1. Combining Well-Tempered Metadynamics Simulation and SPR Assays to Characterize the Binding Mechanism of the Universal T-Lymphocyte Tetanus Toxin Epitope TT830-843.
- Author
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Brandt AAML, Rodrigues-da-Silva RN, Lima-Junior JC, Alves CR, and de Souza-Silva F
- Subjects
- Epitopes, T-Lymphocyte chemistry, Hydrogen Bonding, Static Electricity, Thermodynamics, Epitopes, T-Lymphocyte immunology, Molecular Dynamics Simulation, Surface Plasmon Resonance, Tetanus Toxin immunology
- Abstract
Peptide TT830-843 from the tetanus toxin is a universal T-cell epitope. It helps in vaccination and induces T-cell activation. However, the fine molecular interaction between this antigen and the major histocompatibility complex (MHC) remains unknown. Molecular analysis of its interaction with murine MHC (H-2) was proposed to explore its immune response efficiency. Molecular dynamics simulations are important mechanisms for understanding the basis of protein-ligand interactions, and metadynamics is a useful technique for enhancing sampling in molecular dynamics. SPR (surface plasmon resonance) assays were used to validate whether the metadynamics results are in accordance with the experimental results. The peptide TT830-843 unbinding process was simulated, and the free energy surface reconstruction revealed a detailed conformational landscape. The simulation described the exiting path as a stepwise mechanism between progressive detachment states. We pointed out how the terminus regions act as anchors for binding and how the detachment mechanism includes the opening of α -helices to permit the peptide's central region dissociation. The results indicated the peptide/H-2 receptor encounter occurs within a distance lesser than 27.5 Å, and the encounter can evolve to form a stable complex. SPR assays confirmed the complex peptide/H-2 as a thermodynamically stable system, exhibiting enough free energy to interact with TCR on the antigen-presenting cell surface. Therefore, combining in silico and in vitro assays provided significant evidence to support the peptide/H-2 complex formation., Competing Interests: The authors declare that there are no conflicts of interest. Artur Brandt is a research fellow of FAPERJ, Franklin S. Silva is a research fellow of CAPES institution, and Carlos R. Alves and Josué C. Lima-Júnior are research fellows of CNPq institution., (Copyright © 2021 Artur A. M. L. Brandt et al.)
- Published
- 2021
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