Abstract
Structure-based clustering technique is useful for identifying superfamilies of major histocompatibility complex (MHC) proteins with similar binding specificities. The resolved MHC superfamilies play an important role in vaccine development, from discovering new targets for broad-based vaccines and therapeutics to optimizing the affinity and selectivity of hits. Here, we describe a protocol and provide a summary for grouping MHC proteins according to their structural interaction characteristics.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sidney J, Peters B, Frahm N, Brander C, Sette A (2008) HLA class I supertypes: a revised and updated classification. BMC Immunol 9:1
Brusic V, Petrovsky N, Zhang G, Bajic B (2002) Prediction of promiscuous peptides that bind HLA class I molecules. Immunol Cell Biol 80:280–285
Doytchinova IA, Guan P, Flower DR (2004) Identifying human MHC supertypes using bioinformatic methods. J Immunol 172:4314–4323
Tong JC, Tan TW, Ranganathan S (2007) In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. Bioinformatics 23:177–183
Lefranc M-P, Giudicelli V, Ginesoux C, Jabado-Michaloud J, Folch G, Bellahcene F et al (2009) IMGT®, the international ImMunoGeneTics information system®. Nucleic Acids Res 37:D1006–D1012
Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N et al (2010) The immune epitope database 2.0. Nucleic Acids Res 38:D854–D862
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H et al (2000) The Protein Data Bank. Nucleic Acids Res 28:D235–D242
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815
Wang Q, Canutescu AA, Dunbrack RL Jr (2008) SCWRL and MollDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc 3:1832–1847
Gilat A (2004) MATLAB: an introduction with applications, 2nd edn. Wiley, Canada
McDonald IK, Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777–793
Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Biol 13(323–330):307–308
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291
Abagyan RA, Totrov MM, Kuznetsov DA (1994) ICM: a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488–506
Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85–94
Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci U S A 93:13–20
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Tong, J.C., Tan, T.W., Ranganathan, S. (2014). Structure-Based Clustering of Major Histocompatibility Complex (MHC) Proteins for Broad-Based T-Cell Vaccine Design. In: De, R., Tomar, N. (eds) Immunoinformatics. Methods in Molecular Biology, vol 1184. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1115-8_27
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1115-8_27
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1114-1
Online ISBN: 978-1-4939-1115-8
eBook Packages: Springer Protocols