Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry
Tài liệu tham khảo
Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925
Afonine, 2012, Towards automated crystallographic structure refinement with phenix, Refine. Acta Crystallogr. Sect. D Biol. Crystallogr., 68, 352, 10.1107/S0907444912001308
Ahmad, 2012, ScFv antibody: principles and clinical application, Clin. Dev. Immunol., 2012, 980250, 10.1155/2012/980250
Bachman, 2013, Site-directed mutagenesis, Methods Enzymol., 529, 241, 10.1016/B978-0-12-418687-3.00019-7
Banatao, 2006, An approach to crystallizing proteins by synthetic symmetrization, PNAS, 103, 16230, 10.1073/pnas.0607674103
Banisadr, 2018, Production of a germline-humanized cetuximab scFv and evaluation of its activity in recognizing EGFR- overexpressing cancer cells, Hum. Vaccin. Immunother., 14, 856, 10.1080/21645515.2017.1407482
Bauman, 2008, Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design, Nucleic Acids Res., 36, 5083, 10.1093/nar/gkn464
Borras, 2010, Generic approach for the generation of stable humanized single-chain Fv fragments from rabbit monoclonal antibodies, J. Biol. Chem., 285, 9054, 10.1074/jbc.M109.072876
Clark, 1995, Crystallization of human immunodeficiency virus type 1 reverse transcriptase with and without nucleic acid substrates, inhibitors, and an antibody Fab fragment, Methods Enzymol., 262, 171, 10.1016/0076-6879(95)62017-6
Derewenda, 2010, Application of protein engineering to enhance crystallizability and improve crystal properties, Acta Crystallogr. - Sect. D Biol. Crystallogr., 66, 604, 10.1107/S090744491000644X
Ding, 1998, Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution, J. Mol. Biol., 284, 1095, 10.1006/jmbi.1998.2208
Emsley, 2010, Features and development of Coot, Acta Crystallogr. - Sect. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493
Forse, 2011, Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima, Protein Sci., 20, 168, 10.1002/pro.550
Gaciarz, 2016, Systematic screening of soluble expression of antibody fragments in the cytoplasm of E. coli, Microb. Cell Fact., 15, 22, 10.1186/s12934-016-0419-5
Goldschmidt, 2007, Toward rational protein crystallization: a Web server for the design of crystallizable protein variants, Protein Sci., 16, 1569, 10.1110/ps.072914007
Hino, 2013, Generation of functional antibodies for mammalian membrane protein crystallography, Curr. Opin. Struct. Biol., 23, 2, 10.1016/j.sbi.2013.04.007
Ho, 1989, Site-directed mutagenesis by overlap extension using the polymerase chain reaction, Gene, 77, 51, 10.1016/0378-1119(89)90358-2
Holcomb, 2017, Protein crystallization: eluding the bottleneck of X-ray crystallography, AIMS Biophys., 4, 557, 10.3934/biophy.2017.4.557
Holliger, 1993, “Diabodies”: small bivalent and bispecific antibody fragments, PNAS, 90, 6444, 10.1073/pnas.90.14.6444
Hopkins, 2017, BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis, J. Appl. Crystallogr., 50, 1545, 10.1107/S1600576717011438
Illiams, 1997, The 2.0-Å resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3, Proc. Natl. Acad. Sci., 94, 9637, 10.1073/pnas.94.18.9637
Jacobo-Molina, 1991, Crystals of a ternary complex of human immunodeficiency virus type 1 reverse transcriptase with a monoclonal antibody Fab fragment and double-stranded DNA diffract x-rays to, PNAS, 88, 10895, 10.1073/pnas.88.23.10895
Jacobo-Molina, 1993, Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA, Proc. Natl. Acad. Sci., 90, 6320, 10.1073/pnas.90.13.6320
Kabat, 1991
Kim, 2011, Rapid identification of recombinant Fabs that bind to membrane proteins, Methods, 55, 303, 10.1016/j.ymeth.2011.09.012
Kim, 2016, Crystal structures of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface, Sci. Rep., 6, 34515, 10.1038/srep34515
Krishnamurthy, 2012, X-ray structures of LeuT in substrate-free outward-open and apo inward-open states, Nature, 481, 469, 10.1038/nature10737
Krissinel, 2007, Inference of macromolecular assemblies from crystalline state, J. Mol. Biol., 372, 774, 10.1016/j.jmb.2007.05.022
Kunik, 2012, Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure, Nucleic Acids Res., 40, 521, 10.1093/nar/gks480
Laganowsky, 2011, An approach to crystallizing proteins by metal-mediated synthetic symmetrization, Protein Sci., 20, 1876, 10.1002/pro.727
Leibly, 2015, A suite of engineered GFP molecules for oligomeric scaffolding, Structure, 23, 1754, 10.1016/j.str.2015.07.008
Lieberman, 2011, Crystallization chaperone strategies for membrane proteins, Methods, 55, 293, 10.1016/j.ymeth.2011.08.004
Lim, 2011, High-efficiency screening of monoclonal antibodies for membrane protein crystallography, PLoS One, 6, e24653, 10.1371/journal.pone.0024653
Lobstein, 2012, SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm, Microb. Cell Fact., 11, 56, 10.1186/1475-2859-11-56
Mccoy, 2007, Phaser crystallographic software, J. Appl. Crystallogr., 40, 658, 10.1107/S0021889807021206
Miller, 2016, Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer, Protein Sci., 25, 46, 10.1002/pro.2776
Otwinowski, 1997, Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol., 276, 306
Shaw, 2014, Automation in biological crystallization, Acta Cryst. F, F70, 686, 10.1107/S2053230X14011601
Stahl, 2010, Generation and characterization of a chimeric rabbit/human Fab for co-crystallization of HIV-1 Rev, J. Mol. Biol., 397, 697, 10.1016/j.jmb.2010.01.061
Todorovska, 2001, Design and application of diabodies, triabodies and tetrabodies for cancer targeting, J. Immunol. Methods, 248, 47, 10.1016/S0022-1759(00)00342-2
Yamada, 2007, ‘Crystal lattice engineering,’ an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines, Protein Sci., 16, 1389, 10.1110/ps.072851407