Versatilidade estrutural de aminoácidos agregados: design de nanomateriais orgânicos via dinâmica molecular
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2022-02-25
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Universidade Federal de Goiás
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In this work, we carried out structural and energetic characterization of nine nanomembranes and two nanofibers composed of surfactant-like peptides (SLPs), using Molecular Dynamics (MD) simulations with atomistic resolution. The nanomembranes [nanofibers] studied are formed by the peptides I3V3A3G3K3 and K3G3A3V3I3 [G3A3V3I3K3 and
K3I3V3A3G3]; A6Hε and A6Hδ; and I3XGK (X = Q, S, N, G or L). The nanomembranes
I3V3A3G3K3 and K3G3A3V3I3 are formed by the same amino acids, but linked in inverted
primary sequences, which changes torsions, the side chains, and the C and N peptide terminals, affecting the hydration and stability of the nanomembranes. The A6Hε and A6Hδ
nanomembranes are differentiated by the position of the hydrogen atom attached to the
aromatic ring of histidine (H) residues, alterning the way that this residue is exposed to water, and consequently, the lateral attachment of alanine residues (A). By studying the
I3XGK (X = Q, S, N, G or L) nanomembranes, we realized that the peptides with polar
residues (X = Q, S, or N) present properties of polar zippers connecting β-sheets laterally. Therefore, this work aims at elucidating and characterizing the formation of polar
zippers that, recently, have attracted significant scientific and technological interest. The
nanofibers G3A3V3I3K3 and K3I3V3A3G3 are formed by peptides with the same amino
acids, but linked in inverted primary sequences, similar to the case of the nanomembranes I3V3A3G3K3 and K3G3A3V3. This way, by studying nanomembranes and nanofibers
composed with the same amino acids, this work allows us to understand how changes in
the disposition of the peptide side chains lead to the formation of distinct nanostructures,
evidencing the structural versatility of aggregate amino acids. The analyses performed are
based on the mass density profiles, on nanomembrane thicknesses, on the radial distribution functions, g(r), on the average number of Hydrogen Bonds (HBs) between amino
acids and between each amino acid and water molecules - for a better characterization
of HBs between peptides and consequently the nanomembranes’ hydration, HB’s time
correlation functions are presented - and in the Coulombic and vdW energetic interactions which together with the HBs play a fundamental role in the organization of the
peptides forming the nanostructures. Our results indicate that the C-terminal attached
to the charged lysine (K) leads to the formation of more hydrated nanomembranes; the
A6Hε and A6Hδ are nanostructures with a high degree of organization and with features
of crystalline structures; the polar zippers present an interesting route for the design of
robust and stable nanostructures, by joining neighboring β-sheets; the peptide nanostructures presented in this work have interesting characteristics suggesting that they can be
used to encapsulate and transport drugs, as hydrogels and as an antimicrobial agent. Our
MD results show excellent agreement with experimental data reported in the literature.
In addition, we show that the CHARMM36 force field could be recommended for the
study of the peptide nanomembranes and nanofibers presented. This validation is important because it allows the prediction from the theoretical point of view of new features
of peptide structures of this species, providing advances in the development of organic
nanostructures.
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ANDRADE, D. X. Versatilidade estrutural de aminoácidos agregados: design de nanomateriais orgânicos via dinâmica molecular. 2022. 176 f. Tese (Doutorado em Física) - Universidade Federal de Goiás, Goiânia, 2022.