The role of the concentration scale in the definition of transfer free energies.

The Gibbs free energy of transferring a solute at infinite dilution between two solvents quantifies differences in solute-solvent interactions - if the transfer takes place at constant molarity of the solute. Yet, many calculation formulae and measuring instructions that are commonly used to quantify solute-solvent interactions correspond to transfer processes in which not the molarity of the solute but its concentration measured in another concentration scale is constant. Here, we demonstrate that in this case, not only the change in solute-solvent interactions is quantified but also the entropic effect of a volume change during the transfer.

Relationship between nonlinear pressure-induced chemical shift changes and thermodynamic parameters.

NMR chemical shift analysis is a powerful method to investigate local changes in the environment of the observed nuclear spin of a polypeptide that are induced by application of high hydrostatic pressure. Usually, in the fast exchange regime, the pressure dependence of chemical shifts is analyzed by a second order Taylor expansion providing the first- and second-order pressure coefficient B1 and B2. The coefficients then are interpreted in a qualitative manner.

Unified description of urea denaturation: backbone and side chains contribute equally in the transfer model.

After studying protein denaturation by urea for many decades, conflicting views of the role of the side chains and the backbone have emerged; many results suggest that urea denatures by enhancing the solubility of both the side chains and the backbone, but the frequently applied transfer model (TM) so far ascribes denaturation exclusively to urea's action on the backbone. We use molecular dynamics simulations to rigorously test one of the TM's key assumptions, the proportionality of a molecule's transfer free energy (TFE) and its solvent-accessible surface. The performance of the TM as it is usually implemented turns out to be unsatisfactory, but the proportionality is satisfied very well after an inconsistency in the treatment of the backbone contribution is corrected.

Nuclear inelastic scattering and Mössbauer spectroscopy as local probes for ligand binding modes and electronic properties in proteins: vibrational behavior of a ferriheme center inside a β-barrel protein.

In this work, we present a study of the influence of the protein matrix on its ability to tune the binding of small ligands such as NO, cyanide (CN(-)), and histamine to the ferric heme iron center in the NO-storage and -transport protein Nitrophorin 2 (NP2) from the salivary glands of the blood-sucking insect Rhodnius prolixus. Conventional Mössbauer spectroscopy shows a diamagnetic ground state of the NP2-NO complex and Type I and II electronic ground states of the NP2-CN(-) and NP2-histamine complex, respectively. The change in the vibrational signature of the protein upon ligand binding has been monitored by Nuclear Inelastic Scattering (NIS), also called Nuclear Resonant Vibrational Spectroscopy (NRVS).