The protein state of matter

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

In recent years, interfacial mobility has gained popularity as a model with which to rationalize both affinity in ligand binding and the often observed phenomenon of enthalpy-entropy compensation. While protein contraction and reduced mobility, as demonstrated by computational and NMR techniques respectively, have been correlated to entropies of binding for a variety of systems, to our knowledge, Raman difference spectroscopy has never been included in these analyses. Here, nonresonance Raman difference spectroscopy, isothermal titration calorimetry, and X-ray crystallography were utilized to correlate protein contraction, as demonstrated by an increase in protein interior packing and decreased residual protein movement, with trends of enthalpy-entropy compensation. These results are in accord with the interfacial mobility model and lend additional credence to this view of protein activity.

Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains

Human P-glycoprotein is an ATP-binding cassette transporter that plays an important role in the defence against potentially harmful molecules from the environment. It is involved in conferring resistance against cancer therapeutics and plays an important role for the pharmacokinetics of drugs. The lack of a high resolution structure of P-glycoprotein has hindered its functional understanding and represents an obstacle for structure based drug development. The homologous bacterial exporter Sav1866 has been shown to share a common architecture and overlapping substrate specificity with P-glycoprotein. The structure of Sav1866 suggests that helices in the transmembrane domains diverge at the extracytoplasmic face, whereas cross-link information and a combination of small angle X-ray scattering and cryo-electron crystallography data indicate that helices 6 and 12 of P-glycoprotein are closer in P-glycoprotein than in the crystal structure of Sav1866. Using homology modelling, we present evidence that the protein possesses intrinsic structural flexibility to allow cross-links to occur between helices 6 and 12 of P-glycoprotein, thereby reconciling crystallographic models with available experimental data from cross-linking.

Effect of Tris on catalytic activity of MP-11

The effect of tris(hydroxymethyl)aminomethane (Tris) on the catalytic activity and microstructure of heme undecapeptide, microperoxidase-11 (MP-11) in the aqueous solution was investigated using cyclic voltammetry, circular dichroism (CD) spectroscopy, UV-vis absorption spectroscopy and X-ray photoelectron spectroscopy (XPS). It was found for the first time that Tris would inhibit the catalytic activity and electrochemical reaction of MP-11 at the glassy carbon (GC) electrode. This is mainly due to the fact that Tris would induce more alpha-helix and beta-turn conformations from the random coil conformation of MP-11, cause the asymmetric split-up in the Soret band region of MP-11, increase the non-planarity of the heme of MP-11, and change the electron densities of N, O and S atoms of MP-11. Meanwhile, It was found that the electrochemical reaction of MP-11 with Tris at GC electrode is diffusion-controlled, and the diffusion coefficient of MP-11 and the rate constant for the heterogeneous electron transfer of MP-11 in the presence of Tris are decreased by 19% and 16%, respectively. Further experiments showed that the electrocatalytic current of MP-11 on the reduction of H2O2 is decreased by about 25% after the addition of Tris to the MP-11 solution.

Volumetric properties of proteins

Structural and thermodynamic characterizations of a variety of intra- and intermolecular interactions stabilizing/destabilizing protein systems represent a major part of multidisciplinary efforts aimed at solving the problems of protein folding and binding. To this end, volumetric techniques have been successfully used to gain insights into protein hydration and intraglobular packing. Despite the fact that the use of volumetric measurements in protein-related studies dates back to the 1950s, such measurements still represent a relatively untapped yet potentially informative means for tackling the problems of protein folding and binding. This notion has been further emphasized by recent advances in the development of highly sensitive volumetric instrumentation that has led to intensifying volumetric investigations of protein systems. This paper reviews the volumetric properties of proteins and their low-molecular-weight analogs, in particular, discussing the recent progress in the use of volumetric data for studying conformational transitions of proteins as well as protein-ligand, protein-protein, and protein-nucleic acid interactions.

An electrochemical investigation of ligand-binding abilities of film-entrapped myoglobin

Film-entrapped myoglobin exhibits well-defined electrochemistry which, upon ligand binding, displays a titratable redox potential shift. This effect has been observed to be highly dependent on the charged state of involved films. We have demonstrated that this approach may act as a model system for studies of molecular recognition between proteins and ligands.

Compressibility of protein transitions

We review the results of compressibility studies on proteins and low molecular weight compounds that model the hydration properties of these biopolymers. In particular, we present an analysis of compressibility changes accompanying conformational transitions of globular proteins. This analysis, in conjunction with experimental compressibility data on protein transitions, were used to define the changes in the hydration properties and intrinsic packing associated with native-to-molten globule, native-to-partially unfolded, and native-to-fully unfolded transitions of globular proteins. In addition, we discuss the molecular origins of predominantly positive changes in compressibility observed for pressure-induced denaturation transitions of globular proteins. Throughout this review, we emphasize the importance of compressibility data for characterizing protein transitions, while also describing how such data can be interpreted to gain insight into role that hydration and intrinsic packing play in modulating the stability of and recognition between proteins and other biologically important compounds.

Decomposition of protein tryptophan fluorescence spectra into log-normal components. III. Correlation between fluorescence and microenvironment parameters of individual tryptophan residues

In our previous paper (Reshetnyak, Ya. K., and E. A. Burstein. 2001. Biophys. J. 81:1710-1734) we confirmed the existence of five statistically discrete classes of emitting tryptophan fluorophores in proteins. The differences in fluorescence properties of tryptophan residues of these five classes reflect differences in interactions of excited states of tryptophan fluorophores with their microenvironment in proteins. Here we present a system of describing physical and structural parameters of microenvironments of tryptophan residues based on analysis of atomic crystal structures of proteins. The application of multidimensional statistical methods of cluster and discriminant analyses for the set of microenvironment parameters of 137 tryptophan residues of 48 proteins with known three-dimensional structures allowed us to 1) demonstrate the discrete nature of ensembles of structural parameters of tryptophan residues in proteins; 2) assign spectral components obtained after decomposition of tryptophan fluorescence spectra to individual tryptophan residues; 3) find a correlation between spectroscopic and physico-structural features of the microenvironment; and 4) reveal differences in structural and physical parameters of the microenvironment of tryptophan residues belonging to various spectral classes.

Protein structure and dynamics at high pressure

The effect of pressure on the structure and dynamics of proteins is discussed in the framework of the pressure-temperature stability phase diagram. The elastic (reversible) properties, thermal expansion, compressibility and heat capacity, are correlated with the entropy, volume, and the coupling between entropy and volume fluctuations respectively. The experimental approaches that can be used to measure these quantities are reviewed. The plastic (conformational) changes reflect the changes in these properties in the cold, pressure and heat denaturation.