Entropy gain due to water release upon ligand binding

Entropy gain due to water release upon ligand binding

Experimental thermodynamic data of the ligand-receptor association showed that the entropy changes upon binding are positive and large enough to be important driving forces of the binding process for a considerable number of ligand-receptor complexes [1]. The expected source behind such an entropy increase is the release of the water molecules from the binding pocket and from around the ligand ...

Using Bulk Water to Detect Ligand Binding

Water networks contribute to enthalpy/entropy compensation in protein-ligand binding.

The mechanism (or mechanisms) of enthalpy-entropy (H/S) compensation in protein-ligand binding remains controversial, and there are still no predictive models (theoretical or experimental) in which hypotheses of ligand binding can be readily tested. Here we describe a particularly well-defined system of protein and ligands--human carbonic anhydrase (HCA) and a series of benzothiazole sulfonamid...

Hydrogen Bonding Penalty upon Ligand Binding

Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy ...

Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding

MOTIVATION Protein movements form a continuum from large domain rearrangements (including folding and restructuring) to side-chain rotamer changes and small rearrangements. Understanding side-chain flexibility upon binding is important to understand molecular recognition events and predict ligand binding. METHODS In the present work, we developed a well-curated non-redundant dataset of 188 pr...