A6H polypeptide membranes: molecular dynamics simulation, GIAO-DFT-NMR and TD-DFT spectroscopy analysis
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2020
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In this work, Molecular Dynamics simulation (MD), GIAO-DFT-NMR, and TD-DFT results are obtained to study structural, energetic, dynamics, and spectroscopy properties of polypeptide membranes composed of 6 alanine residue (A6) attached to one histidine residue (H). The histidine residue is simulated with a hydrogen atom bonded in different positions on the aromatic ring: at the epsilon (HSE), or delta (HSD) nitrogen. The results are presented for the A6H(SE or SD) peptide in monomer and membrane configurations to contrast the effects of an organized structure on the peptides' properties studied. Spectroscopy properties are acquired using DFT quantum mechanics calculations combined with MD classical configurations. From 25,000 MD configuration, 100 of them were selected for the calculation of spectroscopic properties. For the A6HSE and A6HSD membranes, in every 100 MD-configurations, we selected just one peptide in the center of the simulation box for quantum mechanics calculation, the other peptides, and water molecules, were considered as charge points. Our results indicate how the absorption spectrum spectroscopy and magnetic shielding constant signature of the A6H(SE or SD) polypeptides are affected when the structure goes from a free monomer in-water solution to a monomer inside a membrane structure in-water solution. The NMR results, acquired at an atomic and molecular level via theoretical studies, reproduce the performance experimentally observed, indicating the reliability of our data. This way, endorsing the methodology used to verify the spectroscopic properties of membranes from a unit monomer.
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Molecular dynamics, GIAO-DFT-NMR, TD-DFT, Polypeptide membrane
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ANDRADE, Douglas; COLHERINHAS, Guilherme. A6H polypeptide membranes: molecular dynamics simulation, GIAO-DFT-NMR and TD-DFT spectroscopy analysis. Journal of Molecular Liquids, Amsterdam, v. 316, e113850, 2020. DOI: 10.1016/j.molliq.2020.113850. Disponível em: https://www.sciencedirect.com/science/article/pii/S0167732220334498. Acesso em: 15 set. 2023.