Computational redesign of a fluorogen activating protein with Rosetta

Bozhanova, Nina G.; Harp, Joel M.; Bender, Brian J.; Gavrikov, Alexey S.; Gorbachev, Dmitry A.; Baranov, Mikhail S.; Mercado, Christina B.; Zhang, Xuan; Lukyanov, Konstantin A.; Mishin, Alexander S.; Meiler, Jens

doi:10.1371/journal.pcbi.1009555

Computational redesign of a fluorogen activating protein with Rosetta

Journal Article · 01 November 2021 · PLOS Comput. Biol.

DOI:https://doi.org/10.1371/journal.pcbi.1009555· OSTI ID:1845526

Bozhanova, Nina G.; Harp, Joel M.; Bender, Brian J.; Gavrikov, Alexey S.; Gorbachev, Dmitry A.; Baranov, Mikhail S.; Mercado, Christina B.; Zhang, Xuan; Lukyanov, Konstantin A.; Mishin, Alexander S.; Meiler, Jens

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science

OSTI ID:: 1845526

Journal Information:: PLOS Comput. Biol., Journal Name: PLOS Comput. Biol. Journal Issue: (11) Vol. 17

Country of Publication:: United States

Language:: ENGLISH

References (41)

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences Sevy, Alexander M.; Jacobs, Tim M.; Crowe, James E. PLOS Computational Biology, Vol. 11, Issue 7 https://doi.org/10.1371/journal.pcbi.1004300	journal	July 2015
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein–protein interactions in vivo Blakeley, Brett D.; Chapman, Alex M.; McNaughton, Brian R. Molecular BioSystems, Vol. 8, Issue 8 https://doi.org/10.1039/c2mb25130b	journal	January 2012
A Pareto-Optimal Refinement Method for Protein Design Scaffolds Nivón, Lucas Gregorio; Moretti, Rocco; Baker, David PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0059004	journal	April 2013
De Novo Enzyme Design Using Rosetta3 Richter, Florian; Leaver-Fay, Andrew; Khare, Sagar D. PLoS ONE, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pone.0019230	journal	May 2011
Self-assembly cloning: a rapid construction method for recombinant molecules from multiple fragments Matsumoto, Akira; Itoh, Taichi BioTechniques, Vol. 51, Issue 1 https://doi.org/10.2144/000113705	journal	July 2011
Collapse and Recovery of Green Fluorescent Protein Chromophore Emission through Topological Effects Tolbert, Laren M.; Baldridge, Anthony; Kowalik, Janusz Accounts of Chemical Research, Vol. 45, Issue 2 https://doi.org/10.1021/ar2000925	journal	August 2011
Computational design of protein-small molecule interfaces Allison, Brittany; Combs, Steven; DeLuca, Sam Journal of Structural Biology, Vol. 185, Issue 2 https://doi.org/10.1016/j.jsb.2013.08.003	journal	February 2014
Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo Plamont, Marie-Aude; Billon-Denis, Emmanuelle; Maurin, Sylvie Proceedings of the National Academy of Sciences, Vol. 113, Issue 3 https://doi.org/10.1073/pnas.1513094113	journal	December 2015
Bright and stable near-infrared fluorescent protein for in vivo imaging Filonov, Grigory S.; Piatkevich, Kiryl D.; Ting, Li-Min Nature Biotechnology, Vol. 29, Issue 8 https://doi.org/10.1038/nbt.1918	journal	July 2011
BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library Kothiwale, Sandeepkumar; Mendenhall, Jeffrey L.; Meiler, Jens Journal of Cheminformatics, Vol. 7, Issue 1 https://doi.org/10.1186/s13321-015-0095-1	journal	September 2015
Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome Shu, X.; Royant, A.; Lin, M. Z. Science, Vol. 324, Issue 5928 https://doi.org/10.1126/science.1168683	journal	May 2009
Red-Shifted Fluorescent Aminated Derivatives of a Conformationally Locked GFP Chromophore Baranov, Mikhail S.; Solntsev, Kyril M.; Baleeva, Nadezhda S. Chemistry - A European Journal, Vol. 20, Issue 41 https://doi.org/10.1002/chem.201403678	journal	August 2014
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes Engler, Carola; Gruetzner, Ramona; Kandzia, Romy PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005553	journal	May 2009
Generation of Families of Construct Variants Using Golden Gate Shuffling Engler, Carola; Marillonnet, Sylvestre Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-065-2_11	book	January 2011
Rosetta and the Design of Ligand Binding Sites Moretti, Rocco; Bender, Brian J.; Allison, Brittany Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-3569-7_4	book	January 2016
A One Pot, One Step, Precision Cloning Method with High Throughput Capability Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre PLoS ONE, Vol. 3, Issue 11, Article No. e3647 https://doi.org/10.1371/journal.pone.0003647	journal	November 2008
A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications Nagai, Takeharu; Ibata, Keiji; Park, Eun Sun Nature Biotechnology, Vol. 20, Issue 1 https://doi.org/10.1038/nbt0102-87	journal	January 2002
The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding Campanacci, Valérie; Nurizzo, Didier; Spinelli, Silvia FEBS Letters, Vol. 562, Issue 1-3 https://doi.org/10.1016/S0014-5793(04)00199-1	journal	March 2004
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/S0021889897006766	journal	December 1997
Reporter proteins for in vivo fluorescence without oxygen Drepper, Thomas; Eggert, Thorsten; Circolone, Franco Nature Biotechnology, Vol. 25, Issue 4 https://doi.org/10.1038/nbt1293	journal	March 2007
Structural and biochemical analyses reveal a monomeric state of the bacterial lipocalin Blc Schiefner, André; Chatwell, Lorenz; Breustedt, Daniel A. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 12 https://doi.org/10.1107/S0907444910039375	journal	November 2010
DiB-splits: nature-guided design of a novel fluorescent labeling split system Bozhanova, Nina G.; Gavrikov, Alexey S.; Mishin, Alexander S. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-67095-2	journal	July 2020
Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy Muslinkina, Liya; Gavrikov, Alexey S.; Bozhanova, Nina G. ACS Chemical Biology, Vol. 15, Issue 9 https://doi.org/10.1021/acschembio.0c00440	journal	August 2020
Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal Bozhanova, Nina G.; Baranov, Mikhail S.; Klementieva, Natalia V. Chemical Science, Vol. 8, Issue 10 https://doi.org/10.1039/C7SC01628J	journal	January 2017
Red-Shifted Aminated Derivatives of GFP Chromophore for Live-Cell Protein Labeling with Lipocalins Bozhanova, Nina; Baranov, Mikhail; Baleeva, Nadezhda International Journal of Molecular Sciences, Vol. 19, Issue 12 https://doi.org/10.3390/ijms19123778	journal	November 2018
Structure and function of DNA photolyase Sancar, Aziz Biochemistry, Vol. 33, Issue 1 https://doi.org/10.1021/bi00167a001	journal	January 1994
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
xia2 : an expert system for macromolecular crystallography data reduction Winter, G. Journal of Applied Crystallography, Vol. 43, Issue 1 https://doi.org/10.1107/S0021889809045701	journal	December 2009
A Rainbow of Fluoromodules: A Promiscuous scFv Protein Binds to and Activates a Diverse Set of Fluorogenic Cyanine Dyes Pow, Crystal Lee; Marks, Sarah A.; Jesper, Lawrence D. Journal of the American Chemical Society, Vol. 130, Issue 38 https://doi.org/10.1021/ja805042p	journal	September 2008
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Bradford, Marion M. Analytical Biochemistry, Vol. 72, Issue 1-2 https://doi.org/10.1016/0003-2697(76)90527-3	journal	May 1976
A Bilirubin-Inducible Fluorescent Protein from Eel Muscle Kumagai, Akiko; Ando, Ryoko; Miyatake, Hideyuki Cell, Vol. 153, Issue 7 https://doi.org/10.1016/j.cell.2013.05.038	journal	June 2013
The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids Campanacci, Valérie; Bishop, Russell E.; Blangy, Stéphanie FEBS Letters, Vol. 580, Issue 20 https://doi.org/10.1016/j.febslet.2006.07.086	journal	August 2006
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M. Computer Methods, Part C https://doi.org/10.1016/B978-0-12-381270-4.00019-6	book	January 2011
De novo design of a fluorescence-activating β-barrel Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William Nature, Vol. 561, Issue 7724 https://doi.org/10.1038/s41586-018-0509-0	journal	September 2018
Dependence of alpha-helical and beta-sheet amino acid propensities on the overall protein fold type Fujiwara, Kazuo; Toda, Hiromi; Ikeguchi, Masamichi BMC Structural Biology, Vol. 12, Issue 1 https://doi.org/10.1186/1472-6807-12-18	journal	January 2012
The Chemistry of Small-Molecule Fluorogenic Probes Grimm, Jonathan B.; Heckman, Laurel M.; Lavis, Luke D. Progress in Molecular Biology and Translational Science, p. 1-34 https://doi.org/10.1016/B978-0-12-386932-6.00001-6	book	January 2013
Fluorogen-activating single-chain antibodies for imaging cell surface proteins Szent-Gyorgyi, Christopher; Schmidt, Brigitte F.; Creeger, Yehuda Nature Biotechnology, Vol. 26, Issue 2 https://doi.org/10.1038/nbt1368	journal	December 2007
Synthesis and properties of chromophores of fluorescent proteins Ivashkin, P. E.; Yampolsky, I. V.; Lukyanov, K. A. Russian Journal of Bioorganic Chemistry, Vol. 35, Issue 6 https://doi.org/10.1134/S1068162009060028	journal	November 2009
Plant blue-light receptors Lin, Chentao Trends in Plant Science, Vol. 5, Issue 8 https://doi.org/10.1016/S1360-1385(00)01687-3	journal	August 2000

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