title: Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces.
abstract: The prediction of antigenic epitopes on the surface of proteins is of great importance for vaccine development and to specifically design recombinant antibodies. Computational methods based on the three-dimensional structure of the protein allow for the detection of noncontinuous epitopes in contrast to methods based on the primary amino-acid sequence only. A method recently developed to predict protein-protein binding sites is presented, and the application to predict putative antigenic epitopes is described in detail. The prediction approach is based on the local perturbation of the electrostatic field at the surface of a protein due to a neutral probe of low dielectric constant that represents an approaching binding partner. The calculated change in electrostatic energy corresponds to an energy penalty of desolvating a protein surface region, and antigenic epitope surface regions tend to be associated with a lower penalty compared to the average protein surface. The protocol to perform the calculations is described and illustrated on an example antigen, the outer surface protein A of Borrelia burgdorferi, a pathogenic organism causing lyme disease.
authors.affiliation: Faculté des Sciences, UMR-CNRS 7272, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Nice Cedex 2, 06108, France, Sebastien.Fiorucci@unice.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Fiorucci
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
mesh_terms: D000954:Antigens, Surface / Q000737:chemistry / Q000276:immunology*; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000276:immunology*; D001428:Bacterial Vaccines / Q000737:chemistry / Q000276:immunology*; D025065:Borrelia burgdorferi / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D018604:Epitope Mapping / Q000379:methods*; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D008074:Lipoproteins / Q000737:chemistry / Q000276:immunology*; D008958:Models, Molecular; D011487:Protein Conformation; D011522:Protons; D012984:Software; D055672:Static Electricity
chemical_list: D000954:Antigens, Surface; D001425:Bacterial Outer Membrane Proteins; D001428:Bacterial Vaccines; D000939:Epitopes; D008074:Lipoproteins; C072045:OspA protein; D011522:Protons