Binding mode

Alkanethiolates have two binding modes at the Au(lll) hoUow site, one with a bend angle around the sulfur of 180° (sp) and the other of 104° (sp ). The latter is being more stable by 1.7 kJ/mol (0.41 kcal/mol) (211). Thus, packing requirements may dictate the final surface—S—C angle. Many studies have... 

Figure 11.6 A schematic view of the presumed binding mode of the tetrahedral transition state intermediate for the deacylation step. The four essential features of the serine proteinases are highlighted in yellow the catalytic triad, the oxyanion hole, the specificity pocket, and the unspecific main-chain substrate binding.

In closely related studies, the molecular and crystal structures of lithium, sodium and potassium N,N -di(p-tolyl)formamidinate and N,N -di(2,6-dialkyl-phenyl)formamidinate complexes have been elucidated. These showed the anions to be versatile ligands for alkali metals, exhibiting a wide variety of binding modes. ... 

Collectively, these thermal denaturation studies demonstrated that aPNAs bind to complementary ssDNA targets with high affinity and in a sequence-specific manner consistent with our proposed base-pairing model. Additional electrostatic and hydrophobic binding interactions can be incorporated into the aPNA design without affecting the primary Watson-Crick binding mode. 

The transition of the compressibility, and other properties of the polyelectrolyte brnshes, is most likely accounted for in terms of the transition in the binding mode of the connterion to the polyelectrolytes, from the loosely bonnd state to the tightly bound one, which rednces inter- and intrachain repulsive interactions. The following snpports this ac-connt (1) At the critical density, = 0.20 chain/nm, the separation distance between polyelectrolyte chains, d, is 2.4 nm. This distance is close to the snm, 2.6 nm, of the chain diameter, 1.3 nm, and the size of two hydrated connterions, 1.32 nm, indicating that the abrupt... 

In polyelectrolyte solutions, the counterion condensation on linear polyelectrolyte chains is known to occur when the charge density along the chain exceeds the critical value [40]. Our work indicates the existence of a critical value for the separation distance between chains, where the interchain interaction changes drastically, most likely due to the transition in the binding mode of the counterions (see Fig. 13). Many peculiar forms of behavior, which are often interpreted by the cluster formation or the interchain organization of polyelectrolytes, have been reported for high concentrations of aqueous polyelectrolytes... 

FIG. 13 Schematic drawing of possible binding modes of counterions to polyelectrolyte chains. Counterions loosely bind and form a cloud around the polyelectrolyte chains when the interchain distance (d) is greater than 2.4 0.5 nm, while they strongly bind to form nearly neutral polyelectrolytes at smaller distances d < 2.4 0.5 nm). 

Raha K, Merz KM. Large-scale validation of a quantum mechanics based scoring function predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem 2005 48 4558-75. 

The practical utility of the target-structure-based approach in the design of chemical libraries is still limited because of the requirement of quality crystallographic data, detailed knowledge of the ligand binding mode, and... 

Sprous DG, Lowis DR, Leonard JM, Heritage T, Burkett SN, Baker DS, Clark RD. OptiDock virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space. J Comb Chem 2004 6 530-9. 

AmpC P-Lactamase. A map of hot spots was constructed from the X-ray structure of AmpC P-lactamase and a university version of the program DOCK was used to search for noncovalent inhibitors in 229,810 compounds of the ACD database. Of 56 tested compounds three had values <650pM, for example, compound 41 Ki = 26pM Fig. 16.6) [117]. The experimental X-ray structure of its complex with AmpC P-lactamase closely resembles the predicted binding mode. 

To study the binding mode of the yS-D-galactopyranosyl residue of the Lewis b human blood-group determinant to its monoclonal antibody or to a lectin, methyl 2-acetamido-2-deoxy-3-0-(6-deoxy-6-fluoro-2-0-a-L-fuco-pyranosyl-y -D-galactopyranosyl)-4-0-a-L-fucopyranosyl-/ -D-glucopyrano-side was synthesized. ... 

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