Cold Denaturation Of Proteins Research Articles

Mitigating the Effects of Starch Derivatives on Cold Denaturation of Gluten Protein: Insights from Hydration Capacity and Conformation Behavior.

Mitigating the cold denaturation of gluten protein during frozen storage is crucial for the quality improvement of frozen cereal products. Our previous study observed that starch derivatives, especially short-clustered maltodextrin (SCMD), could significantly improve frozen dough quality, alleviating the deterioration of gluten-network structure. To further reveal the cryoprotection mechanism of SCMD on gluten protein during frozen storage, the modulatory roles of SCMD in the hydration capacity and conformation behavior of gluten protein were explored, in comparison with DE2 maltodextrin (MD) and pregelatinized starch (PGS). Results demonstrated that SCMD significantly facilitated the reservation of bound water and decreased the surface hydrophobicity of gluten protein after 8 weeks of frozen storage. Remarkable effects of SCMD on stabilizing the secondary structure and microenvironment of aromatic amino acids of gluten protein were observed. Further mechanistic investigation showed that when the temperature dropped from 300 to 250 K, the short-clustered structure could stabilize the α-helixes more evidently than linear structures through hydrogen bonds with water and steric hindrance effect, rather than directly with protein. Our findings will provide novel insights into the cold denaturation of gluten protein and useful guidance in selecting the optimum structure to suppress this denaturation, improving the quality of frozen cereal products.

Salt-Specific Suppression of the Cold Denaturation of Thermophilic Multidomain Initiation Factor 2.

Thermophilic proteins and enzymes are attractive for use in industrial applications due to their resistance against heat and denaturants. Here, we report on a thermophilic protein that is stable at high temperatures (Ttrs, hot 67 °C) but undergoes significant unfolding at room temperature due to cold denaturation. Little is known about the cold denaturation of thermophilic proteins, although it can significantly limit their applications. We investigated the cold denaturation of thermophilic multidomain protein translation initiation factor 2 (IF2) from Thermus thermophilus. IF2 is a GTPase that binds to ribosomal subunits and initiator fMet-tRNAfMet during the initiation of protein biosynthesis. In the presence of 9 M urea, measurements in the far-UV region by circular dichroism were used to capture details about the secondary structure of full-length IF2 protein and its domains during cold and hot denaturation. Cold denaturation can be suppressed by salt, depending on the type, due to the decreased heat capacity. Thermodynamic analysis and mathematical modeling of the denaturation process showed that salts reduce the cooperativity of denaturation of the IF2 domains, which might be associated with the high frustration between domains. This characteristic of high interdomain frustration may be the key to satisfying numerous diverse contacts with ribosomal subunits, translation factors, and tRNA.

On the emerging of thawing drip: Role of myofibrillar protein renaturation

This study aimed to facilitate the understanding on the origin of thawing drip under different freezing rate. Eventually we observed significantly greater thaw loss produced by slow freezing (8.58%) as compared to fast freezing (6.41%) after 24 h of thawing. Back to the freezing, ice crystallization induced decline in pH and the cold denaturation of myofibrillar protein. However, independent of freezing rate, we noticed protein renaturation with pH restoring during thawing, evidenced by the decreasing surface hydrophobicity, increasing solubility and thermal stability, and gradually stabilized secondary structure. Meanwhile, the water-holding of myofibrils increased with thawing process along with the rising water mobility. Under fast freezing, the results indicated less extensive protein cold denaturation and lower water mobility during thawing. Besides, we proposed that the microenvironment of lower ionic strength in fast freezing should benefit the protein renaturation and water re-absorption, ultimately contributed to lower thaw loss.

Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage.

The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.

Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage.

The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable‐temperature ion mobility mass spectrometry (VT IM‐MS) allows us to measure the structure of molecules at sub‐ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep‐freezing minimizes denaturation and maintains the native fold and VT IM‐MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.

A simple model of protein cold denaturation

Cold denaturation is a general feature of the conformational stability of globular proteins. Its modelization is still an important goal of biophysics. We present a modified version of the Schellman-Brandts model that is able to reproduce the occurrence of two conformational transitions, cold and hot denaturations. The model suggests that: (a) globular protein cooperativity can be obtained by distinguishing an inner core, buried from water contact, in a spherical globule; (b) the latter is stabilized by the hydrophobic effect that can be modelled by the Gibbs free energy gain associated with the burial of nonpolar side chains in the inner core; (c) cold denaturation comes from the decrease in the stabilization provided by the hydrophobic effect at low temperature.

Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions.

Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the ΔG becoming more negative for the former and less negative for the latter with increasing temperature. Dissection of the free energy curves into enthalpy and entropy contributions, and further separation of the enthalpy term into solute-solute, solute-solvent, and solvent-solvent components provides insight into the physical molecular causes for the distinctive thermodynamic results. Finally, it is reasoned how the opposite temperature dependencies of the two types of hydrophilic interactions provide a rationale for the cold denaturation of proteins.

Protein dynamics implications of the low- and high-temperature denaturation of myoglobin

We reinvestigate a simple model used in the literature concerning the thermodynamic analysis of protein cold denaturation. We derive an exact thermodynamic expression for cold denaturation and give a better approximation than exists in the literature for predicting cold denaturation temperatures in the two-state model. We discuss the "dark-side" implications of this work for previous temperature-dependent protein dynamics experiments and discuss microfluidic experimental technologies, which could explore the thermal stability range of proteins below the bulk freezing point of water.

Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein

Study of cold denaturation is relevant for understanding the freeze tolerant activity of organism at sub-zero environment. The proteins responsible for the survival of these organisms contain abundance of alpha-helix. Here we study the effect of cold temperature on the alpha-helical region of a widely used model system, Trp-cage miniprotein by means of extensive atomistic molecular dynamics simulations in conjunction with replica exchange scheme. We find a helix-to-helix transition when the usual ~3.59 alpha-helix transforms to ~3.7 helix upon cooling below ~230 K. This transition is primarily driven by enthalpy gain from water-water interactions with the significant enhancement of low-density liquid (LDL)-like water at cold temperature. Because the transition from ~3.59-helix to ~3.7-helix occurs at cold temperature, it may be accompanied by cold denaturation of protein. Like the cold denatured state of Trp-cage, type-1 antifreeze proteins (AFP) also have ~3.7 or more residues per helical turn. However, unlike Trp-cage, AFP has the 3.7-helix in its biological active form. Such helical arrangement in AFP facilitates the hydrogen bonding with the surrounding clathrate or ice-like water molecules, which is crucial for the antifreeze activity of AFP.

Cold Denaturation of Proteins: Where Bioinformatics Meets Thermodynamics to Offer a Mechanistic Understanding: Pea Protein As a Case Study.

Protein structure can be altered with heat, but models which predict denaturation show that globular proteins also spontaneously unfold at low temperatures through cold denaturation. By an analysis of the primary structure of pea protein using bioinformatic modeling, a mechanism of pea protein cold denaturation is proposed. Pea protein is then fractionated into partially purified legumin and vicilin components, suspended in ethanol, and subjected to low temperatures (-10 to -20 °C). The structural characterizations of the purified fractions are conducted through FTIR, ζ potential, dynamic light scattering, and oil binding, and these are compared to the results of commercial protein isolates. The observed structural changes suggest that pea protein undergoes changes in structure as the result of low-temperature treatments, which could lead to innovative industrial processing techniques for functionalization by low-temperature processing.

Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach.

Proteins are stable over a narrow temperature range, with hot and cold denaturation occurring outside of this window, both of which adversely affect protein function. While hot unfolding is entropically driven, cold denaturation, on the other hand, results from a more favorable free energy associated with the interaction of water with apolar groups at low temperature. Because of the key role of water in this latter process, capturing cold denaturation using implicit solvent models is challenging. We propose here a novel computational approach to develop an implicit solvent model that accounts for both hot and cold denaturation in simulations involving atomistically detailed protein representations. By mining a large number of protein structures solved by nuclear magnetic resonance, we derive transfer free energy contributions for the backbone and amino acids side chains representing the transfer of these moieties between water at two different temperatures. Using Trp-cage as a model system, we show that the implicit solvent model constructed using these temperature-dependent free energies of transfer recovers the parabolic temperature dependence of protein stability, capturing both hot and cold denaturation. The resulting cold-unfolded conformations show reduced secondary structure content but preserve most of their internal hydrogen-bonding network, in contrast to the extended configurations with no hydrogen-bonding populated during heat-induced denaturation.

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins

Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.

Heightened Cold-Denaturation of Proteins at the Ice-Water Interface.

The process of freezing proteins is widely used in applications ranging from processing and storage of biopharmaceuticals to cryo-EM analysis of protein complexes. The formation of an ice-water interface is a critical destabilization factor for the protein, which can be offset by the use of cryo-protectants. Using molecular dynamics simulation, we demonstrate that the presence of the ice-water interface leads to a lowering of the free-energy barrier for unfolding, resulting in rapid unfolding of the protein. The unfolding process does not require direct adsorption of the protein to the surface, but is rather mediated by nearby liquid molecules that show an increased tendency for hydrating nonpolar groups. The observed enhancement in the cold denaturation process upon ice formation can be mitigated by addition of glucose, which acts as a cryoprotectant through preferential exclusion from side chains of the protein.

The Cold Thermal Response of an Amyloid Oligomer Differs from Typical Globular Protein Cold Denaturation.

In contrast with the general behavior of folded proteins, the cold thermal response of amyloid assemblies is difficult to elicit with simple models. We exploit exhaustive simulations to evaluate the thermal response of a barrel-shaped model amyloid oligomer, with a distinct hydrophobic core akin to that of folded proteins. Cumulative thermal data over the range of 210-483 K indicate a sharp inflection and rise in structural stability as the temperature is decreased below the melting temperature of the water model. This is not commensurate with the equilibrium free energy profile obtained with core packing as the order parameter. However, energetic analyses and the size of their fluctuations indicate the crucial role of hydration in mediating structural transitions, beyond the expected temperature-dependent hydrophobic effect. Structural ordering of the hydration layer over bulk water is maximized at the transition and vanishes at high temperatures. This is a first direct demonstration of the microscopic influence of hydration water on the low-temperature response of an amyloid assembly close to the cryo-regime.

The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin.

An exciting debate arises when microscopic mechanisms involved in the denaturation of proteins at high pressures are explained. In particular, the issue emerges when the hydrophobic effect is invoked, given that hydrophobicity cannot elucidate by itself the volume changes measured during protein unfolding. In this work, we study by the use of molecular dynamics simulations and essential dynamics analysis the relation between the solvation dynamics, volume, and water structure when apomyoglobin is subjected to a hydrostatic pressure regime. Accordingly, the mechanism of cold denaturation of proteins under high-pressure can be related to the disruption of the hydrogen-bond network of water favoring the coexistence of two states, low-density and high-density water, which directly implies in the formation of a molten globule once the threshold of 200 MPa has been overcome.

Water and cold denaturation of small globular proteins

Cold denaturation is an intriguing phenomenon that deserves special attention because its rationalization is surely linked to a deeper understanding of the molecular determinants of the marginal stability of small globular proteins dissolved in water and aqueous solutions. It is here reviewed and discussed a theoretical approach that has offered a reliable explanation for the occurrence of both cold and hot denaturations. A cornerstone of the approach is the recognition of the role played by the density of water and its temperature-dependence that are largely determined by the special energetic and geometric features of H-bonds. In fact, the density of water determines the magnitude of the solvent-excluded volume effect, which is a main ingredient of the hydrophobic effect. The relationship between density and solvent-excluded volume effect establishes a strong connection between the physico-chemical properties of water and the conformational stability of small globular proteins.

The cold denaturation of IscU highlights structure\u2013function 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.

CspB of an arctic bacterium, Polaribacter irgensii KOPRI 22228, confers extraordinary freeze-tolerance.

Freezing temperatures are a major challenge for life at the poles. Decreased membrane fluidity, uninvited secondary structure formation in nucleic acids, and protein cold-denaturation all occur at cold temperatures. Organisms adapted to polar regions possess distinct mechanisms that enable them to survive in extremely cold environments. Among the cold-induced proteins, cold shock protein (Csp) family proteins are the most prominent. A gene coding for a Csp-family protein, cspB, was cloned from an arctic bacterium, Polaribacter irgensii KOPRI 22228, and overexpression of cspB greatly increased the freeze-survival rates of Escherichia coli hosts, to a greater level than any previously reported Csp. It also suppressed the cold-sensitivity of an E. coli csp-quadruple deletion strain, BX04. Sequence analysis showed that this protein consists of a unique domain at its N-terminal end and a well conserved cold shock domain at its C-terminal end. The most common mechanism of Csp function in cold adaption is melting of the secondary structures in RNA and DNA molecules, thus facilitating transcription and translation at low temperatures. P. irgensii CspB bound to oligo(dT)-cellulose resins, suggesting single-stranded nucleic acid-binding activity. The unprecedented level of freeze-tolerance conferred by P. irgensii CspB suggests a crucial role for this protein in survival in polar environments.

Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation.

The hydrophobic effect appears to be a key driving force for many chemical and biological processes, such as protein folding, protein-protein interactions, membrane bilayer self-assembly, and so forth. In this study, we calculated the potential of mean force (PMF) using umbrella sampling technique between different model hydrophobes (methane-methane, cyclobutane-cyclobutane, and between two rodlike hydrophobes) at lower than ambient temperatures (300, 260, and 240 K). We find the appearance of a second solvent-separated minimum at ∼1.0 nm apart from the usual contact and first solvent-separated minimum in the PMF profile of the methane pair at low temperature. In the PMF between both cyclobutane and the rodlike hydrophobe pairs, the second solvent-separated pair (SSSP) becomes even more stable than the first solvent-separated pair (FSSP) at 240 K. Analysis of the water structure shows that, at 240 K, the core water of SSSP for the rodlike hydrophobe pair is more strongly hydrogen bonded and more tetrahedrally oriented than that of the FSSP. Strongly hydrogen-bonded ordered water molecules implicate strong water-water interactions, which are responsible for stabilization of SSSP at low temperature. This weakening of hydrophobic interactions through stabilization of SSSP may play a key role in the cold denaturation of protein.

Yeast Cyclophilins Prevent Cold Denaturation of Proteins

Freezing environments are one of the major challenges faced by many organisms, including Saccharomyces cerevisiae. Exposure to low temperatures reduces protein folding rates and induces the cold denaturation of proteins, necessitating aid from chaperones. In a previous study, we identified 19 chaperone genes, the deletion of which makes the host more vulnerable to freeze‐and‐thaw treatments. Among those, peptidyl–prolyl cis–trans isomerases (PPIases) were the most frequently identified. At low temperatures, peptidyl–prolyl isomerization is a rate‐limiting step in protein folding, and folding intermediates, which are prone to protein aggregation, tend to accumulate. To characterize their mode of function, the identified PPIases were overexpressed in Escherichia coli. Not only did they increase the survival of E. coli during freeze‐and‐thaw treatment at –20 °C, but they also protected β‐galactosidase against freeze‐induced protein denaturation. Purified Cpr1p facilitated the refolding of a slow‐folding substrate protein in vitro. These results suggest that the identified PPIases enhance cold survival of cells by preventing cold‐induced protein denaturation and promoting protein folding.