Figure 2.

Molecular docking analysis of extra domain A fibronectin (EDA-FN) peptide domain binding to the α₄β₁ receptor model. (A) The –TYSSPEDGHIEL-- peptide domain of the EDA-FN protein (green) was utilized as a ligand for molecular docking analysis to the integrin α₄ (blue) β₁ (red) receptor model. From the areas of the receptor analyzed, only the receptor binding cleft (boxed region) returned valid affinity score values. A 180° rotation is shown in order to visualize the peptide within the receptor binding cleft. (B) The top 7 binding modes of the EDA-FN peptide within the integrin receptor binding cleft. Green (–5) to red (+5) gradient colorization relates to the AutoDock affinity (kcal/mol) scores. (C) The electrostatic potential (kT/e) of the receptor binding cleft was predicted and is shown as a red (–5) to blue (+5) gradient. Note that the peptide had an overall stronger binding mode in the positive region of the binding cleft.