Ures 6 and 7). Thus, certain sulfate groups of a saccharide sequence can

Ures 6 and 7). Thus, certain sulfate groups of a saccharide sequence can interdigitate with Lys114, Lys125 and Arg129 of antithrombin. In an appropriate analogy, the H/HS ntithrombin interaction can be thought of as a firm `handshake’ between the two interacting complementary partners. In contrast, the lack of a reasonably sized cavity in exosite II of thrombin does not allow inter-digitation of sulfate groups. This induces a more superficial interaction wherein basic residues of exosite II do interact with sulfate of heparin but without the formation of `more directional’ bonds. Biochemically, this characteristic becomes apparent as less non-ionic forces contributing to interaction, as noted by Olson et al. [17]. Thus, the thrombin-H/HS interaction is more analogous to a superficial `high five’.Prediction of Bound Water in the HBSsBecause 17460038 charged residues bound it, the PBS cavity may reasonably be expected to be occupied by relatively tightly held (i.e., “ordered” or “relevant”) water molecules [41] in the absence of a ligand. Indeed, an analysis of high-resolution crystal structures has shown that such water molecules, presumably ordered, are found in surface grooves three times more often than anywhere else [45]. Displacement of such water molecules upon ligand TA-01 binding provides an additional entropic driving force that supplements the enthalpic factors in the overall binding energetics. The expulsion of a single water molecule upon formation a protein igand complex can result in a change of 21.67 kcal mol21 to DG0 [46] and the energy gain is additive if 68181-17-9 cost multiple water molecules are 11138725 displaced. There are a number of approaches to calculating the thermodynamic contribution of water to the ligand binding process [46]. We utilized tools within HINT [39], [40], [41] to predict the location of conserved water molecules in the aforementioned cavities. As these cavities will be occupied or occluded upon H/HS binding, such conserved water molecules may be ultimately displaced. Four water molecules, w1, w2, w3, and w4, were identified, as shown in Figure 6. Not surprisingly, three of these four water molecules, i.e., w1, w3 and w4, were found to coincide with the locations of the three sulfate groups of heparin pentasaccharide (2SF, 3SF and 6SD, subscripts indicate the residue). Table 3 lists the Relevance [41] and Rank [40] for these water molecules. Waters w1 and w2 display a Rank of 1.9 and 2.1, respectively, while w3 and w4 show a Rank of 0.9 and 0.0, respectively. This implies that, based only on the cavity’sSpecificity of Heparan Sulfate InteractionsFigure 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 igand 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. doi:10.1371/journal.pone.0048632.gproperties (and not those of other waters), w1 and w2 are highly likely to be present in the unliganded binding cavity, w3 i.Ures 6 and 7). Thus, certain sulfate groups of a saccharide sequence can interdigitate with Lys114, Lys125 and Arg129 of antithrombin. In an appropriate analogy, the H/HS ntithrombin interaction can be thought of as a firm `handshake’ between the two interacting complementary partners. In contrast, the lack of a reasonably sized cavity in exosite II of thrombin does not allow inter-digitation of sulfate groups. This induces a more superficial interaction wherein basic residues of exosite II do interact with sulfate of heparin but without the formation of `more directional’ bonds. Biochemically, this characteristic becomes apparent as less non-ionic forces contributing to interaction, as noted by Olson et al. [17]. Thus, the thrombin-H/HS interaction is more analogous to a superficial `high five’.Prediction of Bound Water in the HBSsBecause 17460038 charged residues bound it, the PBS cavity may reasonably be expected to be occupied by relatively tightly held (i.e., “ordered” or “relevant”) water molecules [41] in the absence of a ligand. Indeed, an analysis of high-resolution crystal structures has shown that such water molecules, presumably ordered, are found in surface grooves three times more often than anywhere else [45]. Displacement of such water molecules upon ligand binding provides an additional entropic driving force that supplements the enthalpic factors in the overall binding energetics. The expulsion of a single water molecule upon formation a protein igand complex can result in a change of 21.67 kcal mol21 to DG0 [46] and the energy gain is additive if multiple water molecules are 11138725 displaced. There are a number of approaches to calculating the thermodynamic contribution of water to the ligand binding process [46]. We utilized tools within HINT [39], [40], [41] to predict the location of conserved water molecules in the aforementioned cavities. As these cavities will be occupied or occluded upon H/HS binding, such conserved water molecules may be ultimately displaced. Four water molecules, w1, w2, w3, and w4, were identified, as shown in Figure 6. Not surprisingly, three of these four water molecules, i.e., w1, w3 and w4, were found to coincide with the locations of the three sulfate groups of heparin pentasaccharide (2SF, 3SF and 6SD, subscripts indicate the residue). Table 3 lists the Relevance [41] and Rank [40] for these water molecules. Waters w1 and w2 display a Rank of 1.9 and 2.1, respectively, while w3 and w4 show a Rank of 0.9 and 0.0, respectively. This implies that, based only on the cavity’sSpecificity of Heparan Sulfate InteractionsFigure 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 igand 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. doi:10.1371/journal.pone.0048632.gproperties (and not those of other waters), w1 and w2 are highly likely to be present in the unliganded binding cavity, w3 i.