Figure 6

Results of molecular dynamics simulations of docking fibronectin RGD-containing peptides on to models of integrin surfaces. ( a ) Representation of the 15 lowest-energy models for the docking of the VTGRGDSPAS peptide on αIIbβ3 model surface. Integrin residues are shown in black whereas the 15 peptide models are shown in different colours. For peptide models, the only side chains shown are those from the RGD triad (indicated with red labels). In all models the central Gly residue in the RGD triad is located directly on top of the carbonyl group from Arg 216 in the β3 subunit (shown with blue label). ( b ) Distribution of Cα···O distances in the final models of the molecular dynamics simulations Distances computed between the carbonyl oxygen in Arg216 from the β3 subunit and the central Gly residue from the RGD triad.