Probing volumetric properties of biomolecular systems by pressure perturbation calorimetry (PPC)--the effects of hydration, cosolvents and crowding

Thermal Lens Measurements of Thermal Expansivity in Thermosensitive Polymer Solutions

The weak absorption of a laser beam generates in a fluid an inhomogeneous refractive index profile acting as a negative lens. This self-effect on beam propagation, known as Thermal Lensing (TL), is extensively exploited in sensitive spectroscopic techniques, and in several all-optical methods for the assessment of thermo-optical properties of simple and complex fluids. Using the Lorentz-Lorenz equation, we show that the TL signal is directly proportional to the sample thermal expansivity α, a feature allowing minute density changes to be detected with high sensitivity in a tiny sample volume, using a simple optical scheme. We took advantage of this key result to investigate the compaction of PniPAM microgels occurring around their volume phase transition temperature, and the temperature-driven formation of poloxamer micelles. For both these different kinds of structural transitions, we observed a significant peak in the solute contribution to α, indicating a decrease in the overall solution density-rather counterintuitive evidence that can nevertheless be attributed to the dehydration of the polymer chains. Finally, we compare the novel method we propose with other techniques currently used to obtain specific volume changes.

Volumetric Properties of Four-Stranded DNA Structures

Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute-solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.

Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel

A method is designed to quickly form protein hydrogels, based on the self-assembly of highly concentrated lysozyme solutions in acidic conditions. Their properties can be easily modulated by selecting the curing temperature. Molecular insights on the gelation pathway, derived by in situ FTIR spectroscopy, are related to calorimetric and rheological results, providing a consistent picture on structure–property correlations. In these self-crowded samples, the thermal unfolding induces the rapid formation of amyloid aggregates, leading to temperature-dependent quasi-stationary levels of antiparallel cross β-sheet links, attributed to kinetically trapped oligomers. Upon subsequent cooling, thermoreversible hydrogels develop by the formation of interoligomer contacts. Through heating/cooling cycles, the starting solutions can be largely recovered back, due to oligomer-to-monomer dissociation and refolding. Overall, transparent protein hydrogels can be easily formed in self-crowding conditions and their properties explained, considering the formation of interconnected amyloid oligomers. This type of biomaterial might be relevant in different fields, along with analogous systems of a fibrillar nature more commonly considered.

Properties of Hydrogen-Bonded Liquids at Interfaces

Effects of interfaces on hydrogen-bonded liquids play major roles in nature and technology. Despite their importance, a fundamental understanding of these effects is still lacking. In large parts, this shortcoming is due to the high complexity of these systems, leading to an interference of various interactions and effects. Therefore, it is advisable to take gradual approaches, which start from well designed and defined model systems and systematically increase the level of intricacy towards more complex mimetics. Moreover, it is necessary to combine insights from a multitude of methods, in particular, to link novel preparation strategies and comprehensive experimental characterization with inventive computational and theoretical modeling. Such concerted approach was taken by a group of preparative, experimentally, and theoretically working scientists in the framework of Research Unit FOR 1583 funded by the Deutsche Forschungsgemeinschaft (German Research Foundation). This special issue summarizes the outcome of this collaborative research. In this introductory article, we give an overview of the covered topics and the main results of the whole consortium. The following contributions are review articles or original works of individual research projects.

Influence of cosolvents, self-crowding, temperature and pressure on the sub-nanosecond dynamics and folding stability of lysozyme

We studied the effects of temperature and hydrostatic pressure on the dynamical properties and folding stability of highly concentrated lysozyme solutions in the absence and presence of the osmolytes trimethylamine-N-oxide (TMAO) and urea. Elastic incoherent neutron scattering (EINS) was applied to determine the mean-squared displacement (MSD) of the protein's hydrogen atoms to yield insights into the effects of these cosolvents on the averaged sub-nanosecond dynamics in the pressure range from ambient up to 4000 bar. To evaluate the additional effect of self-crowding, two protein concentrations (80 and 160 mg mL^-1) were used. We observed a distinct effect of TMAO on the internal hydrogen dynamics, namely a reduced mobility. Urea, on the other hand, revealed no marked effect and consequently, no counteracting effect in an urea-TMAO mixture was observed. Different from the less concentrated protein solution, no significant effect of pressure on the MSD was observed for 160 mg mL^-1 lysozyme. The EINS experiments were complemented by Fourier-transform infrared (FTIR) spectroscopy measurements, which led to additional insights into the folding stability of lysozyme under the various environmental conditions. We observed a stabilization of the protein in the presence of the compatible osmolyte TMAO and a destabilization in the presence of urea against temperature and pressure for both protein concentrations. Additionally, we noticed a slight destabilizing effect upon self-crowding at very high protein concentration (160 mg mL^-1), which is attributable to transient destabilizing intermolecular interactions. Furthermore, a pressure-temperature diagram could be obtained for lysozyme at these high protein concentrations that mimics densely packed intracellular conditions.

Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation

In this paper we demonstrate the application of pressure perturbation calorimetry (PPC) to the characterization of 2-propanol/water mixtures. PPC of different 2-propanol/water mixtures provides two useful measurements: (i) the change in heat (ΔQ); and (ii) the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT value. The results demonstrate that the ΔQ values of the mixtures deviate from that expected for a random mixture, with a maximum at ~20–25 mol% 2-propanol. This coincides with the concentration at which molecular dynamics (MD) simulations show a maximum deviation from random distribution, and also the point at which alcohol–alcohol hydrogen bonds become dominant over alcohol–water hydrogen bonds. Furthermore, the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT value showed transitions at 2.5 mol% 2-propanol and at approximately 14 mol% 2-propanol. Below 2.5 mol% 2-propanol the values of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT are negative; this is indicative of the presence of isolated 2-propanol molecules surrounded by water molecules. Above 2.5 mol% 2-propanol \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left[ {\delta \bar{C}_{p} /\delta p} \right]_{T} $$\end{document}δC¯p/δpT rises, reaching a maximum at ~14 mol% corresponding to a point where mixed alcohol–water networks are thought to dominate. The values and trends identified by PPC show excellent agreement not only with those obtained from MD simulations but also with results in the literature derived using viscometry, THz spectroscopy, NMR and neutron diffraction.

Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state. Further, we find a strong interplay between water, salt, and osmolyte in driving the thermodynamics and defining the temperature and pressure stability limit of the RNA. Our results support a universal working mechanism of TMAO and urea to (de)stabilize proteins and the RNA.

Applications of pressure perturbation calorimetry to study factors contributing to the volume changes upon protein unfolding

BACKGROUND

Pressure perturbation calorimetry (PPC) is a biophysical method that allows direct determination of the volume changes upon conformational transitions in macromolecules.

SCOPE OF THIS REVIEW

This review provides novel details of the use of PPC to analyze unfolding transitions in proteins. The emphasis is made on the data analysis as well as on the validation of different structural factors that define the volume changes upon unfolding. Four case studies are presented that show the application of these concepts to various protein systems.

MAJOR CONCLUSIONS

The major conclusions are: 1. Knowledge of the thermodynamic parameters for heat induced unfolding facilitates the analysis of the PPC profiles. 2. The changes in the thermal expansion coefficient upon unfolding appear to be temperature dependent.3.Substitutions on the protein surface have negligible effects on the volume changes upon protein unfolding. 4. Structural plasticity of proteins defines the position dependent effect of amino acid substitutions of the residues buried in the native state. 5. Small proteins have positive volume changes upon unfolding which suggests difference in balance between the cavity/void volume in the native state and the hydration volume changes upon unfolding as compared to the large proteins that have negative volume changes.

GENERAL SIGNIFICANCE

The information provided here gives a better understanding and deeper insight into the role played by various factors in defining the volume changes upon protein unfolding.

Exploring volume, compressibility and hydration changes of folded proteins upon compression

Understanding the physical basis of the structure, stability and function of proteins in solution, including extreme environmental conditions, requires knowledge of their temperature and pressure dependent volumetric properties. One physical-chemical property of proteins that is still little understood is their partial molar volume and its dependence on temperature and pressure. We used molecular dynamics simulations of aqueous solutions of a typical monomeric folded protein, staphylococcal nuclease (SNase), to study and analyze the pressure dependence of the apparent volume, Vapp, and its components by the Voronoi-Delaunay method. We show that the strong decrease of Vapp with pressure (βT = 0.95 × 10(-5) bar(-1), in very good agreement with the experimental value) is essentially due to the compression of the molecular volume, VM, ultimately, of its internal voids, V. Changes of the intrinsic volume (defined as the Voronoi volume of the molecule), the contribution of the solvent to the apparent volume, and of the contribution of the boundary voids between the protein and the solvent have also been studied and quantified in detail. The pressure dependences of the volumetric characteristics obtained are compared with the temperature dependent behavior of these quantities and with corresponding results for a natively unfolded polypeptide.