Computational methods for the design and applications of self-assembled cyclic peptide nanotubes

Abstract

During last decades, and enhanced by the development of the power of computers, Computational Chemistry has emerged as a powerful tool not only for complementing the work that experimental chemists carry out, but also for going beyond the limits of the laboratory. This PhD thesis presents an in-silico study of the nanotubes composed by the self- assembly of disk-shaped cyclic peptides developed by the group of Prof. Juan R. Granja. These tubular-shape structures incorporate non- natural residues (γ- and δ-amino acids), which increases the versatility of these structures. Via Molecular Dynamic simulations and Quantum approaches, these systems have been evaluated, taking advantage of the atomic resolution that these techniques provide us. Using these computational methods, the most stable conformation of the nanotubes, as well as their possible application as transmembrane channels, antibiotic agents or molecule containers, have been systematically analysed. Altogether, this work is expected to provide light in the mechanism of formation and activity of these nanotubes in order to contribute to a more rational design following a bottom-up approach.