directed molecular evolution

Summary

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.

Top Publications

  1. pmc Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    Tom 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
  2. pmc In the light of directed evolution: pathways of adaptive protein evolution
    Jesse D Bloom
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 106:9995-10000. 2009
  3. ncbi Fitness effects of fixed beneficial mutations in microbial populations
    Daniel E Rozen
    Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
    Curr Biol 12:1040-5. 2002
  4. ncbi Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    Manfred T Reetz
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim Ruhr, Germany
    Nat Protoc 2:891-903. 2007
  5. ncbi Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture
    Christopher K Savile
    Codexis, Incorporated, 200 Penobscot Drive, Redwood City, CA 94063, USA
    Science 329:305-9. 2010
  6. pmc Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli
    Hani Goodarzi
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Syst Biol 6:378. 2010
  7. pmc Exploiting models of molecular evolution to efficiently direct protein engineering
    Megan F Cole
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    J Mol Evol 72:193-203. 2011
  8. pmc Evolving thermostability in mutant libraries of ligninolytic oxidoreductases expressed in yeast
    Eva García-Ruiz
    Department of Biocatalysis, Institute of Catalysis, Madrid, Spain
    Microb Cell Fact 9:17. 2010
  9. ncbi Natural diversity to guide focused directed evolution
    Helge Jochens
    Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix Hausdorff Strasse 4, 17487 Greifswald, Germany
    Chembiochem 11:1861-6. 2010
  10. ncbi Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold
    Reinhard Sterner
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    Chem Rev 105:4038-55. 2005

Research Grants

  1. A Novel Technology for Molecular Evolution
    JAMES LARRICK; Fiscal Year: 2003
  2. Novel Therapeutic Vaccines for Chronic HBV
    ROBERT GERALD WHALEN; Fiscal Year: 2012
  3. Vaccines for Eastern and Western Equine Encephalitis Viruses
    Robert Whalen; Fiscal Year: 2006
  4. Vaccines for Eastern and Western Equine Encephalitis Viruses
    Robert Whalen; Fiscal Year: 2007
  5. Improved Vaccines for Influenza B Virus
    ROBERT GERALD WHALEN; Fiscal Year: 2010
  6. IN VITRO SELECTION OF CATALYTIC ANTIBODIES
    Carlos Barbas; Fiscal Year: 1999
  7. IN VITRO SELECTION OF CATALYTIC ANTIBODIES
    Carlos Barbas; Fiscal Year: 1999
  8. Molecular evolution of AAV vectors for anti-HIV gene therapy
    KATHERINE JULIE EXCOFFON; Fiscal Year: 2011
  9. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2000
  10. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2001

Detail Information

Publications228 found, 100 shown here

  1. pmc Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    Tom 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
    ....
  2. pmc In the light of directed evolution: pathways of adaptive protein evolution
    Jesse 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...
  3. ncbi Fitness effects of fixed beneficial mutations in microbial populations
    Daniel 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...
  4. ncbi Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    Manfred 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...
  5. ncbi Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture
    Christopher 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...
  6. pmc Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli
    Hani 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...
  7. pmc Exploiting models of molecular evolution to efficiently direct protein engineering
    Megan 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'...
  8. pmc Evolving thermostability in mutant libraries of ligninolytic oxidoreductases expressed in yeast
    Eva 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...
  9. ncbi Natural diversity to guide focused directed evolution
    Helge 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...
  10. ncbi Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold
    Reinhard Sterner
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    Chem Rev 105:4038-55. 2005
  11. pmc Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution
    Toshihiko Kishimoto
    Faculty of Science, Toho University, Funabashi, Chiba, Japan
    PLoS Genet 6:e1001164. 2010
    ....
  12. pmc Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress
    Takaaki 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...
  13. pmc Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging
    Hui 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...
  14. ncbi Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
    James 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...
  15. pmc Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites
    Swetha 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...
  16. doi Kemp elimination catalysts by computational enzyme design
    Daniela 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...
  17. ncbi Evolution of high mutation rates in experimental populations of E. coli
    P 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...
  18. ncbi Covalent DNA display as a novel tool for directed evolution of proteins in vitro
    Julian 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...
  19. doi Directed molecular evolution to design advanced red fluorescent proteins
    Fedor 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...
  20. doi Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLs
    Shuyun 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)...
  21. ncbi Hypoallergens for allergen-specific immunotherapy by directed molecular evolution of mite group 2 allergens
    Guro 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 ..
  22. ncbi In-vitro selection of highly stabilized protein variants with optimized surface
    A 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...
  23. pmc Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution
    Ilja 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...
  24. pmc Directed evolution of adeno-associated virus to an infectious respiratory virus
    Katherine 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...
  25. doi A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution
    Ali 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...
  26. ncbi A simple selection strategy for evolving highly efficient enzymes
    Martin 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...
  27. ncbi Improving a circularly permuted TEM-1 beta-lactamase by directed evolution
    Joel 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...
  28. ncbi Directed evolution of transketolase activity on non-phosphorylated substrates
    Edward G Hibbert
    Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London, UK
    J Biotechnol 131:425-32. 2007
    ....
  29. ncbi Improving catalytic function by ProSAR-driven enzyme evolution
    Richard J Fox
    Codexis, Inc, 200 Penobscot Drive, Redwood City, California 94063, USA
    Nat Biotechnol 25:338-44. 2007
    ....
  30. ncbi In-vitro protein evolution by ribosome display and mRNA display
    Dasa Lipovsek
    Biological Engineering Division, Massachusetts Institute of Technology, Cambridge 02139, USA
    J Immunol Methods 290:51-67. 2004
    ....
  31. ncbi Directed molecular evolution in plant improvement
    M Lassner
    Maxygen Incorporated, 515 Galveston Drive, California 94063, Redwood City, USA
    Curr Opin Plant Biol 4:152-6. 2001
    b>Directed molecular evolution is a powerful tool to evolve genes with commercial applications...
  32. ncbi Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    Christopher 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...
  33. pmc Experimental evolution of viruses: Microviridae as a model system
    Holly 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...
  34. ncbi DNA display of biologically active proteins for in vitro protein selection
    Masato 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...
  35. pmc Directed evolution of recombinase specificity by split gene reassembly
    Charles 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...
  36. ncbi A ribozyme composed of only two different nucleotides
    John 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...
  37. ncbi Test of synergistic interactions among deleterious mutations in bacteria
    S 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...
  38. ncbi Protein engineering of subtilisin
    P 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
    ....
  39. pmc A highly sensitive selection method for directed evolution of homing endonucleases
    Zhilei 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...
  40. doi Addressing the numbers problem in directed evolution
    Manfred 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...
  41. ncbi Genome shuffling leads to rapid phenotypic improvement in bacteria
    Ying 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...
  42. ncbi HIV-1 proviral DNA excision using an evolved recombinase
    Indrani 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...
  43. ncbi Evolution of programmable zinc finger-recombinases with activity in human cells
    Russell M Gordley
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Mol Biol 367:802-13. 2007
    ....
  44. ncbi Discovery and directed evolution of a glyphosate tolerance gene
    Linda 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...
  45. pmc Molecular evolution of adeno-associated virus for enhanced glial gene delivery
    James 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
    ....
  46. pmc Exceptional convergent evolution in a virus
    J 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...
  47. pmc Protein evolution with an expanded genetic code
    Chang 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...
  48. pmc Development of an in vitro compartmentalization screen for high-throughput directed evolution of [FeFe] hydrogenases
    James 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...
  49. doi Haploids adapt faster than diploids across a range of environments
    A 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...
  50. doi Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage
    Manfred 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...
  51. ncbi Whole plasmid mutagenic PCR for directed protein evolution
    Ichiro 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...
  52. pmc Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolution
    Ilja 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...
  53. ncbi Rapid protein-folding assay using green fluorescent protein
    G 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...
  54. ncbi Directed evolution of high-affinity antibody mimics using mRNA display
    LiHui 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...
  55. doi Evolutionary origins and directed evolution of RNA
    Andrew 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...
  56. doi Directed evolution of transketolase substrate specificity towards an aliphatic aldehyde
    Edward 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...
  57. ncbi Directed molecular evolution by machine learning and the influence of nonlinear interactions
    Richard Fox
    Codexis, Inc, 200 Penobscot Drive, Redwood City, CA 94063, USA
    J Theor Biol 234:187-99. 2005
    ..Simulated molecular evolution on a synthetic protein landscape shows the use of machine learning techniques to guide library design can be a powerful addition to library generation methods such as DNA shuffling...
  58. pmc Cell-free selection of RNA-binding proteins using in vitro compartmentalization
    Yu Chen
    Department of Chemistry and Department of Biochemistry, University of Washington, Seattle WA, USA
    Nucleic Acids Res 36:e128. 2008
    ..After breaking the emulsion, the RBP can be selected based on its affinity for a biotinylated RNA bait. We demonstrate the effectiveness of this method that should enable the selection of RBPs with new specificity or improved affinity...
  59. pmc Tailoring in vitro evolution for protein affinity or stability
    L Jermutus
    Biochemisches Institut, , Winterthurerstrasse 190, , Switzerland
    Proc Natl Acad Sci U S A 98:75-80. 2001
    ..Therefore, by a combination of randomization and appropriate selection strategies, an in vitro evolution of protein properties in a predictable direction is possible...
  60. pmc Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol
    Dae 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...
  61. doi Strategy and success for the directed evolution of enzymes
    Paul 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...
  62. pmc Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Michael 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...
  63. doi Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima
    Yosephine Gumulya
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim an der Ruhr, Germany
    Chembiochem 13:1060-6. 2012
    ..These observations have ramifications for directed evolution in general and for evolutionary biological studies in which protein engineering techniques are applied...
  64. pmc Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis
    David 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...
  65. pmc Directed evolution of an aspartate aminotransferase with new substrate specificities
    T Yano
    Department of Biochemistry, Osaka Medical College, 2 7 Daigakumachi, Takatsuki, Osaka 569, Japan
    Proc Natl Acad Sci U S A 95:5511-5. 1998
    The 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...
  66. ncbi DNA shuffling of a family of genes from diverse species accelerates directed evolution
    A 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...
  67. doi mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries
    Burckhard 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...
  68. pmc Circular permutation in the Ω-loop of TEM-1 β-lactamase results in improved activity and altered substrate specificity
    Gurkan Guntas
    Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 7:e35998. 2012
    ..These variants were circularly permuted in the Ω-loop proximal to the active site. Remarkably, one variant was circularly permuted such that the key catalytic residue Glu166 was located at the N-terminus of the mature protein...
  69. ncbi Distributions of enzyme residues yielding mutants with improved substrate specificities from two different directed evolution strategies
    Janahan 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...
  70. pmc Mechanistic and structural insights into the regioselectivity of an acyl-CoA fatty acid desaturase via directed molecular evolution
    Thomas Vanhercke
    Commonwealth Scientific and Industrial Research Organisation Plant Industry, Canberra, Australian Capital Territory 2601, Australia
    J Biol Chem 286:12860-9. 2011
    ....
  71. ncbi Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method
    Manfred T Reetz
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, 45470 Mulheim an der Ruhr, Germany
    Chem Commun (Camb) 46:8657-8. 2010
    ..Mutants of the lipase from Bacillus subtilis, previously engineered for enhanced thermostability using directed evolution based on the B-FIT method, show significantly increased tolerance to hostile organic solvents...
  72. doi Directed molecular evolution improves the immunogenicity and protective efficacy of a Venezuelan equine encephalitis virus DNA vaccine
    Lesley C Dupuy
    Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
    Vaccine 27:4152-60. 2009
    We employed directed molecular evolution to improve the cross-reactivity and immunogenicity of the Venezuelan equine encephalitis virus (VEEV) envelope glycoproteins...
  73. ncbi Directed evolution of ATP binding proteins from a zinc finger domain by using mRNA display
    Glen S Cho
    Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, USA
    Chem Biol 13:139-47. 2006
    ..Many novel independent sequences were recovered with moderate affinity and high specificity for ATP, validating this scaffold for the generation of functional molecules...
  74. ncbi Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes
    Farid J Ghadessy
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Methods Mol Biol 352:237-48. 2007
    ..aquaticus Pol I (Taq) polymerase with novel and useful properties, such as increased thermostability or resistance to the potent inhibitor, heparin, from a repertoire of randomly mutated Taq polymerase genes...
  75. doi An enhanced system for unnatural amino acid mutagenesis in E. coli
    Travis S Young
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Mol Biol 395:361-74. 2010
    ..The versatility, increased yields, and increased stability of the pEVOL vector will further facilitate the expression of proteins with unnatural amino acids...
  76. ncbi Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray
    David Gresham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Science 311:1932-6. 2006
    ..We applied this approach to elucidate the genetic basis of phenotypic variants and to identify the small number of single-base pair changes accumulated during experimental evolution of yeast...
  77. ncbi Hsp90 as a capacitor for morphological evolution
    S L Rutherford
    Howard Hughes Medical Institute, University of Chicago, Illinois 60637, USA
    Nature 396:336-42. 1998
    ..This provides a plausible mechanism for promoting evolutionary change in otherwise entrenched developmental processes...
  78. ncbi In vitro evolution of a fungal laccase in high concentrations of organic cosolvents
    Miren Zumárraga
    Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Cientificas, Cantoblanco, 28049 Madrid, Spain
    Chem Biol 14:1052-64. 2007
    ..Some mutations at the protein surface stabilized the laccase by allowing additional electrostatic and hydrogen bonding to occur...
  79. ncbi Miniaturising the laboratory in emulsion droplets
    Andrew D Griffiths
    Institut de Science et d Ingénierie Supramoléculaires ISIS, 8 allee Gaspard Monge, BP 70028, F 67083 Strasbourg cedex, France
    Trends Biotechnol 24:395-402. 2006
    ..This review describes the scope and potential of IVC in areas such as in vitro evolution of proteins and RNAs, cell-free cloning and sequencing, genetics, genomics, and proteomics...
  80. ncbi Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection
    Kenny Schlosser
    Department of Biochemistry and Biomedical Sciences and Department of Chemistry, McMaster University, Hamilton, Canada L8N 3Z5
    J Mol Evol 61:192-206. 2005
    ..This is the first study which thoroughly documents the topography of a deoxyribozyme fitness landscape over many generations of in vitro selection...
  81. pmc Optimization and optimality of a short ribozyme ligase that joins non-Watson-Crick base pairings
    M P Robertson
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, 78712, USA
    RNA 7:513-23. 2001
    ..The optimized L1 ligases may be optimal within their sequence spaces, and minimal ligases that span less than 60 nt in length have been engineered based on these results...
  82. pmc Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution
    Kristian M Müller
    Institut fur Biologie III, Universität Freiburg Schänzlestrasse 1, 79104 Freiburg, Germany
    Nucleic Acids Res 33:e117. 2005
    ..1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs...
  83. pmc Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase
    Monal R Parikh
    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
    J Mol Biol 352:621-8. 2005
    ..Site-saturation mutagenesis thus proved faster, less resource-intensive and more effective than DNA shuffling for this particular evolutionary pathway...
  84. ncbi A ribozyme for the aldol reaction
    Stefan Fusz
    Universitat Bonn, Kekule Institut fur Organische Chemie und Biochemie, Gerhard Domagk Strasse 1, 53121 Bonn, Germany
    Chem Biol 12:941-50. 2005
    ....
  85. pmc The effect of cytidine on the structure and function of an RNA ligase ribozyme
    J Rogers
    Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
    RNA 7:395-404. 2001
    ....
  86. pmc Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence
    Atef Nehdi
    RNA Group Groupe ARN, Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Universite de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
    Nucleic Acids Res 34:584-92. 2006
    ..Thus, just because a self-cleaving RNA motif is small does not imply that it occurs easily...
  87. ncbi High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions
    Enrico Mastrobattista
    Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Chem Biol 12:1291-300. 2005
    ..Only two specific mutations were ever seen to provide this improvement in Ebg beta-galactosidase activity in vivo. In contrast, nearly all the improved beta-galactosidases selected in vitro resulted from different mutations...
  88. ncbi Forty years of in vitro evolution
    Gerald F Joyce
    Department of Chemistry and Molecular Biology, La Jolla, CA 92037, USA
    Angew Chem Int Ed Engl 46:6420-36. 2007
    ..This Review summarizes the concepts and methods for the directed evolution of RNA molecules in vitro...
  89. ncbi RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension
    W K Johnston
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Science 292:1319-25. 2001
    ..Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template...
  90. ncbi Protein engineering by cell-surface display
    K D Wittrup
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Curr Opin Biotechnol 12:395-9. 2001
    ..The promise of cell-surface display for directed evolution is being realized, with significant improvements recently reported in protein ligand binding affinity, stability, expression and enzymatic activity...
  91. ncbi Directed evolution of proteins for heterologous expression and stability
    Cintia Roodveldt
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
    Curr Opin Struct Biol 15:50-6. 2005
    ....
  92. pmc In vitro selection of restriction endonucleases by in vitro compartmentalization
    Nobuhide Doi
    Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    Nucleic Acids Res 32:e95. 2004
    ....
  93. ncbi Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase
    Margaret A Chow
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3206, USA
    Biochemistry 43:12780-7. 2004
    ..While HEX is always in the closed conformation, HEX + A293D is observed in both the closed and a novel open conformation, allowing for more rapid product release...
  94. ncbi Genetic screens and directed evolution for protein solubility
    Geoffrey S Waldo
    BN 2, MS M888, Los Alamos National Laboratories, Los Alamos, NM 87545, USA
    Curr Opin Chem Biol 7:33-8. 2003
    ..Efficient, well-established strategies for generating and recombining genetic diversity, driven by new screening and selection methods, can furnish correctly folded, soluble protein...
  95. pmc Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution
    Gavin 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...
  96. ncbi Alteration of Cre recombinase site specificity by substrate-linked protein evolution
    F Buchholz
    Hooper Research Foundation, University of California San Francisco UCSF, 513 Parnassus Ave, San Francisco, CA 94143 0552, USA
    Nat Biotechnol 19:1047-52. 2001
    b>Directed molecular evolution was applied to generate Cre recombinase variants that recognize a new DNA target sequence. Cre was adapted in a three-stage strategy to evolve recombinases to specifically recombine the new site...
  97. pmc Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution
    Cameron Neylon
    School of Chemistry, University of Southampton, Highfield SO17 1BJ, UK
    Nucleic Acids Res 32:1448-59. 2004
    b>Directed molecular evolution and combinatorial methodologies are playing an increasingly important role in the field of protein engineering...
  98. ncbi Directed evolution by in vitro compartmentalization
    Oliver J Miller
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    Nat Methods 3:561-70. 2006
  99. ncbi A covalent chemical genotype-phenotype linkage for in vitro protein evolution
    Viktor Stein
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK
    Chembiochem 8:2191-4. 2007
  100. pmc In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions
    Kenny Schlosser
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Nucleic Acids Res 36:4768-77. 2008
    ..The same deoxyribozymes exhibited approximately 1000-fold lower activity against all RNA substrates, but could potentially be improved through further in vitro evolution and engineering...
  101. ncbi Expanding the genetic code
    Lei Wang
    The Jack H Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Annu Rev Biophys Biomol Struct 35:225-49. 2006
    ..This methodology provides a powerful tool both for exploring protein structure and function in vitro and in vivo and for generating proteins with new or enhanced properties...

Research Grants98

  1. A Novel Technology for Molecular Evolution
    JAMES 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. ..
  2. Novel Therapeutic Vaccines for Chronic HBV
    ROBERT GERALD WHALEN; Fiscal Year: 2012
    ..HBsAg variants containing xenogeneic sequences with novel T epitopes have been identified using a directed molecular evolution approach...
  3. Vaccines for Eastern and Western Equine Encephalitis Viruses
    Robert Whalen; Fiscal Year: 2006
    ..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...
  4. Vaccines for Eastern and Western Equine Encephalitis Viruses
    Robert 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...
  5. Improved Vaccines for Influenza B Virus
    ROBERT GERALD WHALEN; Fiscal Year: 2010
    ..We propose to use a directed molecular evolution approach to address this problem...
  6. IN VITRO SELECTION OF CATALYTIC ANTIBODIES
    Carlos Barbas; Fiscal Year: 1999
    ..In vivo chain shuffling is proposed as a route to facilitate directed molecular evolution of antibodies using iterative selection strategies...
  7. IN VITRO SELECTION OF CATALYTIC ANTIBODIES
    Carlos Barbas; Fiscal Year: 1999
    ..In vivo chain shuffling is proposed as a route to facilitate directed molecular evolution of antibodies using iterative selection strategies...
  8. Molecular evolution of AAV vectors for anti-HIV gene therapy
    KATHERINE JULIE EXCOFFON; Fiscal Year: 2011
    ..We propose to use directed molecular evolution of AAV to tailor make HIV and T cell-specific AAV vectors in order to treat HIV infection with gene-..
  9. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2000
    ....
  10. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2001
    ....
  11. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 1999
    ....
  12. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2002
    ....
  13. Novel Vaccine Immunogens for Pandemic H5 Influenza
    Robert 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 ..
  14. Novel Vaccine Immunogens for Pandemic H5 Influenza
    ROBERT 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 ..
  15. Germline-Specific Immunogens for the Induction of Neutralizing Antibodies to HIV-
    ROBERT GERALD WHALEN; Fiscal Year: 2012
    ..We propose therefore to use a directed molecular evolution approach to identify germline-specific immunogens...
  16. DETAILED ANALYSIS OF SCL/TAL DIMERIZATION WITH E PROTEIN
    Adam 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. ..
  17. DETAILED ANALYSIS OF SCL/TAL DIMERIZATION WITH E PROTEIN
    Adam Goldfarb; Fiscal Year: 1999
    ..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. ..
  18. DETAILED ANALYSIS OF SCL/TAL DIMERIZATION WITH E PROTEIN
    Adam Goldfarb; Fiscal Year: 2000
    ..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. ..
  19. Development of Novel Immunogens for Vaccines to HIV-1
    Robert Whalen; Fiscal Year: 2005
    ..This Proposal employs a powerful technology called directed molecular evolution. This approach involves the use of in vitro recombination to create a large number of chimeric genes ..
  20. Development of Novel Immunogens for Vaccines to HIV-1
    Robert Whalen; Fiscal Year: 2007
    ..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 ..
  21. Development of Novel Immunogens for Vaccines to HIV-1
    Robert Whalen; Fiscal Year: 2006
    ..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 ..
  22. Development of Novel Immunogens for Vaccines to HIV-1
    Robert 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 ..
  23. Development of Novel Immunogens for Vaccines to HIV-1
    Robert Whalen; Fiscal Year: 2005
    ..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 ..
  24. Development of Novel Immunogens for Vaccines to HIV-1
    ROBERT GERALD 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 ..
  25. Novel approaches for the development of live and inactivated viral vaccines
    AARON BRAULT; Fiscal Year: 2009
    ..of attenuation mediated by approaches such as serial passaging of viruses, viral recombination and directed molecular evolution is unpredictable and this characteristic contributes to the lengthy production times for many vaccines ..
  26. STRUCTURE FUNCTION RELATIONSHIP OF TUMOR SUPPRESSORS
    Ming Daw Tsai; Fiscal Year: 1999
    ..The goal is to provide a structural model for the suppressor cdk4 complex, which will be useful in deciphering the "missing functionality" in the disease-related mutants of tumor suppressors, an important information for drug design. ..
  27. Creation of Stable Cleaved Trimers of the HIV-1 Envelope Protein
    Robert Whalen; Fiscal Year: 2006
    ..We propose to use directed molecular evolution to accomplish 2 main objectives...
  28. Engineering high affinity integrin binding proteins
    Jennifer Cochran; Fiscal Year: 2006
    ..period of the award, where integrin binding proteins will be engineered to even higher affinity using directed molecular evolution by yeast surface display...
  29. Engineering high affinity integrin binding proteins
    Jennifer Cochran; Fiscal Year: 2007
    ..period of the award, where integrin binding proteins will be engineered to even higher affinity using directed molecular evolution by yeast surface display...
  30. Engineering high affinity integrin binding proteins
    Jennifer Cochran; Fiscal Year: 2004
    ..period of the award, where integrin binding proteins will be engineered to even higher affinity using directed molecular evolution by yeast surface display...
  31. Engineering high affinity integrin binding proteins
    Jennifer Cochran; Fiscal Year: 2005
    ..period of the award, where integrin binding proteins will be engineered to even higher affinity using directed molecular evolution by yeast surface display...
  32. Dissecting Electrostatic Effects in Cystic Fibrosis Muco
    Gerard 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 ..
  33. Electrostatic Effects in Cystic Fibrosis Mucous
    Gerard Wong; Fiscal Year: 2004
    ..3) To develop, via directed molecular evolution, an anionic DNAzyme which mimics the biofilm suppression action of cationic lactoferrin, but will not ..
  34. Engineering AAV for Enhanced Retrograde Transport
    Brian 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...
  35. Engineering AAV for Enhanced Retrograde Transport
    Brian Kaspar; Fiscal Year: 2005
    ..We therefore propose to employ a directed molecular evolution approach to develop novel AAV capsid variants with enhanced retrograde transport in vivo...
  36. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2005
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  37. Directed Evolution of Nucleic Acid Enzymes
    Gerald F Joyce; Fiscal Year: 2010
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..
  38. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2002
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  39. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2009
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..
  40. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2003
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  41. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2007
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. [unreadable] [unreadable] [unreadable]..
  42. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2008
    ..These decorated nanostructures then will be subject to in vitro evolution, selecting on the basis of both their form and the function of the appended DNAs. ..
  43. Directed Evolution of Nucleic Acid Enzymes
    GERALD JOYCE; Fiscal Year: 2004
    ..The adapter will allow the cofactor to be bound readily by the enzyme, allowing evolution to exploit the bound cofactor for use in catalysis. ..
  44. Directed Evolution of Homing Endonucleases for Human Gene Therapy
    Huimin Zhao; Fiscal Year: 2008
    ..Equally important, we anticipate that this exploratory/developmental (R21) project will establish a technology platform for engineering a wide variety of DNA-modifying enzymes for biomedical research and human gene therapy. ..
  45. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2003
    ..abstract_text> ..
  46. Computation-Guided Protein Recombination and Evolution
    Frances Arnold; Fiscal Year: 2004
    ..abstract_text> ..
  47. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2006
    ..abstract_text> ..
  48. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2004
    ..abstract_text> ..
  49. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2009
    ..We will develop switches designed for the treatment of cancer and switches designed to be used as sensors for the detection and quantification of important protein kinases in vitro and in live cells. ..
  50. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2007
    ..abstract_text> ..
  51. Synthetic Protein Families by Structure-Guided SCHEMA Recombination
    Frances Arnold; Fiscal Year: 2009
    ..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. ..
  52. The Combinatorial Design of Protein Molecular Switches
    MARC A OSTERMEIER; Fiscal Year: 2010
    ..We will develop switches designed for the treatment of cancer and switches designed to be used as sensors for the detection and quantification of important protein kinases in vitro and in live cells. ..
  53. Synthetic Protein Families by Structure-Guided SCHEMA Recombination
    Frances 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. ..
  54. Quantitative Microfluidic Molecular Evolution
    BRIAN PAEGEL; Fiscal Year: 2006
    ....
  55. Creation of site-specific DNA methyltransferases
    Marc Ostermeier; Fiscal Year: 2006
    ..abstract_text> ..
  56. Computation-Guided Protein Recombination and Evolution
    Frances Arnold; Fiscal Year: 2006
    ..abstract_text> ..
  57. Live Cell Fluorescence Imaging Using Molecular Switches
    Marc Ostermeier; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  58. Microfluidic Processors for Directed Evolution and Synthetic Biology
    BRIAN PAEGEL; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  59. Computation-Guided Protein Recombination and Evolution
    Frances Arnold; Fiscal Year: 2005
    ..abstract_text> ..
  60. The Combinatorial Design of Protein Molecular Switches
    Marc Ostermeier; Fiscal Year: 2005
    ..abstract_text> ..
  61. Computation-Guided Protein Recombination and Evolution
    Frances Arnold; Fiscal Year: 2003
    ..abstract_text> ..
  62. HIV-1 Integrase Structural Biology
    Alan Engelman; Fiscal Year: 2009
    ..abstract_text> ..
  63. Mammalian Genomes - Stasis and Change
    HOLLY 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. ..
  64. Interrogation of systems level mechanisms controlling DNA repair processes
    NITIN BALIGA; Fiscal Year: 2008
    ..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. ..
  65. Interrogation of systems level mechanisms controlling DNA repair processes
    Nitin 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. ..
  66. LEDGF-Integrase Structural Biology
    Alan Engelman; Fiscal Year: 2005
    ..abstract_text> ..
  67. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2004
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  68. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2005
    ..abstract_text> ..
  69. HIV-1 Integrase Structural Biology
    Alan Engelman; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  70. MicroRNA Profiles of Pathogen Infection
    Andrew 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. ..
  71. Mammalian Genomes - Stasis and Change
    HOLLY WICHMAN; Fiscal Year: 2006
    ..This proposal will also ask whether changes in patterns of methylation by endocrine disruptors is linked to increased rates of retrotransposition. ..
  72. HIV-1 Integrase Structural Biology
    Alan Engelman; Fiscal Year: 2008
    ..abstract_text> ..
  73. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2009
    ....
  74. Genomic analysis of histone replacement dynamics in yeast
    Oliver Rando; Fiscal Year: 2008
    ..In this proposal we aim to investigate the mechanisms that enable cells to inherit epigenetic information, with the hope that we may eventually use this information to design more directed therapies against cancer. ..
  75. Interrogation of systems level mechanisms controlling DNA repair processes
    NITIN BALIGA; Fiscal Year: 2007
    ..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. ..
  76. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2006
    ....
  77. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 1999
    ..In particular, the peptide motifs identified by physical mapping and selection studies should provide information essential to the synthesis of peptidomimetic drugs. ..
  78. Transgenerational effects of diet in mammals
    Oliver Rando; Fiscal Year: 2009
    ..Thus, our identification and characterization of pathways linking diet in one generation to effects on the next generation is of key importance for understanding and eventually treating a wide range of human diseases. ..
  79. Plant Biofilm Inhibitors to Discover Biofilm Genes
    Thomas Wood; Fiscal Year: 2005
    ..deduce a model for bacterial biofilm formation based on the genetic information (which genes induced/repressed) and protein information discerned (via NMR) ..
  80. A High-throughput Route to Synthetic Antibodies for Array-based Cancer Detection
    JOHN CHAPUT; Fiscal Year: 2008
    ..The relevance of the proposed research resides in the potential for early cancer detection based on routine proteome-wide analysis using synthetic antibody arrays to detect cancer biomarkers presymptomatically. ..
  81. Discovering a Hidden Proteome in the Human Genome
    JOHN CHAPUT; Fiscal Year: 2008
    ..It is expected that such knowledge will lead to new therapeutic interventions that can be used to improve the human condition. ..
  82. BIOCHEMICAL MECHANISM OF HIV DNA INTEGRATION
    Alan Engelman; Fiscal Year: 2002
    ..The results of these experiments will be used to formulate a detailed model of the structural and functional organization of HIV-1 PICs, which will aid the design of antiviral drugs targeted against HIV-1 integration. ..
  83. HIV-1 Preintegration Trafficking and Nuclear Localization
    Alan Engelman; Fiscal Year: 2009
    ..This knowledge in the long run will define novel targets for therapeutic interaction to develop new anti-viral drugs in the fight against HIV/AIDS. ..
  84. Genomic analysis of histone replacement dynamics in yeast
    Oliver Rando; Fiscal Year: 2009
    ..In this proposal we aim to investigate the mechanisms that enable cells to inherit epigenetic information, with the hope that we may eventually use this information to design more directed therapies against cancer. ..
  85. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2002
    ....
  86. Discovering a Hidden Proteome in the Human Genome
    JOHN CHAPUT; Fiscal Year: 2009
    ..It is expected that such knowledge will lead to new therapeutic interventions that can be used to improve the human condition. ..
  87. MECHANISM OF NON-INTEGRASE-MEDIATED HIV-1 REPLICATION
    Alan Engelman; Fiscal Year: 1999
    ..Further aims are to develop gene therapy vectors based on non-integrating retroviruses. ..
  88. BIOCHEMICAL MECHANISM OF HIV DNA INTEGRATION
    Alan Engelman; Fiscal Year: 2007
    ..abstract_text> ..
  89. Plant Biofilm Inhibitors to Discover Biofilm Genes
    Thomas Wood; Fiscal Year: 2006
    ..deduce a model for bacterial biofilm formation based on the genetic information (which genes induced/repressed) and protein information discerned (via NMR) ..
  90. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2004
    ....
  91. Site-specific incorporation of FRET pairs into intracellular proteins
    Andrew 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. ..