Table 1.
Crystal structures used in the analysis of the HBSs in thrombin and antithrombin.
Figure 1.
Relative solvent-exposed surface area for basic residues of the Heparin Binding Site:
The SASA is calculated relative to a reference fully solvent-exposed residue present in a tripeptide. (A) Antithrombin's PBS (PDB ID = 1TB6). (B) Thrombin's exosite II (PDB ID = 1XMN, AB subunits). The exposed Connolly surface was calculated by rolling a sphere of 1.4 Å on the surface. See Methods for details.
Table 2.
Exposed surface area (SA) and radius of gyration (Rg) of arginine and lysine residues in the pentasaccharide binding site of antithrombin and exosite II of thrombin.*
Figure 2.
Radius (Rg) of gyration for HBS basic residues:
the HBSs of the pentasaccharide binding sites of (A) antithrombin and (B) exosite II of thrombin are depicted with gyrational mobility as thick dashed lines that convey the circumference of movement. The radius of gyration (Å) is listed below each basic residue. The basic side chains from (A) 1TB6 and (B) the AB subunits of 1XMN are shown. See text for details.
Figure 3.
Analysis of neighboring groups for HBS residues that display reduced gyrational mobility:
the basic side chains and neighboring amino acids from (A) antithrombin (1TB6) and (B) thrombin (AB subunits of 1XMN) are shown. Dotted lines indicate hydrogen-bonding and/or electrostatic interactions between neighboring residues. Inter-atomic distances (Å) are indicated for each polar interaction. Residues without neighboring interactions display high gyrational mobility. See text for details.
Figure 4.
Two-dimensional symmetry elements in receptor-ligand interactions:
(A) Traditional three-point concept of chiral ligand recognition with non-equivalent interacting pairs. (B) Conceptual representation of receptor–ligand interaction equivalence among receptor and ligand interacting groups with equivalent interacting pairs. Because the interacting pairs are equivalent, the spatial distribution determines the interaction specificity: the higher the degree of symmetry exhibited by the arrangement of interacting points in the receptor (e.g., basic side chains), the greater the number of ways in which a ligand containing a complementary set of interaction points (e.g., sulfate or carboxylate groups) can interact with the receptor.
Figure 5.
Symmetric elements identified among basic residues of HBSs of antithrombin and thrombin:
(A) For antithrombin (1TB6), the three significant (in terms of H/HS binding) residues – Lys114, Lys125 and Arg129 – form a triangular geometry. (B) For thrombin (1XMN), the basic residues are arranged to form a ‘cross’ or ‘square planar’ geometry. See text for details.
Figure 6.
HINT-based detection of cavities and placement of water molecules:
(A) In the antithrombin PBS, the detected cavity region is shown as a white mesh and the placed water molecules are shown with a space-filling representation. Four water molecules (w1, w2, w3 and w4; space-filling representation colored by atom-type) are predicted to bind in this site when unliganded. (B) In thrombin exosite II, no deep cavity regions were identified using the specified VICE parameters (see methods section), although distinct grooves and shallow pockets are apparent. Surface color corresponds to cavity depth where blue indicates shallow regions and yellow indicates deeply buried regions. Figures were generated using the antithrombin–thrombin–heparin ternary complex (PDB ID = 1TB6). See text for details.
Figure 7.
HINT-based hydration of the cavity in the PBS of antithrombin:
A significant cavity is detected in the binding site (transparent blue surface) that is approximately 5–7 Å in depth and 15–20 Å in length. No such cavity was detected in thrombin (see figure 6). Four water molecules (w1, w2, w3 and w4; ball-and-stick representation colored by atom-type) are predicted to bind in this site when unliganded. Co-crystallized pentasaccharide (only units ‘D’–‘F’ are shown; ‘G’ and ‘H’ are situated behind ‘F’ and are omitted here for clarity) is also shown in ball-and-stick rendering. See text for details.
Table 3.
Calculated HINT characteristics of the water molecules in the binding site water array [42].