On the mechanism of cold denaturation

Remarks on Life Feasibility on the Red Planet

The current strong interest in the exploration of Mars leads to the question of the actual possibility of the presence or possible past or future development of life on the planet. Several clues suggest that liquid water could be stably present under the surface of Mars, but on the condition that it is rich in perchlorate salts, abundant in the Martian soil, which would allow for water to remain liquid at the very low temperatures found on the planet. In this work, the main evidence on the permissiveness of Martian environments to microbial life is reviewed, with particular attention to the evaluation of the tolerance limit to the perchlorates of different microorganisms. Furthermore, a reasonable theoretical approach is offered to calculate the stability of globular proteins in aqueous solutions rich in perchlorates, trying to provide, given the current lack of valid experimental data, a rational means to try to understand the behaviour of proteins in environmental conditions very far from those of Earth.

The apo LETM1 F-EF-hand adopts a closed conformation that underlies a multi-modal sensory role in mitochondria

Leucine zipper EF-hand containing transmembrane protein-1 (LETM1) plays a critical role in mitochondrial function, with haploinsufficiency linked to Wolf-Hirschhorn syndrome. Here, we present the solution NMR structure of the calcium (Ca2+)-depleted LETM1 EF-hand domain, revealing a closed conformation facilitated by a distinct F1-helix pivot rather than decreased interhelical angle. Further, we observe regiospecific unfolding in response to hot and cold denaturation and show H662 has a pKa in-line with physiological pH fluctuations. Finally, we demonstrate Ca2+-dependent transient interactions between the EF-hand and other LETM1 or GHITM protein domains. Collectively, our data reveal the apo-to-holo structural dynamics and mechanisms underlying the multi-modal sensing by the LETM1 EF-hand domain, highlighting its role as an adaptable regulatory element within the mitochondrial matrix.

Insights into myofibrillar protein denaturation during freezing: The impact of ice-water interface area

This study investigated the impact of the ice-water interface area on the denaturation of myofibrillar protein (MP) over 1, 3, and 5 freeze-thaw cycles. Experimental systems designed to generate ice-water interfaces with two distinct surface areas were established by employing rapid freezing at -80 °C and slow freezing at -25 °C, resulting in surface areas of 64.63 m2/100 mL and 54.05 m2/100 mL, respectively. Following three freeze-thaw cycles, the process of rapid freezing, characterized by formation of a larger ice-water interface area, was found to significantly influenced the functional properties of MP. The impact was evidenced by a reduction in solubility, total sulfhydryl content, and thermal denaturation temperature. Structural modifications in MP suggested that the larger ice-water interface led an accelerated rate of protein unfolding during freezing. Interfacial pressure and confocal laser scanning microscopy (CLSM) results demonstrated that the larger ice-water interface area could be more able to reduce protein interfacial adsorption and enhanced protein emulsion aggregation. The addition of 0.1 % surfactant Tween 80 prior to freezing markedly enhanced protein stability throughout both the freezing and subsequent freeze-thaw cycles. The findings suggested that to further inhibit MP frozen denaturation, it is important to consider limiting the expansion of ice-water interface area.

Life and death of Yfh1: how cool is cold denaturation

Yeast frataxin (Yfh1) is a small natural protein from yeast that has the unusual property of undergoing cold denaturation at temperatures above the freezing point of water when under conditions of low ionic strength. This peculiarity, together with remarkable resilience, allows the determination, for the whole protein as well as for individual residues, of the stability curve, that is the temperature dependence of the free energy difference between the unfolded and folded forms. The ease of measuring stability curves without the need to add denaturants or introduce ad hoc destabilizing mutations makes this protein an ideal 'tool' for investigating the influence of many environmental factors on protein stability. The present review aims at recapitulating all the open questions that Yfh1 has helped to address, including understanding the differences and commonalities of the cold, heat and pressure unfolded states. This protein thus offers a unique tool for studying aspects of protein stability so far been considered difficult to assess and provides important guidelines that could allow the identification of other similar systems.

On the Stabilizing Effect of Aspartate and Glutamate and Its Counteraction by Common Denaturants

By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents.

Nanocrystallites Modulate Intermolecular Interactions in Cryoprotected Protein Solutions

Studying protein interactions at low temperatures has important implications for optimizing cryostorage processes of biological tissue, food, and protein-based drugs. One of the major issues is related to the formation of ice nanocrystals, which can occur even in the presence of cryoprotectants and can lead to protein denaturation. The presence of ice nanocrystals in protein solutions poses several challenges since, contrary to microscopic ice crystals, they can be difficult to resolve and can complicate the interpretation of experimental data. Here, using a combination of small- and wide-angle X-ray scattering (SAXS and WAXS), we investigate the structural evolution of concentrated lysozyme solutions in a cryoprotected glycerol-water mixture from room temperature (T = 300 K) down to cryogenic temperatures (T = 195 K). Upon cooling, we observe a transition near the melting temperature of the solution (T ≈ 245 K), which manifests both in the temperature dependence of the scattering intensity peak position reflecting protein-protein length scales (SAXS) and the interatomic distances within the solvent (WAXS). Upon thermal cycling, a hysteresis is observed in the scattering intensity, which is attributed to the formation of nanocrystallites in the order of 10 nm. The experimental data are well described by the two-Yukawa model, which indicates temperature-dependent changes in the short-range attraction of the protein-protein interaction potential. Our results demonstrate that the nanocrystal growth yields effectively stronger protein-protein attraction and influences the protein pair distribution function beyond the first coordination shell.

The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins

Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.

Physicochemical characterization of changes in pea protein as the result of cold extrusion

Pea protein is a popular plant-based protein for mimicking textures in meat and dairy analogues which are more sustainable than their animal-based counterparts. However, precise mechanisms for generating specific textures through different processing methods are still being evaluated. This work utilizes a novel low-temperature extrusion process to selectively alter the chemical structure of pea protein. Changes in secondary structure, surface hydrophobicity, electrostatic interactions, and disulfide bonding are characterized through FTIR, ANS- probes, zeta potential, and SDS-PAGE. Extrudates are further characterized using texture parameter analysis. It was found that a linear combination of physicochemical data, generated with multiple linear regression modelling, led to reasonable estimates of the specific mechanical energy and textural properties. This work offers a new method of reactive extrusion to selectively modify interactions in pea protein using low temperature extrusion, and applications may include fatty textures, since the extrudates are found to be largely stabilized through hydrophobic interactions evaluated with surface hydrophobicity measurements.

Folding-unfolding asymmetry and a RetroFold computational algorithm

We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.

Broad-temperature-range mechanically tunable hydrogel microcapsules for controlled active release

Here, we report PNIPAm-co-PEGDA hydrogel shelled microcapsules with a thin oil layer to achieve tunable thermo-responsive release of the encapsulated small hydrophilic actives. We use a microfluidic device integrated with a temperature-controlled chamber for consistent and reliable production of the microcapsules by utilizing triple emulsion drops (W/O/W/O) with a thin oil layer as capsule templates. The interstitial oil layer between the aqueous core and the PNIPAm-co-PEGDA shell provides a diffusion barrier for the encapsulated active until the temperature reaches a critical point above which the destabilization of interstitial oil layer occurs. We find that the destabilization of the oil layer with temperature increase is caused by outward expansion of the aqueous core due to volume increase and the radial inward compression from the deswelling of the thermo-responsive hydrogel shell. The copolymerization of NIPAm with PEGDA increases the biocompatibility of the resulting microcapsule while offering the ability to alter the compressive modulus in broad ranges by simply varying crosslinker concentrations thereby to precisely tune the onset release temperature. Based on this concept, we further demonstrate that the release temperature can be enhanced up to 62 °C by adjusting the shell thickness even without varying the chemical composition of the hydrogel shell. Moreover, we incorporate gold nanorods within the hydrogel shell to spatiotemporally regulate the active release from the microcapsules by illuminating with non-invasive near infrared (NIR) light.

A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion

An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.

Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties

The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.

Some Clues about Enzymes from Psychrophilic Microorganisms

Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.

A Rationalization of the Effect That TMAO, Glycine, and Betaine Exert on the Collapse of Elastin-like Polypeptides

Elastin-like polypeptides (ELPs) are soluble in water at low temperature, but, on increasing the temperature, they undergo a reversible and cooperative, coil-to-globule collapse transition. It has been shown that the addition to water of either trimethylamine N-oxide (TMAO), glycine, or betaine causes a significant decrease of T(collapse) in the case of a specific ELP. Traditional rationalizations of these phenomena do not work in the present case. We show that an alternative approach, grounded in the magnitude of the solvent-excluded volume effect and its temperature dependence (strictly linked to the translational entropy of solvent and co-solute molecules), is able to rationalize the occurrence of ELP collapse in water on raising the temperature, as well as the T(collapse) lowering caused by the addition to water of either TMAO, glycine, or betaine.

Applying text mining to identify relevant literature in food science: Cold denaturation as a case study

In a research environment characterized by the five V's of big data, volume, velocity, variety, value, and veracity, the need to develop tools that quickly screen a large number of publications into relevant work is an increasing area of concern, and the data-rich food industry is no exception. Here, a combination of latent Dirichlet allocation and food keyword searches were employed to analyze and filter a dataset of 6102 publications about cold denaturation. After using the Python toolkit generated in this work, the approach yielded 22 topics that provide background and insight on the direction of research in this field, as well as identified the publications in this dataset which are most pertinent to the food industry with precision and recall of 0.419 and 0.949, respectively. Precision is related to the relevance of a paper in the filtered dataset and the recall represents papers which were not identified in the screening method. Lastly, gaps in the literature based on keyword trends are identified to improve the knowledge base of cold denaturation as it relates to the food industry. This approach is generalizable to any similarly organized dataset, and the code is available upon request. Practical Application: A common problem in research is that when you are an expert in one field, learning about another field is difficult, because you may lack the vocabulary and background needed to read cutting edge literature from a new discipline. The Python toolkit developed in this research can be applied by any researcher that is new to a field to identify what the key literature is, what topics they should familiarize themselves with, and what the current trends are in the field. Using this structure, researchers can greatly speed up how they identify new areas to research and find new projects.

Cryogenic activity and stability of benzaldehyde lyase enzyme in lipidic mesophases-nanoconfined water

Phytantriol-based lipidic mesophases (LMs) are introduced as a platform for cryoenzymology, which relies on the presence of liquid water in LMs at subzero temperatures. After incorporation into LMs, the model enzyme Benzaldehyde lyase (BAL) shows high cryogenic stability and activity. In contrast, BAL in bulk solution undergoes significant secondary structural transitions caused by low temperatures (cold denaturation), demonstrating the potential of this approach to enable in meso cryoenzymology.

General Counteraction Exerted by Sugars against Denaturants

The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis

Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.

Why small proteins tend to have high denaturation temperatures

Data indicate that small globular proteins (consisting of less than about 70 residues) tend to have high denaturation temperatures. This finding is analysed by comparing experimental denaturation enthalpy and entropy changes of a selected set of small proteins with values calculated on the basis of average and common properties of globular proteins. The conclusion is that the denaturation entropy change is smaller than expected, leading to an increase in denaturation temperature. The proposed molecular rationalization considers the existence of long-wavelength, low-frequency vibrational modes in the native state of small proteins due to their large surface-to-interior ratio. The effect of decreasing the conformational entropy gain associated with denaturation on thermal stability is directly verified by means of an already devised theoretical model [G. Graziano, Phys. Chem. Chem. Phys. 2010, 12, 14245-14252; 2014, 16, 21755-21767].

Effect of sodium thiocyanate and sodium perchlorate on poly(N-isopropylacrylamide) collapse

The T(collapse) of poly(N-isopropylacrylamide), PNIPAM, shows a nonlinear dependence on the concentration of NaSCN or NaClO4; in the case of NaClO4, for example, at very low concentrations of the salt, T(collapse) increases with the concentration, while it has an opposite trend at higher NaClO4 concentrations [J. Am. Chem. Soc., 2005, 127, 14505]. These puzzling experimental data can be rationalized by considering that low charge density and poorly hydrated ions, such as thiocyanate and perchlorate, interact preferentially with the surface of the polymer, and cause an increase of the magnitude of the energetic term that stabilizes swollen conformations at low salt concentrations. However, as both swollen and collapsed PNIPAM conformations are accessible to such ions in view of their large conformational freedom, the difference in the number of ions bound to PNIPAM surface upon collapse changes little on increasing the salt concentration. Thus, the energetic term that favors swollen conformations increases with salt concentration to a lesser extent than the solvent-excluded volume term (linked to the density increase caused by salt addition to water), that favors collapsed conformations, leading to a nonlinear trend of T(collapse).

Tuning the electronic structure properties of MoS2 monolayers with carbon doping

The structural and electronic properties of MoS₂ sheets doped with carbon line domains are theoretically investigated through density functional theory calculations. It is primarily studied how the system's electronic properties change when different domain levels are considered. These changes are also reflected in the geometry of the system, which acquires new properties when compared to the pristine structure. We predict, both qualitative and quantitatively, how the energy gap changes as a function of domain types. Strikingly, the band structure for the doped system shows semiconducting behavior with an indirect-bandgap, which is narrower than the one for bulk MoS₂. This is an important feature as far as gap tuning engineering is concerned. It has a profound impact on the applicability of these systems in electronic devices, where an indirect bandgap favors the quantum yield efficiency.

Contrasting the hydration thermodynamics of methane and methanol

The hydration thermodynamics of methane and methanol depend on the cavity creation work and energy of van der Waals and H-bonding attractions.

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.

Cold survival strategies for bacteria, recent advancement and potential industrial applications

Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.

The cold denaturation of IscU highlights structure–function dualism in marginally stable proteins

Proteins undergo both cold and heat denaturation, but often cold denaturation cannot be detected because it occurs at temperatures below water freezing. Proteins undergoing detectable cold as well as heat denaturation yield a reliable curve of protein stability. Here we use bacterial IscU, an essential and ancient protein involved in iron cluster biogenesis, to show an important example of unbiased cold denaturation, based on electrostatic frustration caused by a dualism between iron–sulfur cluster binding and the presence of a functionally essential electrostatic gate. We explore the structural determinants and the universals that determine cold denaturation with the aid of a coarse grain model. Our results set a firm point in our understanding of cold denaturation and give us general rules to induce and predict protein cold denaturation. The conflict between ligand binding and stability hints at the importance of the structure–function dualism in protein evolution.

On the cononsolvency behaviour of hydrophobic clusters in water–methanol solutions

The solvent-excluded volume effect cannot rationalize the cononsolvency phenomenon of polymers, such as PNIPAM, in water–methanol solutions.

Reply to the ‘Comment on “On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility” Phys. Chem. Chem. Phys., 2018, , DOI: 10.1039/C7CP03698A’

In this work we show that a theory aiming to describe solubility must have into account both steric and molecular interaction effects.

Comment on “Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors” by A. Battisti, G. Ciasca, A. Grottesi and A. Tenenbaum, Phys. Chem. Chem. Phys., 2017, 19, 8435

Chain compaction is favoured on raising the temperature because the entropy gain of water molecules due to the decrease in solvent-excluded volume increases with temperature.

Comment on “On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility” Phys. Chem. Chem. Phys., 2016, , 23006

Indole solubility is larger in methanol than in water due to lower magnitude of the cavity creation work.

Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995

In a recent article, Kremer and co-workers have combined NMR measurements and very long, all-atom MD simulations to strengthen their original claim that PNIPAM cononsolvency in water-methanol solutions is driven by the ability of MeOH molecules to bridge different monomers far away along the polymeric chain. In this comment, the results presented by Kremer and co-workers are reviewed, analyzed, and questioned regarding their ability to provide support to the bridging mechanism. Here, some pieces of evidence are provided to show that: (1) the solvent-excluded volume effect plays always a fundamental role in polymer collapse; (2) PNIPAM cononsolvency is caused by the geometric-energetic frustration experienced by the polymer when it can interact with both water and methanol molecules at the same time.

Effect of heavy water on the conformational stability of globular proteins

It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. The latter has to be due to the strength of protein-water van der Waals attractions which are weaker in heavy water due to the smaller molecular polarizability of D₂ O compared with that of H₂ O molecules. Since protein-water van der Waals attractions occur more in the denatured than in the native state, this contribution leads to a stabilization of the latter through a destabilization of the former.

Protein unfolding mechanisms and their effects on folding experiments

In this review, I discuss the various methods researchers use to unfold proteins in the lab in order to understand protein folding both in vitro and in vivo. The four main techniques, chemical-, heat-, pressure- and force-denaturation, produce distinctly different unfolded conformational ensembles. Recent measurements have revealed different folding kinetics from different unfolding mechanisms. Thus, comparing these distinct unfolded ensembles sheds light on the underlying free energy landscape of folding.

An optimized strategy to measure protein stability highlights differences between cold and hot unfolded states

Macromolecular crowding ought to stabilize folded forms of proteins, through an excluded volume effect. This explanation has been questioned and observed effects attributed to weak interactions with other cell components. Here we show conclusively that protein stability is affected by volume exclusion and that the effect is more pronounced when the crowder's size is closer to that of the protein under study. Accurate evaluation of the volume exclusion effect is made possible by the choice of yeast frataxin, a protein that undergoes cold denaturation above zero degrees, because the unfolded form at low temperature is more expanded than the corresponding one at high temperature. To achieve optimum sensitivity to changes in stability we introduce an empirical parameter derived from the stability curve. The large effect of PEG 20 on cold denaturation can be explained by a change in water activity, according to Privalov's interpretation of cold denaturation.

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

Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic pressure can both increase and decrease protein stability. These observations suggest that volume changes upon protein unfolding can be both positive and negative. The molecular details of this difference in sign of volume changes have been puzzling the field for the past 50 years. Here we present a comprehensive thermodynamic model that provides in-depth analysis of the contribution of various molecular determinants to the volume changes upon protein unfolding. Comparison with experimental data shows that the model allows quantitative predictions of volume changes upon protein unfolding, thus paving the way to proteome-wide computational comparison of proteins from different extremophilic organisms.

Proteins can be both stabilized and destabilized by pressure. Here the authors analyse the factors contributing to both negative and positive protein volume change upon denaturation, and shed light on the molecular determinants allowing proteins to be stable at high pressures.