Hybrid Methods for B-Cell Epitope Prediction

Abstract

Many computational approaches to B-cell epitope prediction have been published, including combinations of previously proposed methods, which complicates the tasks of further developing such computational approaches and of selecting those most appropriate for practical applications (e.g., the design of novel immunodiagnostics and vaccines). These tasks are considered together herein to clarify their close but often overlooked interrelationship, thereby providing a guide to their performance in mutual support of one another, with emphasis on key physicochemical and biological considerations that are relevant from an applications perspective. This aims to assist investigators in performing either or both tasks, with the overall goals of successfully applying computational tools towards practical ends and of generating informative new data towards iterative improvement of the tools, particularly as regards the design of peptide-based immunogens for eliciting the production of antipeptide antibodies that modulate biological activity of protein targets via functionally relevant cross-reactivity in relation to the phenomena of protein folding and protein disorder.

Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits

“…The latter sequence itself comprises residues ( 176 VQKP 179 ) predicted to be natively disordered by the PrDOS server and abuts residues ( 174 ES 175 ) likewise predicted by IUPred2 to be disordered. Such disorder among protein epitopes may favor their binding by paratopes through conformational adjustments, for example, to enable binding of native protein targets by antipeptide antibodies that have been produced in response to peptide-based immunogens (e.g., vaccine candidates), wherein peptide epitopes are themselves typically disordered (68). Hence, BBA36 176 VQKPV 180 may constitute or at least form part of an epitope that could be targeted by antibodies for effecting protective immunity, considering that BBA36 is upregulated by cultivation in mammalian hosts, while specific antibodies against BBA36 are bactericidal (69).…”

Recent Progress in Antibody Epitope Prediction

“…Epitopes can be linear or conformational, meaning that they can either be a linear sequence of amino acids or a three-dimensional (3D) structure formed by the folding of the protein. Around 10% of B-cell epitopes are linear, while the rest are non-contiguous sequences and conformational [ 10 ]. When the 3D structure of the antibody–antigen complex is available, the interactions between the paratope and epitope can be mapped and characterized well.…”

iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction

“…B-cell epitopes are broadly classified into two categories: continuous/linear and discontinuous/conformational. Continuous/linear BCEs comprise linear stretches of residues in the antigen protein sequence, while the discontinuous/conformational BCEs comprise residues placed far apart in the antigen protein sequence, which are brought together in three-dimensional space through folding ( 8 , 9 ). Experimental methods to identify BCEs include X-ray crystallography, cryo-EM, nuclear magnetic resonance, hydrogen–deuterium exchange coupled to mass spectroscopy, peptide-based approaches, mutagenesis, and antigen fragmentation ( 5 , 10 ).…”