Ionic peptide aggregation: Exploration of conformational dynamics in aqueous solution by computation techniques

Article Abstract:

The effects of end groups on KEK peptide conformational characteristics and self-assembling properties in water solution are examined by employing long lasting all-atom molecular dynamics simulations. The examination of the structural macroscopic and microscopic properties and the investigation of intra- and intermolecular interactions has indicated the role played by side chains and terminal regions in determining the characteristic features of the assemblages.

Observations, Peptides, Atomic force microscopy, Calorimetry, Chemical bonds, Properties, Structure

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Characterization of supramolecular polyphenol-chromium(III) clusters by molecular dynamics simulations

Article Abstract:

The ability of (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol (FLA) to interact with chromium(III) ions in water solution is investigated by using classical molecular dynamics (MD) simulations starting from the minimum energy conformations that are already identified. The analysis has suggested possible flavonoid-metal ions interaction mechanisms in solution through the intricate characterization of the molecular cluster sampled during nanosecond MD production runs.

Chromium Compounds, Metal ions

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Understanding the structural and binding properties of collagen: a theoretical perspective

Article Abstract:

A study was conducted, by performing a series of nanosecond molecular dynamics simulations, to examine the change in the stability and conformational dynamics of a collagen-like microfibril segment (CMS), 23 amino acid residues long, formaldehyde, and gallic acid. The result shows major changes in the conformation of CMS occur when interacting with water, and other solutions show separate reactions.

Gallium Compounds

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