Discovering neutralizing antibodies targeting the stem epitope of H1N1 influenza hemagglutinin with synthetic phage-displayed antibody libraries

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Tung, Chao Ping ^a   Chen, Ing Chien ^a   Yu, Chung Ming ^a   Peng, Hung Pin ^a   Jian, Jhih Wei ^a,b,c   Ma, Shiou Hwa ^a   Lee, Yu Ching ^a   Jan, Jia Tsrong ^a   Yang, An Suei ^a  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; INFLUENZA VIRUS HEMAGGLUTININ; NEUTRALIZING ANTIBODY; PEPTIDE LIBRARY; PROTEIN BINDING; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY; VIRUS ANTIBODY;

AMINO ACID SEQUENCE; ANIMAL; BIOSYNTHESIS; CHEMISTRY; CROSS REACTION; DOG; EPITOPE MAPPING; GENETICS; HUMAN; IMMUNOLOGY; INFLUENZA A VIRUS (H1N1); MDCK CELL LINE; MOLECULAR GENETICS; PEPTIDE LIBRARY; SERODIAGNOSIS;

AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, NEUTRALIZING; ANTIBODIES, VIRAL; CROSS REACTIONS; DOGS; EPITOPE MAPPING; EPITOPES; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; MADIN DARBY CANINE KIDNEY CELLS; MOLECULAR SEQUENCE DATA; NEUTRALIZATION TESTS; PEPTIDE LIBRARY; PROTEIN BINDING; SINGLE-CHAIN ANTIBODIES;

EID: 84943751764     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep15053     Document Type: Article

References (33)

1. Pappas, L. et al. Rapid development of broadly influenza neutralizing antibodies through redundant mutations. Nature 516, 418-422 (2014).
2. Lingwood, D. et al. Structural and genetic basis for development of broadly neutralizing influenza antibodies. Nature 489, 566-570 (2012).
3. Avnir, Y. et al. Molecular signatures of hemagglutinin stem-directed heterosubtypic human neutralizing antibodies against influenza A viruses. PLoS Pathog 10, e1004103 (2014).
4. Ekiert, D. C. et al. Antibody recognition of a highly conserved influenza virus epitope. Science 324, 246-251 (2009).
5. Dreyfus, C. et al. Highly conserved protective epitopes on influenza B viruses. Science 337, 1343-1348 (2012).
6. Sui, J. et al. Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat Struct Mol Biol 16, 265-273 (2009).
7. Marasco, W. A., Sui, J. The growth and potential of human antiviral monoclonal antibody therapeutics. Nat Biotechnol 25, 1421-1434 (2007).
8. Balazs, A. B. et al. Vectored immunoprophylaxis protects humanized mice from mucosal HIV transmission. Nat Med 20, 296-300 (2014).
9. Schmidt, A. G. et al. Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Proc Natl Acad Sci USA 110, 264-269 (2013).
10. Al-Lazikani, B., Lesk, A. M., Chothia, C. Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 273, 927-948 (1997).
11. Stewart, A., Harrison, J. S., Regula, L. K., Lai, J. R. Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment. BMC Biochem 14, 9 (2013).
12. Adams, J. J., Nelson, B., Sidhu, S. S. Recombinant genetic libraries and human monoclonal antibodies. Methods Mol Biol 1060, 149-170 (2014).
13. Yang, A. S., Honig, B. On the pH dependence of protein stability. J Mol Biol 231, 459-474 (1993).
14. Yang, A. S., Gunner, M. R., Sampogna, R., Sharp, K., Honig, B. On the calculation of pKas in proteins. Proteins 15, 252-265 (1993).
15. Yang, A. S., Honig, B. Electrostatic Effects on Protein Stability. Curr. Opin. Struct. Biol. 2, 40-45 (1992).
16. Chang, H. J. et al. Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. Structure 22, 9-21 (2014).
17. Henikoff, S., Henikoff, J. G. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89, 10915-10919 (1992).
18. Pappas, L. et al. Rapid development of broadly influenza neutralizing antibodies through redundant mutations. Nature 516, 418-422 (2014).
19. Almagro, J. C. et al. Characterization of a high-affinity human antibody with a disulfide bridge in the third complementaritydetermining region of the heavy chain. J Mol Recognit 25, 125-135 (2012).
20. Reed, L. J., Muench, H. A simple method of estimating fifty per cent endpoint. Am J Epidemiol 27, 493-497 (1938).
21. Kunkel, T. A., Roberts, J. D., Zakour, R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol 154, 367-382 (1987).
22. Hsu, H. J. et al. Antibody variable domain interface and framework sequence requirements for stability and function by highthroughput experiments. Structure 22, 22-34 (2014).
23. Sidhu, S. S., Weiss, G. A. in Phage Display, Edn. 1st. (eds. Clackson, T., Lowman, H. B.) Ch. 2, 27-41 (Oxford University Press, New York, 2004).
24. Yu, C. M. et al. Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PLoS One 7, e33340 (2012).
25. Hsu, H. J. et al. Factor Xa active site substrate specificity with substrate phage display and computational molecular modeling. J Biol Chem 283, 12343-12353 (2008).
26. Kapur, K. C., Lamberson, L. R. in Reliability in Engineering Design. Ch. 5, 95-121 (John Wiley & Sons., 1977).
27. Hsu, H.-J. et al. Assessing Computational Amino Acid2-Turn Propensities with a Phage-Displayed Combinatorial Library and Directed Evolution. Structure 14, 1499-1510 (2006).
28. Gorodkin, J., Heyer, L. J., Brunak, S., Stormo, G. D. Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci 13, 583-586 (1997).
29. Yang, A.-S., Wang, L.-Y. Local structure prediction with local structure-based sequence profiles. Bioinformatics 19, 1267-1274 (2003).
30. Peng, H. P., Lee, K. H., Jian, J. W., Yang, A. S. Origins of specificity and affinity in antibody-protein interactions. Proc Natl Acad Sci USA 111, E2656-2665 (2014).
31. Squires, R. B. et al. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses 6, 404-416 (2012).
32. Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome Inform 23, 205-211 (2009).
33. Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res 42, D222-230 (2014).