Rational Epitope Design
for Protein Targeting
Claudio Peri
Paola Gagni
Fabio Combi
Alessandro Gori
Marcella Chiari
Renato Longhi
Marina Cretich
Giorgio Colombo
10.1021/cb300487u.s001
https://acs.figshare.com/articles/journal_contribution/Rational_Epitope_Design_for_Protein_Targeting/2442643
We present a new multidisciplinary strategy integrating
computational
biology with high-throughput microarray analysis aimed to translate
molecular understanding of protein-antibody recognition into the design
of efficient and selective protein-based analytical and diagnostic
tools. The structures of two proteins with different folds and secondary
structure contents, namely, the beta-barrel FABP and the α-helical
S100B, were used as the basis for the prediction and design of potential
antibody-binding epitopes using the recently developed MLCE computational
method. Starting from the idea that the structure, dynamics, and stability
of a protein-antigen play a key role in the interaction with antibodies,
MLCE integrates the analysis of the dynamical and energetic properties
of proteins to identify nonoptimized, low-intensity energetic interaction-networks
on the surface of the isolated antigens, which correspond to substructures
that can aptly be recognized by a binding partner. The identified
epitopes were next synthesized as free peptides and used to elicit
specific antibodies in rabbits. Importantly, the resulting antibodies
were proven to specifically and selectively recognize the original,
full-length proteins in microarray-based tests. Competition experiments
further demonstrated the specificity of the molecular recognition
between the target immobilized proteins and the generated antibodies.
Our integrated computational and microarray-based results demonstrate
the possibility to rationally discover and design synthetic epitopes
able to elicit antibodies specific for full-length proteins starting
only from three-dimensional structural information on the target.
We discuss implications for diagnosis and vaccine development purposes.
2013-02-15 00:00:00
antibody
MLCE
100B
Rational Epitope Design
protein
recognition
FABP
multidisciplinary strategy
Protein TargetingWe
vaccine development purposes
Competition experiments
structure contents
binding partner
analysis
epitope