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Open Access Open Badges Research article

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Matthew N Davies1*, Channa K Hattotuwagama1, David S Moss2, Michael GB Drew3 and Darren R Flower1

Author Affiliations

1 Edward Jenner Institute for Vaccine Research, Compton, Newbury, RG20 7NN, UK

2 School of Crystallography, Birkbeck College, London WC1E 7HX, UK

3 Structural and Computational Chemistry Group, University of Reading, Reading RG6 6AH, UK

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BMC Structural Biology 2006, 6:5  doi:10.1186/1472-6807-6-5

Published: 20 March 2006



MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions.


A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions.


The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.