Conformational Flexibility in Designing Peptides for Immunology: The Molecular Dynamics Approach

Athanassios      Stavrakoudis

Abstract

Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21st century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes.

Keywords: B cell, T cell, TCR, complement system, computer simulation, MHC, antigen, antibody, antibody-antigen interactions, epitope, molecular dynamics, epitope prediction, vaccine design