PMC

Binding of T7 phage displaying CendR peptides to immobilized NRP-1 b1b2 domain. Phage displaying prototypic CendR peptide and its permutations were incubated with hexahistidine-tagged NRP-1 b1b2 immobilized on Ni–NTA magnetic beads, followed by extensive washes to remove unspecifically bound phage, release of phage/NRP-1 b1b2 complexes with 0.4 M imidazole, and phage titering. Phage binding to NRP-1 b1b2 is expressed fold control phage displaying heptaglycine (G7) peptide. Statistical analysis was performed by Student’s t-test. n = 3; error bars indicate s.e.m.

Detailed representations of the final organization obtained for different CendR variants docked into the Rbd system. Non polar hydrogen atoms have been removed, receptor residues are depicted as cartoons unless they participate in a specific interaction RPAR and its counterparts interactions are represented as solid lines following CPK code. Arrows and/or circles point to topological details remarked at the text (the labels indicate the main feature in each case). The images correspond to the following systems: (a) RPDR, (b) RPSR, (c) RPPR, (d) RPRR and, (e) RRAR

(a) The Nb1b2–RPAR complex modeled in Ref.18 used to model the NRP-1–RPAR complex. The b1 domain is colored brown, b2 domain light brown and the inter-domain loop in blue. Interaction loops are labeled and colored in green and RPAR peptide is represented with solid sticks and with CPK color code. (b) The b1 domain binding site. Those residues participating in the binding are explicitly shown as solid sticks and labeled. Interactions between loop residues and RPAR are drawn: blue dashed lines represent hydrogen bonds and red dashed lines depict salt bridges. (c) The simulation box used to represent Rbd model. The inert wall is represented with light pink spheres. The b1 domain linking points are represented by red spheres. Sodium cations (blue small spheres) and Chloride anions (small green spheres) are also depicted. b1 domain is represented by cartoons whereas RXYR peptide is explicitly represented. Non polar hydrogen atoms have been eliminated in all figures.