Abstract
The role of proteins as very effective immunogens for the generation of antibodies is indisputable. Nevertheless, cases in which protein usage for antibody production is not feasible or convenient compelled the creation of a powerful alternative consisting of synthetic peptides. Synthetic peptides can be modified to obtain desired properties or conformation, tagged for purification, isotopically labeled for protein quantitation or conjugated to immunogens for antibody production. The antibodies that bind to these peptides represent an invaluable tool for biological research and discovery. To better understand the underlying mechanisms of antibody–antigen interaction here we present a pipeline developed by us to structurally classify immunoglobulin antigen binding sites and to infer key sequence residues and other variables that have a prominent role in each structural class.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Singh H, Ansari HR, Raghava GPS (2013) Improved method for linear B-cell epitope prediction using antigen’s primary sequence. PLoS One 8(5). ARTN e62216. doi:10.1371/journal.pone.0062216
Wu TT, Kabat EA (2008) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity (Reprinted from J Exp Med, vol 132, pg 211–250, 1970). J Immunol 180(11):7057–7096
Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B (2010) The immune epitope database 2.0. Nucleic Acids Res 38(Database Issue):D854–D862. doi:10.1093/nar/gkp1004
Dutta S, Burkhardt K, Young J, Swaminathan GJ, Matsuura T, Henrick K, Nakamura H, Berman HM (2009) Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol 42(1):1–13. doi:10.1007/S12033-008-9127-7
Al-Lazikani B, Lesk AM, Chothia C (1997) Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 273(4):927–948. doi:10.1006/jmbi.1997.1354
Kabat EA, Wu TT (1991) Identical V-region amino-acid-sequences and segments of sequences in antibodies of different specificities - relative contributions of Vh and Vl genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites. J Immunol 147(5):1709–1719
Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27(1):55–77
Honegger A, Pluckthun A (2001) Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool. J Mol Biol 309(3):657–670. doi:10.1006/Jmbi.2001.4662
Abhinandan KR, Martin AC (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol 45(14):3832–3839. doi:10.1016/j.molimm.2008.05.022
Chothia C, Lesk AM (1987) Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 196(4):901–917
Kunik V, Peters B, Ofran Y (2012) Structural consensus among antibodies defines the antigen binding site. PLoS Comput Biol 8(2). Artn E1002388. doi:10.1371/Journal.Pcbi.1002388.
Zemla A, Venclovas C, Moult J, Fidelis K (1999) Processing and analysis of CASP3 protein structure predictions. Proteins 3:22–29
Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57(4):702–710. doi:10.1002/prot.20264
Rousseeuw PJ (1987) Silhouettes - a graphical aid to the interpretation and validation of cluster-analysis. J Comput Appl Math 20:53–65. doi:10.1016/0377-0427(87)90125-7
Breiman L (2001) Random forests. Mach Learn 45(1):5–32. doi:10.1023/A:1010933404324
Archer KJ, Kirnes RV (2008) Empirical characterization of random forest variable importance measures. Comput Stat Data Anal 52(4):2249–2260. doi:10.1016/J.Csda.2007.08.015
Zemla A (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 31(13):3370–3374
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Chailyan, A., Marcatili, P. (2015). Structural Characterization of Peptide Antibodies. In: Houen, G. (eds) Peptide Antibodies. Methods in Molecular Biology, vol 1348. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2999-3_18
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2999-3_18
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2998-6
Online ISBN: 978-1-4939-2999-3
eBook Packages: Springer Protocols