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Green Fluorescent Protein (GFP) Technical Library

 

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Protein Solubility

LANL Publications

NewCabantous et al. "New Molecular Reporters for Rapid Protein Folding Assays," PLOSone. June 11, 2008.

Chun et al. “Split GFP complementation assay: a novel approach to quantitatively measure aggregation of tau in situ: effects of GSK3beta activation and caspase 3 cleavage”J Neurochem. 103(6):2529-39, December 2007.

Andrews BT, Schoenfish AR, Waldo GS, Jennings PA “The rough energy landscape of sfGFP is linked to the chromophore” (2007) J Mol Biol. 2:476-90, October 2007

Cabantous and Waldo. "In vivo and in vitro protein solubility assays using split GFP," Nature Methods 3(10), 845–854, October 2006.

Cabantous et al. "Recent advances in GFP folding reporter and split-GFP solubility reporter technologies. Application to improving the folding and solubility of recalcitrant proteins from Mycobacterium tuberculosis," Journal of Structural and Functional Genomics 6:113–119, 2005.

Cabantous et al. "Protein tagging and detection with engineered self-assembling fragrments of green fluorescent protein," Nature Biotechnology 23, 102-107, December 2004.

Yang et al. "Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis," PNAS 100: 455-460, 2003

Waldo GS. "Genetic screens and directed evolution for protein solubility" Curr Opin Chem Biol 7(1), 33-8. 2003.

Pédelacq et al. "Engineering soluble proteins for structural genomics," Nature Biotechnology 20, 927-932, September 2002.

Waldo et al. "Rapid protein-folding assay using green flourescent protein," Nature Biotechnology  17, 691 - 695, July 1999.

 

Citations

LANL Presentations

 

Protein Expression Level

[ Top ]

Cava et al. "Expression and use of superfolder green flourescent protein at high temperatures in vivo; a tool to study extreme thermophile biology," Environ Microbiol. 10(3), 605-13, March 2008.

Pédelacq et al. "Engineering and characterization of a superfolder green fluorescent protein,"Nature Biotechnology 24(1), 79–88, January 2006.

Protein-Protein Interactions

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Nature Network: Neuroscience Topic "JOURNAL CLUB: Getting a GRASP on synapse location". March 2008.

Feinberg et al. "GFP reconstitution across synaptic partners (GRASP) defines cell contacts and Synapses in living nervous systems," Neuron. 57(3) 353-363, Feb 2008.

Drug Discovery

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Barakat et al. "Molecular diversity in engineered protein libraries," Chem Biol. 11:335–341, June 2007.

Kim et al. "A high-throughput screen for compounds that inhibit aggregation of the Alzheimer's peptide," ACS Chem Biol. 1(7), 461-9, Aug. 2006

Zaragoza and Hines. "Understanding Proteins,"Innovation, Oct/Nov 2006.

Related Articles

[ Top ]

Protein Complimentation Assays (PCA)

Remy et al. "Application of a protein-fragment complimentation assay in cell biology," Biotechniques. 42(2):137, 139, 141 passim. February 2007.

Remy et al. "Detection of protein-protein interactions using a simple survival protein-fragment complementation assay based on the enzyme dihydrofolate reductase," Nat Protoc. 2(9):2120-5, 2007.

Protein-Protein Interactions

Magliery TJ et al.. "Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: Scope and mechanism," J of Am Chem Soc 127(1):146-157, 2005.

Others

Bellinzoni, M. and G. Riccardi (2003). "Techniques and applications: The heterologous expression of Mycobacterium tuberculosis genes is an uphill road." Trends in Microbiology 11(8): 351-358.

Wurth, C., W. Kim, et al. (2006). "Combinatorial approaches to probe the sequence determinants of protein aggregation and amyloidogenicity." Protein and Peptide Letters 13(3): 279-286.

Delagrave, S. and D. J. Murphy (2003). "In vitro evolution of proteins for drug development." Assay and Drug Development Technologies 1(1): 187-198.

Jayathilaka, L. P., M. Deb, et al. (2004). "Asymmetric synthesis and translational competence of L-alpha-(1-cyclobutenyl)glycine." Organic Letters 6(21): 3659-3662.

Sorensen, H. P. and K. K. Mortensen (2005). "Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli." Microbial Cell Factories 4: 1.

Zhou, C. Z. and Y. X. Chen (2004). "Developments in structural genomics: Protein purification and function interpretation." Current Genomics 5(1): 37-48.

Matsuura, T. and T. Yomo (2006). "In vitro evolution of proteins." Journal of Bioscience and Bioengineering 101(6): 449-456.

Mittl, P. R. E. and M. G. Grutter (2001). "Structural genomics: Opportunities and challenges." Current Opinion in Chemical Biology 5(4): 402-408.

Chambers, S. P. (2002). "High-throughput protein expression for the post-genomic era." Drug Discovery Today 7(14): 759-765.

Kuhn, P., K. Wilson, et al. (2002). "The genesis of high-throughput structure-based drug discovery using protein crystallography." Current Opinion in Chemical Biology 6(5): 704-710.

Heinemann, U., G. Illing, et al. (2001). "High-throughput three-dimensional protein structure determination." Current Opinion in Biotechnology 12(4): 348-354.

Heinemann, U. (2001). The Berlin "Protein structure factory" initiative: A technology-oriented approach to structural genomics

Workshop on Data Mining in Structural Biology. Ernst Schering Research Foundation Workshop SO - Ernst Schering Research Foundation Workshop. Data mining in structural biology; 2001; v.34; p.101-121

Ernst Schering Research Foundation Workshop 34. I. Schlichting, U. Egner, I. Schlichting and U. Egner. BERLIN, GERMANY, 175 Fifth Avenue, New York, NY, 10010-7858, USA : Springer-Verlag New York Inc., 2001 : 101-121.

Sorensen, H. P. and K. K. Mortensen (2005). "Advanced genetic strategies for recombinant protein expression in Escherichia coli." Journal of Biotechnology 115(2): 113-128.

Magliery, T. J. and L. Regan (2004). "Combinatorial approaches to protein stability and structure." European Journal of Biochemistry 271(9): 1595-1608.

Rubin-Pitel, S. B. and H. M. Zhao (2006). "Recent advances in biocatalysis by directed enzyme evolution." Combinatorial Chemistry & High Throughput Screening 9(4): 247-257.

Derewenda, Z. S. (2004). "The use of recombinant methods and molecular engineering in protein crystallization." Methods (Amsterdam) 34(3): 354-363.

Schmidt-Dannert, C. (2001). "Directed evolution of single proteins, metabolic pathways, and viruses." Biochemistry 40(44): 13125-13136.

Terwilliger, T. C., M. S. Park, et al. (2003). "The TB structural genomics consortium: A resource for Mycobacterium tuberculosis biology." Tuberculosis (Amsterdam) 83(4): 223-249.

Stout, T. J., P. G. Foster, et al. (2004). "High-throughput structural biology in drug discovery: Protein kinases." Current Pharmaceutical Design 10(10): 1069-1082.

Buchanan, S. G., J. M. Sauder, et al. (2002). "The promise of structural genomics in the discovery of new antimicrobial agents." Current Pharmaceutical Design 8(13): 1173-1188.

Bradbury, A. R. M. and J. D. Marks (2004). "Antibodies from phage antibody libraries." Journal of Immunological Methods 290(1-2): 29-49.

Brenner, S. E. (2001). "A tour of structural genomics." Nature Reviews Genetics 2(10): 801-809.

March, J. C., G. Rao, et al. (2003). "Biotechnological applications of green fluorescent protein." Applied Microbiology and Biotechnology 62(4): 303-315.

Buchanan, S. G. (2002). "Structural genomics: Bridging functional genomics and structure-based drug design." Current Opinion in Drug Discovery & Development 5(3): 367-381.

Sakanyan, V. (2005). "High-throughput and multiplexed protein array technology: Protein-DNA and protein-protein interactions." Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences 815(1-2): 77-95.

Zhang, J., Z. Liu, et al. (2003). "Three-dimensional localization of divergent region 3 of the ryanodine receptor to the clamp-shaped structures adjacent to the FKBP binding sites." Journal of Biological Chemistry 278(16): 14211-14218.

Liu, Z., J. Zhang, et al. (2002). "Three-dimensional reconstruction of the recombinant type 2 ryanodine receptor and localization of its divergent region 1." Journal of Biological Chemistry 277(48): 46712-46719.

Hardt, M. and R. A. Laine (2004). "Mutation of active site residues in the chitin-binding domain ChBD(ChiAl) from chitinase A1 of Bacillus circulans alters substrate specificity: Use of a green fluorescent protein binding assay." Archives of Biochemistry and Biophysics 426(2): 286-297.

Pengelley, S. C., D. C. Chapman, et al. (2006). "A suite of parallel vectors for baculovirus expression." Protein Expression and Purification 48(2): 173-181.

Fisher, A. C., W. Kim, et al. (2006). "Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway." Protein Science 15(3): 449-458.

Liu, S., R. C. Bugos, et al. (2001). "Green fluorescent protein as a secretory reporter and a tool for process optimization in transgenic plant cell cultures." Journal of Biotechnology 87(1): 1-16.

Benedetti, C. E., J. Kobarg, et al. (2003). "Plasmodium falciparum histidine-rich protein II binds to actin, phosphatidylinositol 4,5-bisphosphate and erythrocyte ghosts in a pH-dependent manner and undergoes coil-to-helix transitions in anionic micelles." Molecular & Biochemical Parasitology 128(2): 157-166.

Heinemann, U., J. Frevert, et al. (2000). "An integrated approach to structural genomics." Progress in Biophysics & Molecular Biology 73(5): 347-62.

Offredi, F., F. Dubail, et al. (2003). "De novo backbone and sequence design of an idealized alpha/beta-barrel protein: Evidence of stable tertiary structure." Journal of Molecular Biology 325(1): 163-174.

Hirano, N., T. Sawasaki, et al. (2006). "Tolerance for random recombination of domains in prokaryotic and eukaryotic translation systems: Limited interdomain misfolding in a eukaryotic translation system." Proteins-Structure Function and Bioinformatics 64(2): 343-354.

Pattenden, L. K., A. P. J. Middelberg, et al. (2005). "Towards the preparative and large-scale precision manufacture of virus-like particles." Trends in Biotechnology 23(10): 523-529.

de Groot, N. S., F. X. Aviles, et al. (2006). "Mutagenesis of the central hydrophobic cluster in A beta 42 Alzheimer's pepticle - Side-chain properties correlate with aggregation propensities." FEBS Journal 273(3): 658-668.

Muddana, S. S. and B. R. Peterson (2003). "Fluorescent cellular sensors of steroid receptor ligands." Chembiochem 4(9): 848-855.

Kim, C. A., M. L. Phillips, et al. (2001). "Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression." EMBO (European Molecular Biology Organization) Journal 20(15): 4173-4182.

Dyson, M. R., S. P. Shadbolt, et al. (2004). "Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression." BMC Biotechnology 4: 32.

Wigley, W. C., R. D. Stidham, et al. (2001). "Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein." Nature Biotechnology 19(2): 131-136.

Card, P. B. and K. H. Gardner (2005). Identification and optimization of protein domains for NMR studies. Nuclear Magnetic Resonance of Biological Macromolecules, Part C SO - Methods in Enzymology; 2005; v.394; p.3-16. T. James, 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA : ELSEVIER ACADEMIC PRESS INC, 2005 : 3-16.

Pritchard, J. B. and D. S. Miller (2005). "Expression systems for cloned xenobiotic transporters." Toxicology and Applied Pharmacology 204(3): 256-262.

Blundell, T. L., H. Jhoti, et al. (2002). "High-throughput crystallography for lead discovery in drug design." Nature Reviews Drug Discovery 1(1): 45-54.

Stevenson, J. D. and S. J. Benkovic (2002). "Combinatorial approaches to engineering hybrid enzymes." Journal of the Chemical Society-Perkin Transactions 2(9): 1483-1493.

Cotlet, M., P. M. Goodwin, et al. (2006). "A comparison of the fluorescence dynamics of single molecules of a green fluorescent protein: One- versus two-photon excitation." Chemphyschem 7(1): 250-260.

Rupp, B. and J. W. Wang (2004). "Predictive models for protein crystallization." Methods (Amsterdam) 34(3): 390-407.

Zagrebelny, S. N. (2005). "Controlled evolution as an approach to the design of efficient biocatalysts." Uspekhi Khimii 74(3): 307-320.

Yao, Y. X., J. Y. Ren, et al. (2003). "Amino terminal interaction in the prion protein identified using fusion to green fluorescent protein." Journal of Neurochemistry 87(5): 1057-1065.

Zhang, F. J. and H. N. Zhu (2006). "Intracellular conformational alterations of mutant SOD1 and the implications for fALS-associated SOD1 mutant induced motor neuron cell death." Biochimica et Biophysica Acta 1760(3): 404-414.

Chen, M. C., C. R. Lambert, et al. (2001). "Photoisomerization of green fluorescent protein and the dimensions of the chromophore cavity." Chemical Physics 270(1): 157-64.

Rabin, S. D. P. and A. R. Hauser (2005). "Functional regions of the Pseudomonas aeruginosa cytotoxin ExoU." Infection and Immunity 73(1): 573-582.

Schwalbach, G., A. P. Sibler, et al. (2000). "Production of fluorescent single-chain antibody fragments in Escherichia coli." Protein Expression and Purification 18(2): 121-132.

Griffith, D. A., C. Delipala, et al. (2003). "A novel yeast expression system for the overproduction of quality-controlled membrane proteins." FEBS Letters 553(1-2): 45-50.

Braud, S., M. Moutiez, et al. (2005). "Dual expression system suitable for high-throughput fluorescence-based screening and production of soluble proteins." Journal of Proteome Research 4(6): 2137-2147.

Belin, P., J. Dassa, et al. (2004). "Toxicity-based selection of Escherichia coli mutants for functional recombinant protein production: application to an antibody fragment." Protein Engineering Design & Selection 17(5): 491-500.

Zuo, X., M. R. Mattern, et al. (2005). "Expression and purification of SARS coronavirus proteins using SUMO-fusions." Protein Expression and Purification 42(1): 100-110.

Hart, D. J. and F. Tarendeau (2006). "Combinatorial library approaches for improving soluble protein expression in Escherichia coli." Acta Crystallographica Section D Biological Crystallography 62(Part 1): 19-26.

Cort, J. R., S. V. S. Mariappan, et al. (2001). "Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase." European Journal of Biochemistry 268(22): 5842-5850.

Pedelacq, J. D., S. Cabantous, et al. (2006). "Engineering and characterization of a superfolder green fluorescent protein." Nature Biotechnology 24(1): 79-88.

Miyazaki, S., Y. Kuroda, et al. (2006). "Identification of putative domain linkers by a neural network - Application to a large sequence database." BMC Bioinformatics 7: 323.

Yokoyama, S. (2003). "Protein expression systems for structural genomics and proteomics." Current Opinion in Chemical Biology 7(1): 39-43.

Sacchetti, A., V. Cappetti, et al. (2001). "Green fluorescent protein variants fold differentially in prokaryotic and eukaryotic cells." Journal of Cellular Biochemistry: 117-128.

Kim, W. and M. H. Hecht (2005). "Sequence determinants of enhanced amyloidogenicity of Alzheimer A beta 42 peptide relative to A beta 40." Journal of Biological Chemistry 280(41): 35069-35076.

Huang, D. and E. V. Shusta (2005). "Secretion and surface display of green fluorescent protein using the yeast Saccharomyces cerevisiae." Biotechnology Progress 21(2): 349-357.

Japrung, D., S. Chusacultanachai, et al. (2005). "A simple dual selection for functionally active mutants of Plasmodium falciparum dihydrofolate reductase with improved solubility." Protein Engineering, Design and Selection 18(10): 457-464.

Wall, M. A., M. Socolich, et al. (2000). "The structural basis for red fluorescence in the tetrameric GFP homolog DsRed." Nature Structural Biology 7(12): 1133-1138.

Pedelacq, J. D., G. S. Waldo, et al. (2005). "Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum." Protein Science 14(10): 2562-2573.

Roodveldt, C., A. Aharoni, et al. (2005). "Directed evolution of proteins for heterologous expression and stability." Current Opinion in Structural Biology 15(1): 50-56.

King, D. A., B. E. Hall, et al. (2006). "Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments." Journal of Biological Chemistry 281(29): 20107-20119.

Matsuura, T., A. Ernst, et al. (2002). "Construction and characterization of protein libraries composed of secondary structure modules." Protein Science 11(11): 2631-2643.

Wurth, C., N. K. Guimard, et al. (2002). "Mutations that reduce aggregation of the Alzheimer's A beta 42 peptide: an unbiased search for the sequence determinants of A beta amyloidogenesis." Journal of Molecular Biology 319(5): 1279-1290.

Nordlund, H. R., O. H. Laitinen, et al. (2005). "Production of Hev b5 as a fluorescent biotin-binding tripartite fusion protein in insect cells." Biochemical and Biophysical Research Communications 336(1): 232-238.

Nakayama, M. and O. Ohara (2003). "A system using convertible vectors for screening soluble recombinant proteins produced in Escherichia coli from randomly fragmented cDNAs." Biochemical and Biophysical Research Communications 312(3): 825-830.

DeLucas, L. J., D. Hamrick, et al. (2005). "Protein crystallization: virtual screening and optimization." Progress in Biophysics & Molecular Biology 88(3): 285-309.

Kaba, S. A., V. Nene, et al. (2002). "Fusion to green fluorescent protein improves expression levels of Theileria parva sporozoite surface antigen p67 in insect cells." Parasitology 125: 497-505.

Ignatova, Z. and L. M. Gierasch (2004). "Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling." Proceedings of the National Academy of Sciences of the United States of America 101(2): 523-528.

Sandrock, T. M., B. Risley, et al. (2001). "Exogenous peptide and protein expression levels using retroviral vectors in human cells." Molecular Therapy 4(5): 398-406.

Last Update June 23, 2008

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