Evaluation of water displacement energetics in protein binding sites with grid cell theory.

Correction: Evaluation of water displacement energetics in protein binding sites with grid cell theory.

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization.

A strategy in drug design is to consider enhancing the affinity of lead molecules with structural modifications that displace water molecules from a protein binding site. Because success of the approach is uncertain, clarification of the associated energetics was sought in cases where similar structural modifications yield qualitatively different outcomes. Specifically, free-energy perturbation...

Energetics of Zn2+ adsorption in silicate MEL-type nanoporous material

Density-functional-based and ab initio calculations were implemented at different computational levels to estimate the binding energy of Zn2+ ion adsorbed on the available sites of a silicate MEL-type adsorbent. B3LYP and MP2 were used in combination with the 6-31G*, 6-31+G*, LanL2DZ, 6-311+G*, and Def2-TZVP basis sets. The zinc cation was found to preferentially occupy the 6MR sites followed b...

Evaluation of Host-Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory.

A previously developed cell theory model of liquid water was used to evaluate the excess thermodynamic properties of confined clusters of water molecules. The results are in good agreement with reference thermodynamic integration calculations, suggesting that the model is adequate to probe the thermodynamic properties of water at interfaces or in cavities. Next, the grid cell theory (GCT) metho...

Studies of In-Vitro Amlodipine and Arsenic Displacement Interaction at Binding Sites of Bovine Serum Albumin

In this study, the binding of amlodipine (a Ca ++ channel Blocker) and arsenic (metalloid) to bovine serum albumin (BSA) was studied by equilibrium dialysis(ED) method in order to have an insight into their binding chemistry to BSA. Free amlodipine concentration was increased due to addition of arsenic which reduced the binding of the compounds to BSA. However, the free fraction was not increa...