Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface.
We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.
Raffaini
Giuseppina
G
Dipartimento di Chimica, Materiali e Ingegneria Chimica "G Natta", Sez Chimica, Politecnico di Milano, 20131 Milano, Italy.
Ganazzoli
Fabio
F
D000327:Adsorption; D000596:Amino Acids / Q000737:chemistry; D004583:Electrons; D005353:Fibronectins / Q000737:chemistry*; D006108:Graphite / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D005353:Fibronectins; D014867:Water; D006108:Graphite; D010100:Oxygen