Robust Antibody–Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking

作者: Jérémy Loyau , Gérard Didelot , Pauline Malinge , Ulla Ravn , Giovanni Magistrelli

DOI: 10.1016/J.JMB.2015.05.016

关键词: Biological activityIn silico dockingAntibody antigenIn vitroAntibodySystematic evolution of ligands by exponential enrichmentComputational biologyBiologyNeutralizing antibodyStereochemistryDocking (molecular)

摘要: Abstract Hu 15C1 is a potent anti-human Toll-like receptor 4 (TLR4) neutralizing antibody. To better understand the molecular basis of its biological activity, we used multidisciplinary approach to generate an accurate model 15C1–TLR4 complex. By combining site-directed mutagenesis, in vitro antibody evolution, affinity measurements and X-ray crystallography Fab fragments, identified key interactions across interface. These contact points were as restraints predict structure region bound TLR4 using computational docking. This was further evaluated validated by additional mutagenesis studies. The predicted complex indicates that antagonizes dimerization necessary for activation. study exemplifies how iterative cycles engineering can facilitate discovery components antibody-target interactions.

参考文章(40)
Neil S. Greenspan, Enrico Di Cera, Defining epitopes: It's not as easy as it seems. Nature Biotechnology. ,vol. 17, pp. 936- 937 ,(1999) , 10.1038/13590
M. Bardelli, E. Livoti, L. Simonelli, M. Pedotti, A. Moraes, A. P. Valente, L. Varani, Epitope mapping by solution NMR spectroscopy. Journal of Molecular Recognition. ,vol. 28, pp. 393- 400 ,(2015) , 10.1002/JMR.2454
Li Peng, Vaheh Oganesyan, Herren Wu, William F Dall’Acqua, Melissa M Damschroder, Molecular basis for antagonistic activity of anifrolumab, an anti-interferon–α receptor 1 antibody mAbs. ,vol. 7, pp. 428- 439 ,(2015) , 10.1080/19420862.2015.1007810
Leo C James, Pietro Roversi, Dan S Tawfik, Antibody Multispecificity Mediated by Conformational Diversity Science. ,vol. 299, pp. 1362- 1367 ,(2003) , 10.1126/SCIENCE.1079731
Yvonne Chen, Christian Wiesmann, Germaine Fuh, Bing Li, Hans W Christinger, Patrick McKay, Abraham M de Vos, Henry B Lowman, Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. Journal of Molecular Biology. ,vol. 293, pp. 865- 881 ,(1999) , 10.1006/JMBI.1999.3192
Charles Simon Bond, Alexander Wolfgang Schüttelkopf, ALINE: a WYSIWYG protein‐sequence alignment editor for publication‐quality alignments Acta Crystallographica Section D-biological Crystallography. ,vol. 65, pp. 510- 512 ,(2009) , 10.1107/S0907444909007835
João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, Integrative computational modeling of protein interactions. FEBS Journal. ,vol. 281, pp. 1988- 2003 ,(2014) , 10.1111/FEBS.12771
Mark Ultsch, Jack Bevers, Gerald Nakamura, Richard Vandlen, Robert F. Kelley, Lawren C. Wu, Charles Eigenbrot, Structural Basis of Signaling Blockade by Anti-IL-13 Antibody Lebrikizumab. Journal of Molecular Biology. ,vol. 425, pp. 1330- 1339 ,(2013) , 10.1016/J.JMB.2013.01.024
Jirong Lu, Derrick R. Witcher, Melissa A. White, Xiliang Wang, Lihua Huang, Radhakrishnan Rathnachalam, John M. Beals, Stuart Kuhstoss, IL-1β Epitope Mapping Using Site-Directed Mutagenesis and Hydrogen−Deuterium Exchange Mass Spectrometry Analysis Biochemistry. ,vol. 44, pp. 11106- 11114 ,(2005) , 10.1021/BI0505464
Hetunandan Kamisetty, Sergey Ovchinnikov, David Baker, Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 15674- 15679 ,(2013) , 10.1073/PNAS.1314045110