Docking server for the identification of heparin binding sites on proteins

Abstract

Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined pockets, rather than for docking polysaccharides to highly charged shallow crevices that usually bind heparin. We have extended the program PIPER and the automated protein-protein docking server ClusPro to heparin docking. Using a molecular mechanics energy function for scoring and the fast Fourier transform correlation approach, the method generates and evaluates close to a billion poses of a heparin tetrasaccharide probe. The docked structures are clustered using pairwise root-mean-square deviations as the distance measure. It was shown that clustering of heparin molecules close to each other but having different orientations and selecting the clusters with the highest protein-ligand contacts reliably predicts the heparin binding site. In addition, the centers of the five most populated clusters include structures close to the native orientation of the heparin. These structures can provide starting points for further refinement by methods that account for flexibility such as molecular dynamics. The heparin docking method is available as an advanced option of the ClusPro server at http://cluspro.bu.edu/ .

Figure 1

Best results and contact maps of the five test systems. (left) Unbound protein shown with the actual heparin pose (in green sticks). The best predicted pose is shown in thin, cyan sticks. (right) Contact maps. Red (hot) areas have large number of contacts with the docked heparin poses, white areas have fewer, and dark areas have none.

Figure 2

Atom–atom contacts between heparin chains and protein residues. Predicted heparin chains are shown in blue; actual chains (normalized) are in orange. The x-axis is protein residue sorted by residue number where only residues that had at least one atom–atom contact are included for clarity.

Figure 3

Results for Annexin V (PDB IDs 1G5N for the bound structure, 2IE7 for the unbound). Calcium ions are shown as green spheres. (A) Best predicted structure shown as thin cyan sticks. The native binding mode is shown in green. Notice that as in many other cases, the predicted structure is closer to the surface than the native one. (B) Heat map based on heparin docking. Red (hot) areas have large number of contacts with the docked heparin poses, white areas have fewer, and dark areas have none.

Figure 4

Results for human fibronectin (Unbound PDB 1FNH). Subunit FN13 is on the left and FN14 is on the right. (A) Predicted heparin binding residues are shown in blue. For FN13 we show the predicted heparin poses ranked 1 (magenta) and 8 (green). For FN14 we show the poses ranked 1 (cyan) and 2 (yellow). (B) Same as A with the protein shown as a cartoon. The R and K residues of the heparin binding site are shown as sticks. Only the top ranked heparin poses are shown.