Epitope modeling and MHC project

Peptides that come from the fractionation of pathogen proteins in intracellular lysosomes are recognised by the immune system by the binding of antigen-presenting proteins known as the histocompatibility complex (MHC) class I and II type. In order to design peptide vaccines I investigated the binding of short chain peptides candidates that could start an immune response as antigens and activate the T lymphocytes in order to initiate the immune response. The prediction of peptide fragments with potential affinity to bind to the MHC I or II could lead to the development of an optimal immune response to promote immunity in organisms such as humans or animals.

In this project I worked in collaboration with colleagues of University of Chile and a Chilean Veterinary company to find out potential peptide sequences to treat diseases in Salmon species such as *Salmon Salar* type. In order to predict peptide affinity in MHC-peptide complexes and to design antigens a molecular modelling protocol has been developed from studies involving techniques such as homology modelling of MHC I and II, prediction and design of peptide structures using *de novo* methods.

The *Salmon Salar* MHC models were obtained using homology modeling using *Modeller* and taking protein templates from Protein Data Bank. Different de novo design techniques based on Monte Carlo calculations available on Rosetta were studied to model peptides of 9 amino acid length. The affinity of best candidate peptide models with MHC was evaluated using Molecular Dynamics (GROMACS) and then calculated using the free energy calculation by the MMPBSA approach.