BACKGROUND Site-specific protein-DNA complexes vary greatly in structural properties and in the thermodynamic strategy for achieving an appropriate binding free energy. A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins. RESULTS A novel analysis of ten site-specific protein-DNA complexes reve...

A localized change in a protein, which occurs as a result of either ligand binding or single amino acid substitution, necessarily encounters the conformational uctuation of the rest of the protein. Both the entropy and the enthalpy associated with the change consist of contributions from uctuations in the atoms surrounding the localized site, but they compensate. A novel thermodynamic ensemble ...

The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, pr...

The changes in excess thermodynamic quantities upon the contact of two solutes immersed in a solvent are analyzed using the radial-symmetric and three-dimensional versions of the integral equation theory. A simple model mimicking a solute in water is employed. The solute-solute interaction energy is not included in the calculations. Under the isochoric condition, the solute contact always leads...

Reaction rates and selectivities were measured for transacylation of fatty acid esters in solvents catalysed by Candida antarctica lipase B and by cutinase from Humicola insolens. With these enzymes classical water-based enzymology can be expanded to many different solvents allowing large variations in interaction energies between the enzymes, the substrates and the surrounding. Further, hydrol...

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...