LocaPep: Localization of Epitopes on Protein Surfaces Using Peptides from Phage Display Libraries

Abstract

The use of peptides from a phage display library selected by binding to a given antibody is a widespread technique to probe epitopes of antigenic proteins. However, the identification of interaction sites mimicked by these peptides on the antigen surface is a difficult task. LocaPep is a computer program developed to localize epitopes using a new clusters algorithm that focuses on protein surface properties. The program is constructed with the aim of providing a flexible computational tool for predicting the location of epitopes on protein structures. As a first set of testing results, the localization of epitope regions in eight different antigenic proteins for which experimental data on their antibody interactions exist is correctly identified by LocaPep. These results represent a disparate sample of biologically different systems. The program is freely available at http://atenea.montes.upm.es.

A comprehensive analysis of the allergenicity and IgE epitopes of myosinogen allergens in Scylla paramamosain

“…Mimotopes obtained from phage display experiments were aligned using the multiple sequence alignment program ClustalW, to find a consensus pattern of amino acids . For conformational epitope mapping, the parameter of amino acids in mimotopes was calculated, analysed using LocaPep (http://atenea.montes.upm.es), and mapped onto the three‐dimensional structure of allergens by PyMOL (https://pymol.org/2/). Analysis of the frequency of single amino acids was performed by ExPASy (https://web.expasy.org/protparam).…”

“…BAT was performed with heparinized whole blood stimulated by allergens for 30 minutes at 37°C as described by Mukai et al 25 One hundred microlitres of whole blood was mixed with 100 μL of RPMI medium or with the flowing stimulants: purified AK, SCP, TIM, and Mimotopes obtained from phage display experiments were aligned using the multiple sequence alignment program ClustalW, to find a consensus pattern of amino acids. 27 For conformational epitope mapping, the parameter of amino acids in mimotopes was calculated, analysed using LocaPep (http://atenea.montes.upm.es), 28 and mapped onto the three-dimensional structure of allergens by PyMOL (https://pymol.org/2/). Analysis of the frequency of single amino acids was performed by ExPASy (https://web.expasy.org/ protparam).…”

Mapping and characterization of antigenic epitopes of arginine kinase of Scylla paramamosain

“…To act as a seed, a residue must display a significantly large exposed surface area and have a small number of contacts compared with mean and extreme values for the corresponding amino acid in the protein (Pacios et al, 2011). The AK surface was scanned for seeds among the residues belonging to each cluster.…”

Antibody–antigen complex modelling in the era of immunoglobulin repertoire sequencing

“…However, the types of contacts found in Ab-Ag complexes were soon shown to be different from those found in general protein-protein interactions [85][86][87] , displaying a unique pattern both in terms of amino acid usage and in binding site interactions 70,85,86 . More recent predictors seek improved performance by accounting for this specialised binding, for example by retraining existing protein-protein interaction predictors only on Ab-Ag structures [88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103] . While progress has been made, prediction precision is still close to random for most tools, meaning we remain unable to distinguish the region(s) of an antigen surface that are generally more prone to being bound by antibodies.…”