beijing, China
PLoS ONE 6:e16228. 2011..coli...
- In vivo molecular evolution reveals biophysical origins of organismal fitnessRafael Couñago
Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
Mol Cell 22:441-9. 2006..Thus, continuous evolution of a single gene permits a quantitative approach that extends from the phenotypes of the microbial populations to their underlying biophysical basis...
- Laboratory evolution of high-redox potential laccasesDiana Maté
Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid, Spain
Chem Biol 17:1030-41. 2010....
- Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme foldReinhard Sterner
Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
Chem Rev 105:4038-55. 2005
- Natural diversity to guide focused directed evolutionHelge Jochens
Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix Hausdorff Strasse 4, 17487 Greifswald, Germany
Chembiochem 11:1861-6. 2010..2) towards 3-PBA-ethyl ester, a significant number of hits with improved rates (up to 240-fold) and enantioselectivities (up to E(true)=80) were identified in these "smart" libraries...
- Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stressTakaaki Horinouchi
Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1 5 Yamadaoka, Suita, Osaka, Japan
BMC Genomics 11:579. 2010..Hence, we performed parallel-evolution experiments using Escherichia coli cells under ethanol stress to determine the phenotypic changes necessary for ethanol tolerance...
- Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imagingHui Wang Ai
Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
Biochem J 400:531-40. 2006..85) makes it particularly suitable as a replacement for ECFP (enhanced CFP) or Cerulean as a FRET (fluorescence resonance energy transfer) donor to either a yellow or orange FP acceptor...
- Viral evolution as a tool to improve the tetracycline-regulated gene expression systemAtze T Das
Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
J Biol Chem 279:18776-82. 2004..Our results demonstrate that the viral evolution strategy can be used to improve the activity of genes by making them an integral and essential part of the virus...
- The past, present and future of cell-free protein synthesisFederico Katzen
Invitrogen Corporation, 1600 Faraday Avenue, Carlsbad, CA 92008, USA
Trends Biotechnol 23:150-6. 2005..We review the advances on this expanding technology and highlight the growing list of associated applications...
- Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolutionToshihiko Kishimoto
Faculty of Science, Toho University, Funabashi, Chiba, Japan
PLoS Genet 6:e1001164. 2010....
- DNA shuffling of adeno-associated virus yields functionally diverse viral progenyJames T Koerber
Department of Chemical Engineering, University of California at Berkeley, Berkeley, California 94720 1462, USA
Mol Ther 16:1703-9. 2008..Thus, directed evolution can potentially yield unlimited numbers of new AAV variants with novel gene-delivery properties, and subsequent analysis of these variants can further extend basic knowledge of AAV biology...
- Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolutionM Lehmann
F Hoffmann La Roche Ltd, Vitamins and Fine Chemicals Division, Department VFB, Building 203, CH 4070 Basel, Switzerland
Curr Opin Biotechnol 12:371-5. 2001..The potential benefits of the underlying, semirational 'consensus concept' are compared with those of rational design and directed evolution approaches...
- Rapid protein-folding assay using green fluorescent proteinG S Waldo
Structural Biology Group, MS M888, Los Alamos National Laboratory, NM 87545, USA
Nat Biotechnol 17:691-5. 1999..This approach to improving protein folding does not require functional assays for the protein of interest and provides a simple route to improving protein folding and expression by directed evolution...
- Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificityJames C Samuelson
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
J Mol Biol 319:673-83. 2002..Moreover, cleavage of the GGATCC sequence is no longer detected. This study provides further evidence that laboratory evolution strategies offer a powerful alternative to structure-guided protein design...
- Evolution of high mutation rates in experimental populations of E. coliP D Sniegowski
Department of Biology, University of Pennsylvania, Philadelphia 19104, USA
Nature 387:703-5. 1997..Our results corroborate computer simulations of mutator evolution in adapting clonal populations, and may help to explain observations that associate high mutation rates with emerging pathogens and with certain cancers...
- Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sitesSwetha Bolusani
School of Biological Sciences IfM, 911 Hergot Avenue, Louisiana Tech University, Ruston, LA 71272, USA
Nucleic Acids Res 34:5259-69. 2006..We demonstrate the ability of an Flp variant to mediate integration of a reporter cassette in Escherichia coli via recombination at one of the IL10-derived sites...
- Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolutionGavin J Williams
School of Biochemistry and Molecular Biology, Department of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
Proc Natl Acad Sci U S A 100:3143-8. 2003..This demonstration is of considerable significance to synthetic chemists requiring efficient syntheses of complex stereoisomeric products, such as carbohydrate mimetics...
- Experimental evolution of viruses: Microviridae as a model systemHolly A Wichman
Department of Biological Sciences, University of Idaho, Moscow, ID, USA
Philos Trans R Soc Lond B Biol Sci 365:2495-501. 2010..Elucidation of these mechanisms is aided by the availability of capsid and pro-capsid structures for phiX174 and builds on years of genetic studies of the phage life history...
- Expression system of CotA-laccase for directed evolution and high-throughput screenings for the oxidation of high-redox potential dyesVânia Brissos
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
Biotechnol J 4:558-63. 2009..The enzymatic assays developed were tested for the screening of one mutant library from CotA-laccase created by error-prone PCR...
- Addressing the numbers problem in directed evolutionManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
Chembiochem 9:1797-804. 2008..This type of approach accelerates the process of laboratory evolution considerably and can be expected to be broadly applicable when engineering functional proteins in general...
- Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coliHani Goodarzi
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Mol Syst Biol 6:378. 2010..Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape...
- Engineering of single Ig superfamily domain of intercellular adhesion molecule 1 (ICAM-1) for native fold and functionRoisin M Owens
Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA
J Biol Chem 285:15906-15. 2010..The systematic approach demonstrated in this study to engineer a single Ig superfamily fold in ICAM-1 can be broadly applicable to the engineering of modular Ig superfamily domains in other cell surface molecules...
- Evolving thermostability in mutant libraries of ligninolytic oxidoreductases expressed in yeastEva García-Ruiz
Department of Biocatalysis, Institute of Catalysis, Madrid, Spain
Microb Cell Fact 9:17. 2010..The current work describes how to achieve this goal by engineering ligninolytic oxidoreductases (a high-redox potential laccase -HRPL- and a versatile peroxidase, -VP-) functionally expressed in Saccharomyces cerevisiae...
- Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutationsTom M Conrad
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093 0332, USA
Genome Biol 10:R118. 2009....
- Molecular evolution of adeno-associated virus for enhanced glial gene deliveryJames T Koerber
Department of Chemical Engineering, Helen Wills Neuroscience Institute, The University of California, Berkeley, California 94720 1462, USA
Mol Ther 17:2088-95. 2009....
- The influence of cellular physiology on the initiation of mutational pathways in Escherichia coli populationsLucinda Notley-McRobb
School of Molecular and Microbial Biosciences, G08, University of Sydney, Sydney, NSW 2006, Australia
Proc Biol Sci 270:843-8. 2003....
- Development of chimeric laccases by directed evolutionIsabel Pardo
Centro de Investigaciones Biologicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
Biotechnol Bioeng 109:2978-86. 2012..Using this approach, we identified chimeras with up to six crossover events in the whole sequence, and we obtained active hybrid laccases with combined characteristics in terms of pH activity and thermostability...
- Directed molecular evolution reveals Gaussia luciferase variants with enhanced light output stabilityM Hannah Degeling
Experimental Therapeutics and Molecular Imaging Laboratory, Neuroscience Center, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, United States
Anal Chem 85:3006-12. 2013..To overcome these limitations, a library of Gluc variants was generated using directed molecular evolution and screened for relative light output, a shift in emission spectrum, and glow-type light emission ..
- A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cellsThomas Gaj
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Nucleic Acids Res 41:3937-46. 2013..This study demonstrates the feasibility of generating customized ZFRs and the potential of ZFR technology for a diverse range of applications, including genome engineering, synthetic biology and gene therapy...
- Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59Olga Khersonsky
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 109:10358-63. 2012..Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies...
- A system for the continuous directed evolution of biomoleculesKevin M Esvelt
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Nature 472:499-503. 2011..By greatly accelerating laboratory evolution, PACE may provide solutions to otherwise intractable directed evolution problems and address novel questions about molecular evolution...
- In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptideM Wecker
Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder 80304, USA
RNA 2:982-94. 1996..This hairpin structure is also implicated in the recognition of the peptide substrate...
- Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel foldB Höcker
Universitat zu Koln, Institut fur Biochemie, Otto Fischer Strasse 12 14, D 50674 Köln, Germany
Curr Opin Biotechnol 12:376-81. 2001..Recently, the (beta alpha)(4)-half-barrel was identified as a possible structural subdomain...
- Covalent DNA display as a novel tool for directed evolution of proteins in vitroJulian Bertschinger
Institute of Pharmaceutical Sciences, ETH Honggerberg, Wolfgang Pauli Strasse 10, HCI G394, 8093 Zurich, Switzerland
Protein Eng Des Sel 17:699-707. 2004..M.Hae III could be fused to small globular proteins (such as calmodulin and fibronectin domains), which are ideally suited for the generation of combinatorial libraries and for the isolation of novel binding specificities...
- In-vitro selection of highly stabilized protein variants with optimized surfaceA Martin
, , Bayreuth, D-95440, Germany
J Mol Biol 309:717-26. 2001..In an ionic denaturant non-polar surface interactions were optimized, whereas at elevated temperature variants with improved electrostatics were selected, pointing to two different strategies for stabilization at protein surfaces...
- Improving catalytic function by ProSAR-driven enzyme evolutionRichard J Fox
Codexis, Inc, 200 Penobscot Drive, Redwood City, California 94063, USA
Nat Biotechnol 25:338-44. 2007....
- A simple selection strategy for evolving highly efficient enzymesMartin Neuenschwander
Laboratory of Organic Chemistry, ETH Zurich, Hönggerberg HCI F 339, CH 8093 Zurich, Switzerland
Nat Biotechnol 25:1145-7. 2007..Numerous selection formats and cell-based screening methodologies may benefit from the large dynamic range afforded by this easily implemented strategy...
- Hypoallergens for allergen-specific immunotherapy by directed molecular evolution of mite group 2 allergensGuro Gafvelin
Department of Medicine, Clinical Immunology and Allergy Unit, Karolinska Institutet, 17176 Stockholm, Sweden
J Biol Chem 282:3778-87. 2007..It may, however, be difficult to predict how to modify an allergen to create a hypoallergen. Directed molecular evolution by DNA shuffling and screening provides a means by which to evolve proteins having novel or improved ..
- Directed evolution of transketolase activity on non-phosphorylated substratesEdward G Hibbert
Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London, UK
J Biotechnol 131:425-32. 2007....
- Improving a circularly permuted TEM-1 beta-lactamase by directed evolutionJoel Osuna
Instituto de Biotecnologia, UNAM, Apdo Postal 510 3 Cuernavaca, Morelos 62250, Mexico
Protein Eng 15:463-70. 2002..We also analyze some of the data collected on the outcomes and paths of these evolutionary experiments. A purified sixth cycle variant with connector peptide GGS showed catalytic efficiency values approximately 8% of the natural enzyme...
- Directed molecular evolution in plant improvementM Lassner
Maxygen Incorporated, 515 Galveston Drive, California 94063, Redwood City, USA
Curr Opin Plant Biol 4:152-6. 2001b>Directed molecular evolution is a powerful tool to evolve genes with commercial applications...
- In-vitro protein evolution by ribosome display and mRNA displayDasa Lipovsek
Biological Engineering Division, Massachusetts Institute of Technology, Cambridge 02139, USA
J Immunol Methods 290:51-67. 2004....
- Selection and evolution of enzymes from a partially randomized non-catalytic scaffoldBurckhard Seelig
Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology CCIB, 7215 Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
Nature 448:828-31. 2007..The resulting ligases exhibit multiple turnover with rate enhancements of more than two-million-fold...
- Predictive behavior within microbial genetic networksIlias Tagkopoulos
Department of Electrical Engineering, Princeton University, Princeton, NJ 08544, USA
Science 320:1313-7. 2008..We further show that these internal correlations reflect a true associative learning paradigm, because they show rapid decoupling upon exposure to novel environments...
- Protein engineers turned evolutionistsSergio G Peisajovich
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
Nat Methods 4:991-4. 2007....
- Improved solubility of TEV protease by directed evolutionSusanne van den Berg
Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE 171 77 Stockholm, Sweden
J Biotechnol 121:291-8. 2006..We identified a mutant, TEV(SH), in which three amino acid substitutions result in a five-fold increase in the yield of purified protease with retained activity...
- Functional expression and stabilization of horseradish peroxidase by directed evolution in Saccharomyces cerevisiaeB Morawski
Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
Biotechnol Bioeng 76:99-107. 2001..Site-directed mutagenesis to replace each of the four methionine residues in HRP (M83, M181, M281, M284) with isoleucine revealed no mutation that significantly increased the enzyme's stability to hydrogen peroxide...
- Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostabilityManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
Angew Chem Int Ed Engl 45:7745-51. 2006
- Functional expression of a fungal laccase in Saccharomyces cerevisiae by directed evolutionThomas Bulter
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
Appl Environ Microbiol 69:987-95. 2003..Hyperglycosylation, corresponding to a 120-monomer glycan on one N-glycosylation site, is responsible for this increase. This S. cerevisiae expression system makes MtL available for functional tailoring by directed evolution...
- An evolutionary route to xylanase process fitnessNisha Palackal
Diversa Corp, 4955 Directors Place, San Diego, CA 92121, USA
Protein Sci 13:494-503. 2004..The use of two evolution strategies in combination enabled the rapid discovery of the enzyme variant with the highest degree of fitness (greater thermal tolerance and activity relative to the wild-type parent)...
- In vitro evolution suggests multiple origins for the hammerhead ribozymeK Salehi-Ashtiani
Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
Nature 414:82-4. 2001..Our results suggest that the evolutionary process may have been channelled, in nature as in the laboratory, towards repeated selection of the simplest solution to a biochemical problem...
- A ribozyme composed of only two different nucleotidesJohn S Reader
Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
Nature 420:841-4. 2002..This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages...
- A highly sensitive selection method for directed evolution of homing endonucleasesZhilei Chen
Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
Nucleic Acids Res 33:e154. 2005..003%. This system should also be readily applicable for directed evolution of other DNA cleavage enzymes...
- Protein engineering of subtilisinP N Bryan
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, 20850, Rockville, MD, USA
Biochim Biophys Acta 1543:203-222. 2000....
- Directed evolution of recombinase specificity by split gene reassemblyCharles A Gersbach
The Skaggs Institute for Chemical Biology, Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Nucleic Acids Res 38:4198-206. 2010..This enhanced evolution system will translate recombinase engineering and genome editing into a practical and expedient endeavor for academic, industrial and clinical applications...
- DNA display of biologically active proteins for in vitro protein selectionMasato Yonezawa
Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522
J Biochem 135:285-8. 2004..Thus, DNA display should be useful for rapidly screening or evolving proteins based on affinity selection...
- Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescaleChristopher D Herring
Department of Bioengineering, University of California, San Diego, California 92093, USA
Nat Genet 38:1406-12. 2006..The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts...
- Test of synergistic interactions among deleterious mutations in bacteriaS F Elena
Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
Nature 390:395-8. 1997..Several pairs exhibit significant interactions for fitness, but they are antagonistic as often as they are synergistic. These results do not support the mutational deterministic hypothesis for the evolution of sex...
- Evolution of programmable zinc finger-recombinases with activity in human cellsRussell M Gordley
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
J Mol Biol 367:802-13. 2007....
- Genome shuffling leads to rapid phenotypic improvement in bacteriaYing Xin Zhang
Maxygen, 515 Galveston Drive, Redwood City, California 94063, USA
Nature 415:644-6. 2002..This approach has the potential to facilitate cell and metabolic engineering and provide a non-recombinant alternative to the rapid production of improved organisms...
- Discovery and directed evolution of a glyphosate tolerance geneLinda A Castle
Verdia, Inc Redwood City, CA 94063, USA
Science 304:1151-4. 2004..Glyphosate acetylation provides an alternative strategy for supporting glyphosate use on crops...
- Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenasesJames A Stapleton
Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
PLoS ONE 5:e15275. 2010..Recent advances have allowed [FeFe] hydrogenases to be expressed and activated in the cell-free protein synthesis reactions on which IVC is based; however, IVC is a demanding technique with which many enzymes have proven incompatible...
- Whole plasmid mutagenic PCR for directed protein evolutionIchiro Matsumura
Department of Biochemistry, Center for Fundamental and Molecular Evolution, Emory University School of Medicine, Rollins Research Center, Room 4119, 1510 Clifton Road, Atlanta, GA 30322, USA
Biomol Eng 22:73-9. 2005..This latter result clearly demonstrates the utility of whole plasmid mutagenic PCR for directed protein evolution...
- Protein evolution with an expanded genetic codeChang C Liu
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Proc Natl Acad Sci U S A 105:17688-93. 2008..These experiments suggest that an expanded "synthetic" genetic code can confer a selective advantage in the directed evolution of proteins with specific properties...
- Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stageManfred T Reetz
Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, D 45470 Mulheim Ruhr, Germany
J Am Chem Soc 131:7334-43. 2009..Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible...
- Haploids adapt faster than diploids across a range of environmentsA C Gerstein
Biodiversity Research Centre and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
J Evol Biol 24:531-40. 2011..These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes...
- Directed evolution of high-affinity antibody mimics using mRNA displayLiHui Xu
Phylos, Inc, Lexington, MA 02421, USA
Chem Biol 9:933-42. 2002..10Fn3-based scaffold libraries and mRNA-display allow the isolation of high-affinity, specific antigen binding proteins; potential applications of such binding proteins include diagnostic protein microarrays and protein therapeutics...
- Evolutionary origins and directed evolution of RNAAndrew D Ellington
Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
Int J Biochem Cell Biol 41:254-65. 2009..Self-replication would have inexorably led to life...
- Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesisDavid P Nannemann
Chemistry Department, 7330 Stevenson Center, Vanderbilt University, Nashville, TN 37235, USA
Future Med Chem 3:809-19. 2011..4, 3 and 15.6. Further analysis by enzyme class, library-generation methodology and screening methodology explores relationships between successful campaigns and the methodologies employed...
- Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediolDae Hee Lee
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
Appl Environ Microbiol 76:4158-68. 2010..These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate...
- Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategiesJanahan Paramesvaran
The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
Protein Eng Des Sel 22:401-11. 2009..The results suggest ways in which directed evolution by SDSM could be improved for greater efficiency in terms of reducing the library sizes required to obtain beneficial mutations that alter substrate specificity...
- Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeastMichael W Traxlmayr
University of Natural Resources and Life Sciences, Vienna, Austria
Biochim Biophys Acta 1824:542-9. 2012..These data clearly demonstrate the importance and efficacy of the presented strategy for selection of stabilizing mutations in proteins of high intrinsic stability within reasonable time...
- Strategy and success for the directed evolution of enzymesPaul A Dalby
Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
Curr Opin Struct Biol 21:473-80. 2011..Finally, the combined use of several strategies is likely to be required in practice to improve multiple target properties of an enzyme, as successfully shown by a recent industrial example...
- DNA shuffling of a family of genes from diverse species accelerates directed evolutionA Crameri
Maxygen Inc, Santa Clara, California 95051, USA
Nature 391:288-91. 1998..Molecular breeding by shuffling can efficiently mix sequences from different species, unlike traditional breeding techniques. The power of family shuffling may arise from sparse sampling of a larger portion of sequence space...
- Directed evolution of an aspartate aminotransferase with new substrate specificitiesT Yano
Department of Biochemistry, Osaka Medical College, 2 7 Daigakumachi, Takatsuki, Osaka 569, Japan
Proc Natl Acad Sci U S A 95:5511-5. 1998The substrate specificity of aspartate aminotransferase was successfully modified by directed molecular evolution using a combination of DNA shuffling and selection in an auxotrophic Escherichia coli strain...
- Directed evolution of transketolase substrate specificity towards an aliphatic aldehydeEdward G Hibbert
Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
J Biotechnol 134:240-5. 2008..This suggests that saturation mutagenesis can be more selectively guided for evolution towards either natural or non-natural substrates, using both structural and sequence information...
- mRNA display for the selection and evolution of enzymes from in vitro-translated protein librariesBurckhard Seelig
Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
Nat Protoc 6:540-52. 2011..This method is demonstrated by the generation of new RNA ligase enzymes...
- Mechanistic and structural insights into the regioselectivity of an acyl-CoA fatty acid desaturase via directed molecular evolutionThomas Vanhercke
Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory 2601, Australia
J Biol Chem 286:12860-9. 2011....
- A Novel Technology for Molecular EvolutionJAMES LARRICK; Fiscal Year: 2003..These will be expressed, purified and characterized by binding and affinity measurements. This simple yet high-yield system should contribute significantly to proteomics research in the post-genome era. ..
- Novel Therapeutic Vaccines for Chronic HBVROBERT GERALD WHALEN; Fiscal Year: 2013..HBsAg variants containing xenogeneic sequences with novel T epitopes have been identified using a directed molecular evolution approach...
- Novel Vaccine Immunogens for Pandemic H5 InfluenzaROBERT GERALD WHALEN; Fiscal Year: 2009..We propose here a novel way to approach this problem, using the power of directed molecular evolution. This technology encompasses a method for creating novel protein sequences coupled with a means of ..
- Germline-Specific Immunogens for the Induction of Neutralizing Antibodies to HIV-ROBERT GERALD WHALEN; Fiscal Year: 2013..We propose therefore to use a directed molecular evolution approach to identify germline-specific immunogens...
- Germline-Specific Immunogens for the Induction of Neutralizing Antibodies to HIV-ROBERT GERALD WHALEN; Fiscal Year: 2013..We propose therefore to employ a directed molecular evolution approach to the problem of identifying germline-specific immunogens...
- Molecular Fluorescent ToolkitVLADISLAV VERKHUSHA; Fiscal Year: 2013..We will apply directed molecular evolution techniques consisting of rational structure-based design and random mutagenesis of candidate proteins, ..
- Engineering Morphogenetic Factors for Enhanced Genetic ReprogrammingCharles A Gersbach; Fiscal Year: 2011..these limitations, we propose to enhance the intrinsic properties of the reprogramming factors through directed molecular evolution. This represents a new conceptual direction in the area of genetic reprogramming and capitalizes on the ..
- Development of a Computational Framework for TCR EngineeringZhiping Weng; Fiscal Year: 2013..Perform flexible redesign of TCR loops with multiple substitutions to further improve and redirect binding;Aim 3. Bias specific pairing of engineered TCR chains via computationally designed constant regions. ..
- Function of Astrocytic GPCR Signaling Cascades in Physiology and Mental IllnessKEN DOUGLAS MCCARTHY; Fiscal Year: 2013..DREADD receptors were prepared by directed molecular evolution of M3-ACh receptor DREADD receptors, fail to respond to any known endogenous GPCR ligand, and are ..
- MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASESJON THORSON; Fiscal Year: 2002....
- DETAILED ANALYSIS OF SCL/TAL DIMERIZATION WITH E PROTEINAdam Goldfarb; Fiscal Year: 2001..Candidate antagonists of SCL/tal will be characterized first in in vitro interaction assays and then tested for the induction of apoptosis in T-ALL cells. ..
- Development of Novel Immunogens for Vaccines to HIV-1Robert Whalen; Fiscal Year: 2009..HIVRAD Proposal is to identify one or more novel HIV-1 envelope (Env) antigens, identified by use of directed molecular evolution, that are capable of inducing broadly neutralizing antibody responses to primary isolates of the HIV-1 ..
- Dissecting Electrostatic Effects in Cystic Fibrosis MucoGerard Wong; Fiscal Year: 2005..3) To develop, via directed molecular evolution, an anionic DNAzyme which mimics the biofilm suppression action of cationic lactoferrin, but will not ..
- Engineering AAV for Enhanced Retrograde TransportBrian Kaspar; Fiscal Year: 2006..We therefore propose to employ a directed molecular evolution approach to develop novel AAV capsid variants with enhanced retrograde transport in vivo...
- Creation of site-specific DNA methyltransferasesMarc Ostermeier; Fiscal Year: 2006..abstract_text> ..
- Synthetic Protein Families by Structure-Guided SCHEMA RecombinationFrances H Arnold; Fiscal Year: 2010..Finally, this research represents a fundamentally new approach to study protein stability using recombination, with results that can be applied to understanding enzymes in general. ..
- Live Cell Fluorescence Imaging Using Molecular SwitchesMarc Ostermeier; Fiscal Year: 2007..unreadable] [unreadable]..
- Quantitative Microfluidic Molecular EvolutionBRIAN PAEGEL; Fiscal Year: 2006....
- Microfluidic Processors for Directed Evolution and Synthetic BiologyBRIAN PAEGEL; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- A Selective Approach to Metastatic Gene DiscoveryCarlos Barbas; Fiscal Year: 2006..The net result of this study should be an increased understanding of the cell biology of metastasis and the discovery of novel molecular targets for diagnostic, prognostic and therapeutic application. ..
- Genetic Analysis of the Escherichia coli Tat PathwayGeorge Georgiou; Fiscal Year: 2007..abstract_text> ..
- Strategies for Selective Covalent Conjugation of Proteins with Small MoleculesFujie Tanaka; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Vaccines for Eastern and Western Equine Encephalitis VirusesRobert Whalen; Fiscal Year: 2007..glycoproteins of VEEV have already been obtained using in vitro multigene DNA recombination and directed molecular evolution. This demonstrates the potential of this approach for improving EEEV and WEEV immunogens...
- Transcriptional Blockades of HIV-1Carlos F Barbas; Fiscal Year: 2010..The new approach we develop will be applicable to other diseases. ..
- Engineering and Analysis of T cell CD3 and IL2R SignalsKARL WITTRUP; Fiscal Year: 2008..These studies will provide insights into T cell regulation as well as develop CDS and IL-2 stimulatory molecules of potential therapeutic value. ..
- Drosophila as a model genetic system to study neuropsychiatric disordersCharles Nichols; Fiscal Year: 2008..The development and utilization of this model system will lead to an enhanced discovery rate of novel targets for therapeutics to treat these conditions. [unreadable] [unreadable]..
- DRUG DISCOVERY BY MIRROR IMAGE LIGAND DISPLAYANTHONY FORSTER; Fiscal Year: 2003..3. To apply this strategy for drug discovery to other potential therapeutic targets, including the gp41 subunit of the HIV envelope glycoprotein and the breast-cancer specific, cell- surface glycoprotein MUC1. ..
- Plant Biofilm Inhibitors to Discover Biofilm GenesThomas Wood; Fiscal Year: 2008..deduce a model for bacterial biofilm formation based on the genetic information (which genes induced/repressed) and protein information discerned (via NMR) ..
- Design and Selection of Aptamer BeaconsAndrew Ellington; Fiscal Year: 2008..abstract_text> ..
- T7 RNA polymerase engineering and RNA amplificationAndrew Ellington; Fiscal Year: 2008..This will enable microarray gene analysis with as little as 1 ng of total RNA with a single round of amplification or microarray profiling from a single cell (-10 pg of total RNA) after two rounds of amplification. ..
- Chemically Programmed Antibodies for Cancer TherapyCarlos F Barbas; Fiscal Year: 2010..It is anticipated that the results of this work will provide a promising new approach to the treatment of cancer. ..
- BIOCHEMICAL MECHANISM OF HIV DNA INTEGRATIONAlan Engelman; Fiscal Year: 2009..abstract_text> ..
- Transducing Tumor Cell Antigens to AmpliconsAndrew Ellington; Fiscal Year: 2006..abstract_text> ..
- Targeted Activation of Fetal HemoglobinCarlos Barbas; Fiscal Year: 2004..It is anticipated that the results of this work will provide a novel approach to study the molecular mechanisms of hemoglobinopathies as well as new strategies to treat them. ..
- Phage Binding for Continuous Anthrax Spore DetectionVALERY PETRENKO; Fiscal Year: 2004..Parallel experiments will also be conducted with antibody-derived probes for comparison evaluation of specificity, selectivity and longevity of the sensors. ..
- Ribozymes for Peptide- and Protein- Sensing Chip ArraysAndrew Ellington; Fiscal Year: 2002..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
- Auto Selection of aptamers binding to pX01 proteomeAndrew Ellington; Fiscal Year: 2004..abstract_text> ..
- PROTEIN FOLDING AND STABILITY OF SUBTILISINPhilip Bryan; Fiscal Year: 2004..Understanding the relationships between facile folding and stability should advance the fields of protein engineering, protein structure prediction and de novo protein design. ..
- DNA REPAIR IN DRUG RESISTANCE MUTATIONSusan Rosenberg; Fiscal Year: 2003....
- Engineered alkaline phosphatases as biosensorsIchiro Matsumura; Fiscal Year: 2004..These experiments will test the feasibility of our evolutionary hypothesis and demonstrate the utility of novel protein engineering techniques. ..
- Modeling of Multivalent Vaccination for Variable VirusesMICHAEL DEEM; Fiscal Year: 2005..The proposed work allows investigation and determination of the qualitative and quantitative features that govern the interaction between an effective multivalent vaccine and the variability of the virus. ..
- Nuclear receptor probed with designer binding proteinsShohei Koide; Fiscal Year: 2005..We expect that results from this project will fill a large gap that presently exists between out knowledge gained from the static ..
- IN VITRO EVOLUTION OF HUMAN ANTIHIV ANTIBODIESCarlos Barbas; Fiscal Year: 2002....
- Creation of Stable Cleaved Trimers of the HIV-1 Envelope ProteinRobert Whalen; Fiscal Year: 2006..We propose to use directed molecular evolution to accomplish 2 main objectives...
- Novel HIV-1 Envelope Proteins Based on Consensus SequencesRobert Whalen; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- MECHANISM OF NON-INTEGRASE-MEDIATED HIV-1 REPLICATIONAlan Engelman; Fiscal Year: 2001..Further aims are to develop gene therapy vectors based on non-integrating retroviruses. ..
- APTAMER BASED DETECTOR TO QUANTIFY MACROMOLECULESAndrew Ellington; Fiscal Year: 2006....
- Gene transfer of antibodies targeting tumor angiogenesisCarlos Barbas; Fiscal Year: 2006..In addition, they are designed to facilitate a faster transition from preclinical to clinical development based on (i) cross-reactivity with human and mouse antigen and (ii) established antibody humanization strategies. ..
- STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETSShohei Koide; Fiscal Year: 2005..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
- Glycosylation Variants of HIV-1 EnvelopeRobert Whalen; Fiscal Year: 2005....
- Prolyl endopeptidases to treat Celiac SprueJeremy Minshull; Fiscal Year: 2005..4) Use the results from activity testing to derive sequence-activity relationships and thus design further improved variants. ..
- ENDOGENOUS GENE REGULATION FOR CANCER AND ANGIOGENESISCarlos Barbas; Fiscal Year: 2004..It is anticipated that the results of this work will provide researchers with novel tools to study the molecular mechanisms of disease as well as a new strategy to treat it. ..
- Improving nucleoside phosphorylation with hybrid kinasesStefan Lutz; Fiscal Year: 2009..Finally, the structural diversity of the hybrid proteins will be a rich source for fundamental structure-function studies. ..
- Targeting a novel regulatory RNA with novel antibioticsJennifer V Hines; Fiscal Year: 2010....
- Interrogation of systems level mechanisms controlling DNA repair processesNitin S Baliga; Fiscal Year: 2010..e. a predictive model for regulatory mechanisms for repair. This basic model will serve as a template for designing systems approaches to model higher complexities of eukaryotic repair processes. ..
- Ribozymes for Peptide- and Protein- Sensing Chip ArraysAndrew Ellington; Fiscal Year: 2004..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
- LEDGF-Integrase Structural BiologyAlan Engelman; Fiscal Year: 2005..abstract_text> ..
- MicroRNA Profiles of Pathogen InfectionAndrew Ellington; Fiscal Year: 2005..3. Apply these methods to the detection of changes in microRNA expression during influenza infection. 4. Apply these methods to the detection of changes in microRNA expression with other infectious agents. ..
- Mammalian Genomes - Stasis and ChangeHOLLY WICHMAN; Fiscal Year: 2009..This proposal will also ask whether changes in patterns of methylation by endocrine disruptors is linked to increased rates of retrotransposition. ..
- REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENTAndrew Ellington; Fiscal Year: 2004....
- Site-specific incorporation of FRET pairs into intracellular proteinsAndrew Ellington; Fiscal Year: 2009..This will allow us to follow and track proteins in a cell, and to determine where, when, and how proteins reside next to one another, in either normal or malformed complexes. ..