Toward the supramolecular structure of collagen: A molecular dynamics approach

TitleToward the supramolecular structure of collagen: A molecular dynamics approach
Publication TypeJournal Article
Year of Publication2005
AuthorsMonti, S, Bronco, S, Cappelli, C
JournalJournal of Physical Chemistry B
ISSN15206106 (ISSN)
Keywordsamino acid, Amino acids, Article, Carboxylic Acids, Chemical, chemical model, chemical structure, chemistry, Collagen, Computer simulation, Conformational dynamics, Conformations, Extracellular fibers, Formaldehyde, Gallic Acid, hydrogen bond, Hydrogen Bonding, Hydrogen-Ion Concentration, hydrophobicity, Models, Molecular, molecular dynamics, Molecular Structure, pH, Protein Conformation, protein secondary structure, Protein Structure, Quasi-crystalline hexagonal packing, Quasicrystals, Secondary, solution and solubility, Solutions, Supramolecular chemistry, Supramolecular structure, Tensile strength, Transmission electron microscopy, water, X ray diffraction analysis

The structure, stability, and conformational dynamics of an assembly of two pentameric bundles made of collagen-like triple helical segments are explored using 1.2 ns molecular dynamics simulations in three environments: 8.0% (v/v) formaldehyde/water solution, 1.4% (v/v) gallic acid/water solution, and pure water. Stable supramolecular arrangements, where the two collagen units are very close to each other at interacting distances, are identified via docking and energy minimization procedures. Analysis of the interaction with formaldehyde and gallic acid suggests that they perturb the protein in a similar way depending on hydrogen-bonding capability, Hydrophobic association properties, and the size and concentration of the compound. © 2005 American Chemical Society.