Applications of Molecular Dynamics Simulations in Immunology: A Useful Computational Method in Aiding Vaccine Design

Molecular dynamics (MD) simulation methods have been an effective source of generating biomolecular-level structural information in immunology, as feedback to understand basic science and to design new experiments, leading to the discovery of drugs and vaccines. Different soluble or surface-bound proteins secreted by immune cells exchange signals through the formation of specialized molecular complexes. Molecules involved in the complex formation are complement proteins, antibodies, T cell receptors, MHC encoded HLA molecules, endogenous peptide antigens, and pathogenic peptides. Understanding the molecular details of the complex formation is very important to systematic design of drugs and vaccines. Experimental data provide only macroscopic reasoning and in many cases fail to perceive subtle differences in behaviors of two apparently very similar systems. Formation of stable complexes depends on complementary residues in proteins and peptides and their matching conformations. Here we present a comprehensive review of applications of MD simulations in immunology. In addition, a short section on computational predictive methods to identify T cell epitopes has been included.