Jim Swartz

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 4:e7565. 2009
  2. pmc A cell-free microtiter plate screen for improved [FeFe] hydrogenases
    James A Stapleton
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 5:e10554. 2010
  3. pmc An integrated cell-free metabolic platform for protein production and synthetic biology
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    Mol Syst Biol 4:220. 2008
  4. pmc Cell-free H-cluster synthesis and [FeFe] hydrogenase activation: all five CO and CN⁻ ligands derive from tyrosine
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 6:e20346. 2011
  5. pmc New insights into [FeFe] hydrogenase activation and maturase function
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, USA
    PLoS ONE 7:e45850. 2012
  6. pmc Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation
    Cem Albayrak
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305, USA
    Nucleic Acids Res 41:5949-63. 2013
  7. pmc High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, USA
    PLoS ONE 5:e15491. 2010
  8. 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
  9. ncbi request reprint Developing cell-free biology for industrial applications
    Jim Swartz
    Department of Chemical Engineering, Stauffer III, Rm 113, Stanford University, Stanford, CA 94305 5025, USA
    J Ind Microbiol Biotechnol 33:476-85. 2006
  10. doi request reprint Cell-free production of Gaussia princeps luciferase--antibody fragment bioconjugates for ex vivo detection of tumor cells
    Kedar G Patel
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305 5025, USA
    Biochem Biophys Res Commun 390:971-6. 2009

Collaborators

  • Jeanne Bonomo
  • John P Welsh
  • Michael C Jewett
  • JOSEPH PUGLISI
  • Cem Albayrak
  • Jon M Kuchenreuther
  • Aaron R Goerke
  • Kara A Calhoun
  • James A Stapleton
  • Kurtis G Knapp
  • Junhao Yang
  • Marcus E Boyer
  • Kim A Woodrow
  • Ronald Levy
  • Gregory Kanter
  • Kedar G Patel
  • Alexei Voloshin
  • Simon J George
  • Stephen P Cramer
  • Celestine S Grady-Smith
  • William C Yang
  • Bradley C Bundy
  • Jessica J Wuu
  • Shoshana Levy
  • Chia Wei Wang
  • Alexei M Voloshin
  • Kelly A Underwood
  • David V Liu
  • Gang Yin
  • Dong Myung Kim
  • R David Britt
  • Alyssa S Bingham
  • Jieun Lee
  • Yohannes T Ghebremariam
  • Chiung Chi Kuo
  • Patrick P Ng
  • John P Cooke
  • H Edward Wong
  • Marc J Franciszkowicz
  • Andreas M Loening
  • Sanjiv S Gambhir
  • Isoken O Airen
  • Nathalie Michel-Reydellet
  • James F Zawada
  • Hendrik Velkeen

Detail Information

Publications42

  1. pmc Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 4:e7565. 2009
    ..This unique [6Fe-6S] complex contains multiple non-protein moieties and requires several maturation enzymes for its assembly. The pathways and biochemical precursors for H-cluster biosynthesis have yet to be elucidated...
  2. pmc A cell-free microtiter plate screen for improved [FeFe] hydrogenases
    James A Stapleton
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 5:e10554. 2010
    ..Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms...
  3. pmc An integrated cell-free metabolic platform for protein production and synthetic biology
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    Mol Syst Biol 4:220. 2008
    ....
  4. pmc Cell-free H-cluster synthesis and [FeFe] hydrogenase activation: all five CO and CN⁻ ligands derive from tyrosine
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 6:e20346. 2011
    ....
  5. pmc New insights into [FeFe] hydrogenase activation and maturase function
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, USA
    PLoS ONE 7:e45850. 2012
    ....
  6. pmc Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation
    Cem Albayrak
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305, USA
    Nucleic Acids Res 41:5949-63. 2013
    ..This new platform can also be used to screen scissile ribozymes for improved catalysis...
  7. pmc High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli
    Jon M Kuchenreuther
    Department of Chemical Engineering, Stanford University, Stanford, California, USA
    PLoS ONE 5:e15491. 2010
    ..The realization of hydrogenase-based technologies for renewable H(2) production is presently limited by the need for scalable and high-yielding methods to supply active hydrogenases and their required maturases...
  8. 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...
  9. ncbi request reprint Developing cell-free biology for industrial applications
    Jim Swartz
    Department of Chemical Engineering, Stauffer III, Rm 113, Stanford University, Stanford, CA 94305 5025, USA
    J Ind Microbiol Biotechnol 33:476-85. 2006
    ..Although many challenges remain, this newly expanded ability to activate and control protein production holds much promise for both research and commercial applications...
  10. doi request reprint Cell-free production of Gaussia princeps luciferase--antibody fragment bioconjugates for ex vivo detection of tumor cells
    Kedar G Patel
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305 5025, USA
    Biochem Biophys Res Commun 390:971-6. 2009
    ..GLuc-scFv conjugates were shown to differentiate between cells expressing a surface target of the scFv and cells that did not carry this marker...
  11. ncbi request reprint Multiply mutated Gaussia luciferases provide prolonged and intense bioluminescence
    John P Welsh
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305 5025, USA
    Biochem Biophys Res Commun 389:563-8. 2009
    ....
  12. ncbi request reprint Rapid expression of vaccine proteins for B-cell lymphoma in a cell-free system
    Junhao Yang
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Bioeng 89:503-11. 2005
    ..Between the two amino-terminal GM-CSF fusion proteins, GM-VL-VH showed a higher total and soluble yield than GM-VH-VL...
  13. pmc Cell-free production of scFv fusion proteins: an efficient approach for personalized lymphoma vaccines
    Gregory Kanter
    Department of Medicine, Division of Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
    Blood 109:3393-9. 2007
    ..The cell-free E coli system offers a platform for rapidly generating individualized vaccines, thereby allowing much more efficient application in the clinic...
  14. ncbi request reprint Cell-free metabolic engineering promotes high-level production of bioactive Gaussia princeps luciferase
    Aaron R Goerke
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
    Metab Eng 10:187-200. 2008
    ..The cell-free product had a specific activity of 4.2x10(24)photons/s/mol, the highest reported activity for any characterized luciferase...
  15. ncbi request reprint Total amino acid stabilization during cell-free protein synthesis reactions
    Kara A Calhoun
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    J Biotechnol 123:193-203. 2006
    ..The extract from strain KC6 maintains stable amino acid concentrations of all 20 amino acids in a 3-h batch reaction. Yields for three different proteins improved 75-250% relative to cell-free expression using the control extract...
  16. ncbi request reprint Development of cell-free protein synthesis platforms for disulfide bonded proteins
    Aaron R Goerke
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Bioeng 99:351-67. 2008
    ..Establishing general CFPS platforms enhances the potential for cell-free protein synthesis to reliably produce complex protein products at low production and capital costs with very rapid process development timelines...
  17. doi request reprint High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids
    Aaron R Goerke
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Bioeng 102:400-16. 2009
    ..The desired specificity for incorporation of the nnAA by the cell-free system was confirmed. Additionally, the modified proteins were enzymatically active and reactive for copper(I)-catalyzed (3 + 2) cycloadditions (click chemistry)...
  18. pmc Continued protein synthesis at low [ATP] and [GTP] enables cell adaptation during energy limitation
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    J Bacteriol 191:1083-91. 2009
    ..We anticipate that cell-free studies in which complex metabolic systems are activated will be valuable tools for elucidating the behavior of such systems...
  19. ncbi request reprint Escherichia coli-based cell-free synthesis of virus-like particles
    Bradley C Bundy
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 100:28-37. 2008
    ..The scalability of this technology was tested without loss in production yields. To our knowledge, this is the first time a prokaryote-based in vitro transcription/translation system has generated a virus-like particle...
  20. pmc Comparing the functional properties of the Hsp70 chaperones, DnaK and BiP
    Jeanne Bonomo
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305 5025, USA
    Biophys Chem 149:58-66. 2010
    ..Our results support previous reports suggesting that DnaK provides both post-translational and co-translational folding assistance while BiP predominantly provides folding assistance that is contemporaneous with translation...
  21. ncbi request reprint Energy systems for ATP regeneration in cell-free protein synthesis reactions
    Kara A Calhoun
    Department of Chemical Engineering, Stanford University, Stanford, CA, USA
    Methods Mol Biol 375:3-17. 2007
    ..We describe the various types of energy sources used in cell-free reactions, give examples of the major classes, and demonstrate protocols for successful use of three recently developed energy systems: PANOxSP, cytomim, and glucose...
  22. pmc Cell-free production of transducible transcription factors for nuclear reprogramming
    William C Yang
    Department of Bioengineering, Stanford University, California 94305, USA
    Biotechnol Bioeng 104:1047-58. 2009
    ....
  23. ncbi request reprint Cell-free synthesis and maturation of [FeFe] hydrogenases
    Marcus E Boyer
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, California 94305, USA
    Biotechnol Bioeng 99:59-67. 2008
    ....
  24. ncbi request reprint Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 86:19-26. 2004
    ....
  25. ncbi request reprint Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 87:465-72. 2004
    ..4 mg/mL of CAT. These results underscore the critical role that nucleotides play in the combined transcription-translation reaction and highlight the importance of understanding metabolic processes influencing substrate depletion...
  26. ncbi request reprint Expression of active murine granulocyte-macrophage colony-stimulating factor in an Escherichia coli cell-free system
    Junhao Yang
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Prog 20:1689-96. 2004
    ..Finally, successful folding of the cell-free synthesized GM-CSF-his6 was confirmed by its cell-proliferation activity after purification with a Ni2+ chelating column...
  27. ncbi request reprint Cell-free protein synthesis with prokaryotic combined transcription-translation
    James R Swartz
    Department of Chemical Engineering, Stanford University, CA, USA
    Methods Mol Biol 267:169-82. 2004
    ..We describe the preparation of materials necessary for the expression, quantification, and purification of rDNA proteins from active Escherichia coli extracts...
  28. ncbi request reprint Efficient and scalable method for scaling up cell free protein synthesis in batch mode
    Alexei M Voloshin
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 91:516-21. 2005
    ..We believe that this approach provides a general reaction scale-up technology that will be suitable for any protein target, cell free system, and reaction volume...
  29. ncbi request reprint Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis
    Kelly A Underwood
    Biophysics Program, D118 Fairchild Science Building, Stanford, California 94305 5126, USA
    Biotechnol Bioeng 91:425-35. 2005
    ....
  30. ncbi request reprint An economical method for cell-free protein synthesis using glucose and nucleoside monophosphates
    Kara A Calhoun
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    Biotechnol Prog 21:1146-53. 2005
    ..The glucose/NMP cell-free reaction system dramatically reduces reagent costs while supplying high protein yields...
  31. ncbi request reprint Cell-free production of active E. coli thioredoxin reductase and glutathione reductase
    Kurtis G Knapp
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    FEBS Lett 559:66-70. 2004
    ..The specific activity for both TR and GR decreased without FAD supplementation. This research demonstrates that CFPS can be used to produce enzymes that are multimeric and require a cofactor...
  32. ncbi request reprint Evidence for an additional disulfide reduction pathway in Escherichia coli
    Kurtis G Knapp
    Department of Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305, USA
    J Biosci Bioeng 103:373-6. 2007
    ..However, significant glutathione reductase activity remained. The unknown glutathione reductase pathway is disabled by iodoacetamide, is inhibited by NADH, and appears to use NADPH as an electron source...
  33. ncbi request reprint Enhancing multiple disulfide bonded protein folding in a cell-free system
    Gang Yin
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 86:188-95. 2004
    ..Taken together, the modifications enabled the production of more than 60 microg/mL of bioactive PA in a simple 3-h batch reaction...
  34. ncbi request reprint Efficient production of a bioactive, multiple disulfide-bonded protein using modified extracts of Escherichia coli
    Dong Myung Kim
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Bioeng 85:122-9. 2004
    ..This result not only demonstrates efficient production of complex proteins, it also emphasizes the control and flexibility offered by the cell-free approach...
  35. ncbi request reprint A sequential expression system for high-throughput functional genomic analysis
    Kim A Woodrow
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305 5025, USA
    Proteomics 7:3870-9. 2007
    ..This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities...
  36. ncbi request reprint Streamlining Escherichia coli S30 extract preparation for economical cell-free protein synthesis
    David V Liu
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Prog 21:460-5. 2005
    ..These insights suggest that consistent cell extract can be produced more quickly and with considerably less expense for large-scale cell-free protein production, especially when combined with high-density fermentation protocols...
  37. ncbi request reprint Rapid expression of functional genomic libraries
    Kim A Woodrow
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    J Proteome Res 5:3288-300. 2006
    ..These improvements in the parallel synthesis of linear ETs combined with enhanced in vitro enzyme activation help to make CFPS systems more attractive platforms for high-throughput evaluation of protein function...
  38. ncbi request reprint Simultaneous expression and maturation of the iron-sulfur protein ferredoxin in a cell-free system
    Marcus E Boyer
    Department of Chemical Engineering, Stanford University, California 94305, USA
    Biotechnol Bioeng 94:128-38. 2006
    ..To our knowledge, this is the first demonstration of directed, high-yield production and maturation of an Fe-S protein in a cell-free system...
  39. ncbi request reprint Energizing cell-free protein synthesis with glucose metabolism
    Kara A Calhoun
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Bioeng 90:606-13. 2005
    ....
  40. ncbi request reprint Cell-free synthesis of proteins that require disulfide bonds using glucose as an energy source
    Kurtis G Knapp
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    Biotechnol Bioeng 97:901-8. 2007
    ..This new protocol offers an economically feasible cell-free system for the production of secreted mammalian proteins as human therapeutics or vaccines...
  41. doi request reprint High yield cell-free production of integral membrane proteins without refolding or detergents
    Jessica J Wuu
    Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
    Biochim Biophys Acta 1778:1237-50. 2008
    ..Whereas TetA incorporates efficiently into vesicle membranes with over two-thirds of the synthesized protein being inserted, MtlA yields appear to be limited by insufficient concentrations of a membrane-associated chaperone...
  42. ncbi request reprint Rapid expression and purification of 100 nmol quantities of active protein using cell-free protein synthesis
    Michael C Jewett
    Department of Chemical Engineering, Stanford University, Stanford, California 94305 5025, USA
    Biotechnol Prog 20:102-9. 2004
    ..To our knowledge, this is the largest amount of actively expressed protein to be reported in a simple, fed-batch cell-free protein synthesis reaction...

Research Grants4

  1. Increasing The Utility Of Cell-Free Protein Synthesis
    James Swartz; Fiscal Year: 2001
    ..When successful, this project will provide exciting new technology for the efficient synthesis and modification of a wide variety of proteins. ..
  2. Increasing The Utility Of Cell-Free Protein Synthesis
    James Swartz; Fiscal Year: 2002
    ..When successful, this project will provide exciting new technology for the efficient synthesis and modification of a wide variety of proteins. ..
  3. Increasing The Utility Of Cell-Free Protein Synthesis
    James Swartz; Fiscal Year: 2003
    ..When successful, this project will provide exciting new technology for the efficient synthesis and modification of a wide variety of proteins. ..
  4. Designing Proximal Chaperones for Cell-Free Protein Synthesis
    James Swartz; Fiscal Year: 2007
    ..If successful, the project will produce new knowledge about eukaryotic protein folding and will also produce improved technology for the production of important protein therapeutics. ..