Mapping conformational epitopes by NMR spectroscopy

Current Opinion in Virology - Tập 49 - Trang 1-6 - 2021
Ana P Valente1, Mariana Manzano-Rendeiro1
1National NMR Center, Cenabio, Department of Structural Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

Tài liệu tham khảo

Nelson, 2010, Antibody fragments, mAbs, 2, 77, 10.4161/mabs.2.1.10786 Jay, 2018, IgG antibody 3D structures and dynamics, Antibodies, 7, 18, 10.3390/antib7020018 Andersen, 2006, Haste: prediction of residues in discontinuous B-cell epitopes using protein 3D structures, Protein Sci, 15, 2558, 10.1110/ps.062405906 Gershoni, 2007, Epitope mapping, BioDrugs, 21, 145, 10.2165/00063030-200721030-00002 Masoud, 2015, Prediction of epitopes of viral antigens recognized by cytotoxic T lymphocytes as an immunoinformatics approach to anti-HIV/AIDS vaccine design, Int J Vaccines Vaccin, 1, 1 Correia, 2014, Proof of principle for epitope-focused vaccine design, Nature, 507, 201, 10.1038/nature12966 Farrera-Soler, 2020, Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma, PLoS One, 15, 10.1371/journal.pone.0238089 King, 2018, Epitope mapping of antibody-antigen interactions with X-ray crystallography, Methods Mol Biol, 1785, 13, 10.1007/978-1-4939-7841-0_2 Sevvana, 2020, Mapping the diverse structural landscape of the flavivirus antibody repertoire, Curr Opin Virol, 45, 51, 10.1016/j.coviro.2020.07.006 Wilson, 1993, Antibody-antigen interactions, Curr Opin Struct Biol, 3, 113, 10.1016/0959-440X(93)90210-C Addis, 2014, Conformational heterogeneity in antibody-protein antigen recognition: implications for high affinity protein complex formation, J Biol Chem, 289, 7200, 10.1074/jbc.M113.492215 James, 2003, Antibody multispecificity mediated by conformational diversity, Science, 299, 1362, 10.1126/science.1079731 Pauling, 1940, A theory of the structure and process of formation of antibodies, J Am Chem Soc, 62, 2643, 10.1021/ja01867a018 Al Qaraghuli, 2020, Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response, Sci Rep, 10, 1, 10.1038/s41598-020-70680-0 Oldstone, 1991, Mapping the anatomy of the immunodominant domain of the human immunodeficiency virus gp41 transmembrane protein: peptide conformation analysis using monoclonal antibodies and proton nuclear magnetic resonance spectroscopy, J Virol, 65, 1727, 10.1128/jvi.65.4.1727-1734.1991 Adhikary, 2012, Protein dynamics and the diversity of an antibody response, J Biol Chem, 287, 27139, 10.1074/jbc.M112.372698 Moraes, 2016, Antibody binding modulates conformational exchange in domain III of dengue virus E protein, J Virol, 90, 1802, 10.1128/JVI.02314-15 Copperman, 2016, Mode localization in the cooperative dynamics of protein recognition, J Chem Phys, 145, 10.1063/1.4954506 Mittermaier, 2009, Observing biological dynamics at atomic resolution using NMR, Trends Biochem Sci, 34, 601, 10.1016/j.tibs.2009.07.004 Neudecker, 2009, Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding, Biophys J, 96, 2045, 10.1016/j.bpj.2008.12.3907 Grutsch, 2016, NMR methods to study dynamic allostery, PLoS Comput Biol, 12, 1, 10.1371/journal.pcbi.1004620 Akke, 2002, NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis, Curr Opin Struct Biol, 12, 642, 10.1016/S0959-440X(02)00369-X Simonelli, 2018, Mapping antibody epitopes by solution NMR spectroscopy: practical considerations, Methods Mol Biol, 1785, 29, 10.1007/978-1-4939-7841-0_3 Bardelli, 2015, Epitope mapping by solution NMR spectroscopy, J Mol Recognit, 28, 393, 10.1002/jmr.2454 Rosen, 2005, Induced fit in HIV-neutralizing antibody complexes: evidence for alternative conformations of the gp120 V3 loop and the molecular basis for broad neutralization, Biochemistry, 44, 7250, 10.1021/bi047387t Becker, 2018, Investigating protein–ligand interactions by solution nuclear magnetic resonance spectroscopy, ChemPhysChem, 19, 895, 10.1002/cphc.201701253 Williamson, 2013, Using chemical shift perturbation to characterise ligand binding, Prog Nucl Magn Reson Spectrosc, 73, 1, 10.1016/j.pnmrs.2013.02.001 Razzera, 2010, Mapping the interactions between a major pollen allergen and human IgE antibodies, Structure, 18, 1011, 10.1016/j.str.2010.05.012 Pintacuda, 2002, Identification of protein surfaces by NMR measurements with a paramagnetic Gd(III) chelate, J Am Chem Soc, 124, 372, 10.1021/ja016985h Najar, 2017, Mapping protein binding sites and conformational epitopes using cysteine labeling and yeast surface display, Structure, 25, 395, 10.1016/j.str.2016.12.016 Hocking, 2013, Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes, Chem Phys Chem, 14, 3082, 10.1002/cphc.201300219 Osawa, 2012, Functional dynamics of proteins revealed by solution NMR, Curr Opin Struct Biol, 22, 660, 10.1016/j.sbi.2012.08.007 Pervushin, 1997, Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution, Proc Natl Acad Sci U S A, 94, 12366, 10.1073/pnas.94.23.12366 Liang, 2016, Probing the impact of local structural dynamics of conformational epitopes on antibody recognition, Biochemistry, 55, 2197, 10.1021/acs.biochem.5b01354 Li, 2020, A practical perspective on the roles of solution NMR spectroscopy in drug discovery, Molecules, 25, 1 Angulo, 2011, STD-NMR: application to transient interactions between biomolecules — a quantitative approach, Eur Biophys J, 40, 1357, 10.1007/s00249-011-0749-5 Viegas, 2011, A simple and fast method for ligand screening and characterization of protein binding, J Chem Educ, 88, 990, 10.1021/ed101169t Struck, 2012, A hexapeptide of the receptor-binding domain of SARS corona virus spike protein blocks viral entry into host cells via the human receptor ACE2, Antiviral Res, 94, 288, 10.1016/j.antiviral.2011.12.012 Fiege, 2017, Epitope mapping of histo blood group antigens bound to norovirus VLPs using STD NMR experiments reveals fine details of molecular recognition, Glycoconj J, 34, 679, 10.1007/s10719-017-9792-5 Usher, 2020, Mapping invisible epitopes by NMR spectroscopy, J Biol Chem, 295, 17411, 10.1074/jbc.H120.016607 Di Muzio, 2020, Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins, J Biol Chem, 295, 17398, 10.1074/jbc.RA120.014243