Molecular determinant of the effects of hydrostatic pressure on protein folding stability

On the Origin of Microtubules' High-Pressure Sensitivity

For over 50 years, it has been known that the mitosis of eukaryotic cells is inhibited already at high hydrostatic pressure conditions of 30 MPa. This effect has been attributed to the disorganization of microtubules, the main component of the spindle apparatus. However, the structural details of the depolymerization and the origin of the pressure sensitivity have remained elusive. It has also been a puzzle how complex organisms could still successfully inhabit extreme high-pressure environments such as those encountered in the depth of oceans. We studied the pressure stability of microtubules at different structural levels and for distinct dynamic states using high-pressure Fourier-transform infrared spectroscopy and Synchrotron small-angle x-ray scattering. We show that microtubules are hardly stable under abyssal conditions, where pressures up to 100 MPa are reached. This high-pressure sensitivity can be mainly attributed to the internal voids and packing defects in the microtubules. In particular, we show that lateral and longitudinal contacts feature different pressure stabilities, and they define also the pressure stability of tubulin bundles. The intactness of both contact types is necessary for the functionality of microtubules in vivo. Despite being known to dynamically stabilize microtubules and prevent their depolymerization, we found that the anti-cancer drug taxol and the accessory protein MAP2c decrease the pressure stability of microtubule protofilaments. Moreover, we demonstrate that the cellular environment itself is a crowded place and accessory proteins can increase the pressure stability of microtubules and accelerate their otherwise highly pressure-sensitive de novo formation.

A high pressure cell using metallic windows to investigate the structure of molecular solutions up to 600 MPa by small-angle neutron scattering

We report on a high pressure (HP) cell designed for the determination of the structure of molecular solutions by small-angle neutron scattering (SANS). The HP cell is fitted up with two thick metallic windows that make the device very resistant under hydrostatic pressures up to 600 MPa (or 6 kbar). The metallic windows are removable, offering the possibility to adapt the HP cell to a given study with the pressure desired on an appropriate spatial range to study the structure of various molecular solutions by SANS. In this context, we report the absorption, transmission, and scattering properties of different metallic windows. Finally, we describe, as a proof of principle, the solution structure changes of myoglobin, a small globular protein.

On empirical decomposition of volumetric data

Volumetric characterization of proteins and their recognition events has been instrumental in providing information on the role of intra- and intermolecular interactions, including hydration, in stabilizing biomolecules. The credibility of molecular models and interpretation schemes used to rationalize experimental data are essential for the validity of microscopic insights derived from volumetric results. Current empirical schemes used to interpret volumetric data suffer from a lack of theoretical and computational substantiation. In this contribution, we take advantage age of recent MD simulations of proteins in solution coupled with Voronoi-Delaunay tessellation of simulated structures that have provided an exceptional level of structural detail on the nature of protein-water interfaces. We use these structural insights to re-evaluate empirical frameworks used for interpretation of volumetric data. An important issue in this respect is the actual dividing surface between water and protein atoms that is used in volumetric studies when the solute and solvent are treated as hard spheres enclosed within their respective van der Waals surfaces. In one development, using Voronoi tessellation of MD simulated protein-water systems the dividing surface has been defined as the points equidistant from the water and protein atoms. The interstitial void volume between the solute and the dividing surface corresponds to thermal volume envisaged by Scaled Particle Theory. In this communication, we explicitly account for the contributions of thermal volume to the partial molar volume, compressibility, and expansibility of proteins and re-examine and redefine the intrinsic and hydration volumetric contributions. We discuss the implications of our results for protein transitions and association events.

Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents

DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.

Enhanced Oxygen Solubility in Metastable Water under Tension

Despite its relevance in numerous natural and industrial processes, the solubility of molecular oxygen has never been directly measured in capillary-condensed liquid water. In this article, we measure oxygen solubility in liquid water trapped within nanoporous samples, in metastable equilibrium with a subsaturated vapor. We show that solubility increases two fold at moderate subsaturations (relative humidity ∼0.55). This evolution with relative humidity is in good agreement with a simple thermodynamic prediction using properties of bulk water, previously verified experimentally at positive pressure. Our measurement thus verifies the validity of this macroscopic thermodynamic theory to strong confinement and large negative pressures, where significant nonidealities are expected. This effect has strong implications for important oxygen-dependent chemistries in natural and technological contexts.

Lessons from pressure denaturation of proteins

Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.

Hydration Promoted by a Methylene Group: A Volumetric Study on Alkynes in Water

Hydrocarbons including a methylene group are generally considered a hydrophobic building block, in the sense that the density of their hydration water is lower than that of bulk water. However, is the methylene group always hydrophobic? In this study, we experimentally determined the partial molar volume of a methylene group in water as 14.01 ± 0.46 cm³ mol^-1 for 1-alkyne, 9.83 ± 0.35 cm³ mol^-1 for 2-alkyne, and 11.39 ± 0.55 cm³ mol^-1 for 3-alkyne. These values are all unusually small compared to the ∼16 cm³ mol^-1 for model compounds from the literature. The subsequent volumetric analysis on the basis of the Kirkwood-Buff parameter indicates that the hydration water is enriched by the addition of a methylene group for 2-alkyne, while it is depleted for the reported model compounds that contain hydrophilic functional groups, 1-alkyne, and 3-alkyne. Our findings suggest that the triple bonded carbons in 2-alkyne that reduce hydration water act as a hydrophobic group in 2-alkyne. Thus, the methylene group should be called "hydrophilic" in this case because it actually recovers the hydration water when placed next to more hydrophobic groups. Therefore, we conclude that the hydrophobicity of a methylene group varies depending on its hydration environment due to other functional groups in the solute.

Effects of Cosolvents and Macromolecular Crowding on the Phase Transitions and Temperature-Pressure Stability of Chiral and Racemic Poly-Lysine

FTIR spectroscopy has been used to reveal the effects of different types of cosolvents (TMAO, urea) as well as macromolecular crowding (using the crowding agent Ficoll) on the temperature and pressure dependent structure of poly-L-lysine, poly-D-lysine and their racemic mixture. Compared to the effects of cosolvents on the unfolding transition of proteins, their effects on the α-helix to aggregated β-sheet transition of polylysine are quite small. High hydrostatic pressure has been found to favor the α-helical state over the aggregated β-sheet structure which is reflected in a volume decrease of ΔV=−32 mL mol−1, indicating that the packing mode is more efficient in the α-helical structure. Both, addition of urea and TMAO lead to a decrease in pressure stability of the aggregated β-sheet structure, which is accompanied by a three-fold decrease in ΔV, whereas the macromolecular crowder has little effect on the β-to-α transition. The more than 3 kbar higher β-to-α transition pressure of the racemic mixture compared with PLL confirms the drastic stabilization of β-sheet aggregates if the stereoisomers PLL and PDL are combined. Changes in hydration and packing of the polypeptide occurs upon interaction and fine packing of the polypeptide’s chains of opposed chirality, which are slightly modulated by the properties of cosolute and crowding, only. The underlying solvational and packing mechanisms observed here may be decisive factors responsible for the spontaneous protein aggregation in general and, as such, may shed additional light on the molecular basis of amyloid-associated diseases.

Folding of maltose binding protein outside of and in GroEL

The GroEL/ES chaperonin is known to prevent protein aggregation during folding by passive containment within the central cavity. The possible role of more active intervention is controversial. The HX MS method documents an organized hydrophobically stabilized folding preintermediate in the collapsed ensemble of maltose binding protein. A mutational defect destabilizes the preintermediate and greatly slows folding of the subsequent on-pathway H-bonded intermediate. GroEL encapsulation alone, without ATP and substrate protein cycling, restabilizes the preintermediate and restores fast folding. The mechanism appears to depend on forceful compression during confinement. More generally, these results suggest that GroEL can repair different folding defects in different ways.

We used hydrogen exchange–mass spectrometry (HX MS) and fluorescence to compare the folding of maltose binding protein (MBP) in free solution and in the GroEL/ES cavity. Upon refolding, MBP initially collapses into a dynamic molten globule-like ensemble, then forms an obligatory on-pathway native-like folding intermediate (1.2 seconds) that brings together sequentially remote segments and then folds globally after a long delay (30 seconds). A single valine to glycine mutation imposes a definable folding defect, slows early intermediate formation by 20-fold, and therefore subsequent global folding by approximately twofold. Simple encapsulation within GroEL repairs the folding defect and reestablishes fast folding, with or without ATP-driven cycling. Further examination exposes the structural mechanism. The early folding intermediate is stabilized by an organized cluster of 24 hydrophobic side chains. The cluster preexists in the collapsed ensemble before the H-bond formation seen by HX MS. The V9G mutation slows folding by disrupting the preintermediate cluster. GroEL restores wild-type folding rates by restabilizing the preintermediate, perhaps by a nonspecific equilibrium compression effect within its tightly confining central cavity. These results reveal an active GroEL function other than previously proposed mechanisms, suggesting that GroEL possesses different functionalities that are able to relieve different folding problems. The discovery of the preintermediate, its mutational destabilization, and its restoration by GroEL encapsulation was made possible by the measurement of a previously unexpected type of low-level HX protection, apparently not dependent on H-bonding, that may be characteristic of proteins in confined spaces.

The effects of glycine, TMAO and osmolyte mixtures on the pressure dependent enzymatic activity of α-chymotrypsin

Different natural osmolytes modulate the pressure dependent enzyme kinetics in different ways.

Monitoring protein folding through high pressure NMR spectroscopy

High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.

Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding

Pressure is a well-known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilized proteins at high pressures. High temperature often accompanies high pressure, for example, in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding. Here, we present a comprehensive analysis of the temperature dependence of the volumetric components of proteins, showing that hydration volume is the primary component that defines expansivities of the native and unfolded states and void volume only contributes slightly to the folded state expansivity.

Putting the Piezolyte Hypothesis under Pressure

A group of small molecules that stabilize proteins against high hydrostatic pressure has been classified as piezolytes, a subset of stabilizing cosolutes. This distinction would imply that piezolytes counteract the effects of high hydrostatic pressure through effects on the volumetric properties of the protein. The purpose of this study was to determine if cosolutes proposed to be piezolytes have an effect on the volumetric properties of proteins through direct experimental measurements of volume changes upon unfolding of model proteins lysozyme and ribonuclease A, in solutions containing varying cosolute concentrations. Solutions containing the proposed piezolytes glutamate, sarcosine, and betaine were used, as well as solutions containing the denaturants guanidinium hydrochloride and urea. Changes in thermostability were monitored using differential scanning calorimetry whereas changes in volume were monitored using pressure perturbation calorimetry. Our findings indicate that increasing stabilizing cosolute concentration increases the stability and transition temperature of the protein, but does not change the temperature dependence of volume changes upon unfolding. The results suggest that the pressure stability of a protein in solution is not directly affected by the presence of these proposed piezolytes, and so they cannot be granted this distinction.