A multidisciplinary approach to probing enthalpy-entropy compensation and the interfacial mobility model

Introduction of a tailor made anion receptor into the side chain of small peptides allows fine-tuning the thermodynamic signature of peptide–DNA binding

Replacing lysine by a tailor made anion binding motif, switches the DNA binding of small peptides from entropy to enthalpy control.

Quasithermodynamic contributions to the fluctuations of a protein nanopore

Proteins undergo thermally activated conformational fluctuations among two or more substates, but a quantitative inquiry on their kinetics is persistently challenged by numerous factors, including the complexity and dynamics of various interactions, along with the inability to detect functional substates within a resolvable time scale. Here, we analyzed in detail the current fluctuations of a monomeric β-barrel protein nanopore of known high-resolution X-ray crystal structure. We demonstrated that targeted perturbations of the protein nanopore system, in the form of loop-deletion mutagenesis, accompanying alterations of electrostatic interactions between long extracellular loops, produced modest changes of the differential activation free energies calculated at 25 °C, ΔΔG(⧧), in the range near the thermal energy but substantial and correlated modifications of the differential activation enthalpies, ΔΔH(⧧), and entropies, ΔΔS(⧧). This finding indicates that the local conformational reorganizations of the packing and flexibility of the fluctuating loops lining the central constriction of this protein nanopore were supplemented by changes in the single-channel kinetics. These changes were reflected in the enthalpy-entropy reconversions of the interactions between the loop partners with a compensating temperature, TC, of ∼300 K, and an activation free energy constant of ∼41 kJ/mol. We also determined that temperature has a much greater effect on the energetics of the equilibrium gating fluctuations of a protein nanopore than other environmental parameters, such as the ionic strength of the aqueous phase as well as the applied transmembrane potential, likely due to ample changes in the solvation activation enthalpies. There is no fundamental limitation for applying this approach to other complex, multistate membrane protein systems. Therefore, this methodology has major implications in the area of membrane protein design and dynamics, primarily by revealing a better quantitative assessment on the equilibrium transitions among multiple well-defined and functionally distinct substates of protein channels and pores.

An enthalpic basis of additivity in biphenyl hydroxamic acid ligands for stromelysin-1

Fragment based drug discovery remains a successful tool for pharmaceutical lead discovery. Although based upon the principle of thermodynamic additivity, the underlying thermodynamic basis is poorly understood. A thermodynamic additivity analysis was performed using stromelysin-1 and a series of biphenyl hydroxamate ligands identified through fragment additivity. Our studies suggest that, in this instance, additivity arises from enthalpic effects, while interaction entropies are unfavorable; this thermodynamic behavior is masked by proton transfer. Evaluation of the changes in constant pressure heat capacities during binding suggest that solvent exclusion from the binding site does not account for the dramatic affinity enhancements observed.