Toward the supramolecular structure of collagen: a molecular dynamics approach.
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.
Monti
Susanna
S
Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy. s.monti@ipcf.cnr.it
Bronco
Simona
S
Cappelli
Chiara
C
D000596:Amino Acids / Q000737:chemistry; D003094:Collagen / Q000737:chemistry*; D003198:Computer Simulation; D005557:Formaldehyde; D005707:Gallic Acid / Q000737:chemistry; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012996:Solutions; D014867:Water
D000596:Amino Acids; D012996:Solutions; D014867:Water; D005557:Formaldehyde; D005707:Gallic Acid; D003094:Collagen