Measuring the Thermal Unfolding of Lysozyme: A Critical Comparison of Differential Scanning Fluorimetry and Differential Scanning Calorimetry

The thermal unfolding of lysozyme in aqueous solution has been analyzed by (nano) differential scanning fluorimetry (nanoDSF) and differential scanning calorimetry (DSC). In addition, dynamic light scattering (DLS) acquired in parallel to the DSF measurements, was used to confirm that the change in hydrodynamic radius upon unfolding is rather small (RH,f =1.75 nm in the folded state; and RH,u=1.91 nm in the unfolded state). NanoDSF measurements were evaluated to characterize the folding/unfolding transition within the classical two-state folding model. The temperature of unfolding (Tm) is found to be the most robust quantity. The unfolding enthalpyΔ H u ${{\rm \Delta }{H}_{u}}$ and the change of specific heat were also obtained and errors in the range of 5-10 % and 30-50 % were determined, respectively. A comparison of thermodynamic parameters from nanoDSF and DSC measurements provides evidence for an increasing unfolding enthalpyΔ H u ${{\rm \Delta }{H}_{u}}$ with protein concentration. A comparison with data from literature suggests that a weak association in the folded state can lead to the observed change of the unfolding enthalpy. For Δcp significantly higher values is deduced from the analysis of temperature dependent nanoDSF measurements (10 kJ/(K mol)) as compare to DSC (3-5 kJ/(K mol)).

Differential scanning calorimetry of proteins and Zimm-Bragg model in water

Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. Hydrogen bonds play a crucial role in stabilizing the three-dimensional structure of proteins. Naturally, information about the strength of hydrogen bonds is contained in the measured DSC profiles. Despite its obvious importance, there is no approach that would allow the extraction of such information from the heat capacity measurements. In order to connect the measured profile to microscopic properties of a polypeptide chain, a proper model is required to fit. Using recent advances in the Zimm-Bragg (ZB) theory of protein folding in water, we propose a new and efficient algorithm to process the DSC experimental data and to extract the H-bonding energy among other relevant constants. Thus, for the randomly picked set of 33 proteins, we have found a quite narrow distribution of hydrogen bonding energies from 1 to 8 kJ/mol with the average energy of intra-protein hydrogen bonds h¯=4.2±1.5 kJ/mol and the average energy of water-protein bonds as hps¯=3.8±1.5 kJ/mol. This is an important illustration of a tiny disbalance between the water-protein and intraprotein hydrogen bonds. Fitted values of the nucleation parameter σ belong to the range from 0.001 to 0.01, as expected. The reported method can be considered as complementary to the classical two-state approach and together with other parameters provides the protein-water and intraprotein H-bonding energies, not accessible within the two-state paradigm.

Protein conformation and biomolecular condensates

Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.

Denaturation of proteins: electrostatic effects vs. hydration

The unfolding transition of proteins in aqueous solution containing various salts or uncharged solutes is a classical subject of biophysics. In many cases, this transition is a well-defined two-stage equilibrium process which can be described by a free energy of transition ΔG u and a transition temperature T m. For a long time, it has been known that solutes can change T m profoundly. Here we present a phenomenological model that describes the change of T m with the solute concentration c s in terms of two effects: (i) the change of the number of correlated counterions Δn ci and (ii) the change of hydration expressed through the parameter Δw and its dependence on temperature expressed through the parameter dΔc p/dc s. Proteins always carry charges and Δn ci describes the uptake or release of counterions during the transition. Likewise, the parameter Δw measures the uptake or release of water during the transition. The transition takes place in a reservoir with a given salt concentration c s that defines also the activity of water. The parameter Δn ci is a measure for the gain or loss of free energy because of the release or uptake of ions and is related to purely entropic effects that scale with ln c s. Δw describes the effect on ΔG u through the loss or uptake of water molecules and contains enthalpic as well as entropic effects that scale with c s. It is related to the enthalpy of transition ΔH u through a Maxwell relation: the dependence of ΔH u on c s is proportional to the dependence of Δw on temperature. While ionic effects embodied in Δn ci are independent of the kind of salt, the hydration effects described through Δw are directly related to Hofmeister effects of the various salt ions. A comparison with literature data underscores the general validity of the model.

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.

VDAC Gating Thermodynamics, but Not Gating Kinetics, Are Virtually Temperature Independent

The voltage-dependent anion channel (VDAC) is the most abundant protein in the mitochondrial outer membrane and an archetypical β-barrel channel. Here, we study the effects of temperature on VDAC channels reconstituted in planar lipid membranes at the single- and multichannel levels within the 20°C to 40°C range. The temperature dependence of conductance measured on a single channel in 1 M KCl shows an increase characterized by a 10°C temperature coefficient Q₁₀ = 1.22 ± 0.02, which exceeds that of the bathing electrolyte solution conductivity, Q₁₀ = 1.17 ± 0.01. The rates of voltage-induced channel transition between the open and closed states measured on multichannel membranes also show statistically significant increases, with temperatures that are consistent with activation energy barriers of ∼10 ± 3 kcal/mol. At the same time, the gating thermodynamics, as characterized by the gating charge and voltage of equipartitioning, does not display any measurable temperature dependence. The two parameters stay within 3.2 ± 0.2 elementary charges and 30 ± 2 mV, respectively. Thus, whereas the channel kinetics, specifically its conductance and rates of gating response to voltage steps, demonstrates a clear increase with temperature, the conformational voltage-dependent equilibria are virtually insensitive to temperature. These results, which may be a general feature of β-barrel channel gating, suggest either an entropy-driven gating mechanism or a role for enthalpy-entropy compensation.

Effects of Polar Head Nature and Tail Length of Single-Chain Lipids on the Conformational Stability of β-Lactoglobulin

Interaction between β-lactoglobulin and single-chain lipids, differing for either the length of the aliphatic chain or the molecular properties of the headgroup, was investigated at neutral and acidic pH to determine the impact on the thermal stability of the protein. Differential scanning calorimetry results with different fatty acids (from C10:0 to C18:0) show a correlation of both melting temperature and unfolding enthalpy of the protein with the ligand binding affinity, and the maximum effect was found for palmitic acid (PLM). The influence of the lipid polar head was investigated by comparing PLM with lyso-palmitoylphosphatidylcholine (LPC), which possesses the same aliphatic chain. At neutral pH, the stabilizing effect of LPC is less favorable compared to PLM. However, fluorescence results revealed that LPC can bind into the protein calyx even at acidic pH, at variance with fatty acids. Molecular dynamics simulations indicated that this difference is due to the ability of the polar head of LPC to interact with the protein loop that regulates the shift (Tanford transition) between open and closed state of the binding site of β-lactoglobulin. The results provide a rationale for how a ligand has the ability to access the protein active site at acidic conditions by overcoming the Tanford transition, and they demonstrate that β-lactoglobulin can deliver ligands with tailored properties of the polar head in a wide pH range.

Ionic liquids and protein folding-old tricks for new solvents

One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. In this short note, we briefly outline the nature of the parameters associated with different empirical and model-based characterization procedures and point out factors which affect their interpretation when using a base solvent different from water. This review principally describes arguments developed by Wakayama et al., Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry, 2019, edited by Y. Kuroda and F. Arisaka; CMC Publishing House. Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.

Active site-targeted carbon dots for the inhibition of human insulin fibrillation

This work aimed to study the inhibitory mechanism of carbon dots for HI fibrillation using isothermal titration calorimetry.

Use of isothermal titration calorimetry to study surfactant aggregation in colloidal systems

BACKGROUND

Isothermal titration calorimetry (ITC) is a general technique that allows for precise and highly sensitive measurements. These measurements may provide a complete and accurate thermodynamic description of association processes in complex systems such as colloidal mixtures.

SCOPE OF THE REVIEW

This review will address uses of ITC for studies of surfactant aggregation to form micelles, with emphasis on the thermodynamic studies of homologous surfactant series. We will also review studies on surfactant association with polymers of different molecular characteristics and with colloidal particles.

GENERAL SIGNIFICANCE

ITC studies on the association of different homologous series of surfactants provide quantitative information on independent contribution from their apolar hydrocarbon chains and polar headgroups to the different thermodynamic functions associated with micellization (Gibbs energy, enthalpy and entropy). Studies on surfactant association to polymers by ITC provide a comprehensive description of the association process, including examples in which particular features revealed by ITC were elucidated by using ancillary techniques such as light or X-ray scattering measurements. Examples of uses of ITC to follow surfactant association to biomolecules such as proteins or DNA, or nanoparticles are also highlighted. Finally, recent theoretical models that were proposed to analyze ITC data in terms of binding/association processes are discussed.

MAJOR CONCLUSIONS

This review stresses the importance of using direct calorimetric measurements to obtain and report accurate thermodynamic data, even in complex systems. These data, whenever possible, should be confirmed and associated with other ancillary techniques that allow elucidation of the nature of the transformations detected by calorimetric results, providing a complete description of the process under scrutiny.

On the mechanism of cold denaturation

A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.

Cold denaturation of α-synuclein amyloid fibrils

Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α-Synuclein fibrils cold-denatured to monomers at 0-20 °C and heat-denatured at 60-110 °C. Meanwhile, the fibrils of β2-microglobulin, Alzheimer's Aβ1-40/Aβ1-42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α-synuclein fibrils. We propose that although cold-denaturation is common to both native proteins and misfolded fibrillar states, the main-chain dominated amyloid structures may explain amyloid-specific cold denaturation arising from the unfavorable burial of charged side-chains in fibril cores.

Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.

Notable Stabilization of α-Chymotrypsin by the Protic Ionic Additive, [ch][dhp]: Calorimetric Evidence for a Fine Enthalpy/Entropy Balance

An impact of 0.5 to 3 M choline dihydrogen phosphate, [ch][dhp], the biotechnologically relevant ionic substance, on the thermal stability of a model globular protein, α-chymotrypsin (α-CT), has been studied exploiting the highly sensitive differential scanning calorimetry (DSC) technique. The notable overall stabilizing effect of 11 ± 2 K regarding the thermal transition (melting) temperature, T m , has been detected. For this kind of series, for the first time, the calorimetric melting enthalpy (ΔH cal) and transition entropy (ΔS m ) parameters have been determined simultaneously throughout. The first analysis indicated a two-phase impact implying (a) the initial, dramatic drop in both ΔH cal and ΔS m , obviously connected to specific, direct interaction between the [ch][dhp] components and α-CT's charged groups (within 0 to 1 mol/L [ch][dhp]), leading to the essential rearrangement of the interfacial hydrogen-bonded (HB) network; and (b) the follow-up (within 1 to 3.0 mol/L [ch][dhp]), modest changes in ΔH cal and lack of changes in ΔS m , seemingly connected with a subsequent steady strengthening of already reformed HB network, respectively. These changes, presumably, are primarily facilitated by Coulombic interactions between the [dhp] anions and solvent-exposed positively charged amino groups of α-CT.

Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative

The thermodynamics of binding reactions is usually studied in the framework of the linear van't Hoff analysis of the temperature dependence of the equilibrium constant. The logarithm of the equilibrium constant is plotted versus inverse temperature to discriminate between two terms: an enthalpic contribution that is linear in the inverse temperature, and a temperature-independent entropic contribution. When we apply this approach to a particular case-blockage of the anthrax PA(63) channel by a multicharged cyclodextrin derivative-we obtain a nearly linear behavior with a slope that is characterized by enthalpy of about 1 kcal/mol. In contrast, from blocker partitioning between the channel and the bulk, we estimate the depth of the potential well for the blocker in the channel to be at least 8 kcal/mol. To understand this apparent discrepancy, we use a simple model of particle interaction with the channel and show that this significant difference between the two estimates is due to the temperature dependence of the physical forces between the blocker and the channel. In particular, we demonstrate that if the major component of blocker-channel interaction is van der Waals interactions and/or Coulomb forces in water, the van't Hoff enthalpy of the binding reaction may be close to zero or even negative, including cases of relatively strong binding. The results are quite general and, therefore, of importance for studies of enzymatic reactions, rational drug design, small-molecule binding to proteins, protein-protein interactions, and protein folding, among others.

Physical origin of hydrophobicity studied in terms of cold denaturation of proteins: comparison between water and simple fluids

A clue to the physical origin of the hydrophobicity is in the experimental observations, which show that it is weakened at low temperatures. By considering a solvophobic model protein immersed in water and three species of simple solvents, we analyze the temperature dependence of the changes in free energy, energy, and entropy of the solvent upon protein unfolding. The angle-dependent and radial-symmetric integral equation theories and the morphometric approach are employed in the analysis. Each of the changes is decomposed into two terms, which depend on the excluded volume and on the area and curvature of the solvent-accessible surface, respectively. The excluded-volume term of the entropy change is further decomposed into two components representing the protein-solvent pair correlation and the protein-solvent-solvent triplet and higher-order correlation, respectively. We show that water crowding in the system becomes more serious upon protein unfolding but this effect becomes weaker as the temperature is lowered. If the hydrophobicity originated from the water structuring near a nonpolar solute, it would be strengthened upon lowering of the temperature. Among the three species of simple solvents, considerable weakening of the solvophobicity at low temperatures is observed only for the solvent where the particles interact through a strong attractive potential and the particle size is as small as that of water. Even in the case of this solvent, however, cold denaturation of a protein cannot be reproduced. It would be reproducible if the attractive potential was substantially enhanced, but such enhancement causes the appearance of the metastability limit for a single liquid phase.

On the molecular origin of cold denaturation of globular proteins

A polypeptide chain can adopt very different conformations, a fundamental distinguishing feature of which is the water accessible surface area, WASA, that is a measure of the layer around the polypeptide chain where the center of water molecules cannot physically enter, generating a solvent-excluded volume effect. The large WASA decrease associated with the folding of a globular protein leads to a large decrease in the solvent-excluded volume, and so to a large increase in the configurational/translational freedom of water molecules. The latter is a quantity that depends upon temperature. Simple calculations over the -30 to 150 °C temperature range, where liquid water can exist at 1 atm, show that such a gain decreases significantly on lowering the temperature below 0 °C, paralleling the decrease in liquid water density. There will be a temperature where the destabilizing contribution of the polypeptide chain conformational entropy exactly matches the stabilizing contribution of the water configurational/translational entropy, leading to cold denaturation.

A theoretical analysis on characteristics of protein structures induced by cold denaturation

Yeast frataxin is a protein exhibiting cold denaturation at an exceptionally high temperature (280 K). We show that the microscopic mechanism of cold denaturation, which has recently been suggested by us [Yoshidome and Kinoshita, Phys. Rev. E 79, 030905(R) (2009)], is also applicable to yeast frataxin. The hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach is employed for calculating hydration thermodynamic quantities of the protein with a prescribed structure. In order to investigate the characteristics of the cold-denatured structures of yeast frataxin, we consider the entropy change upon denaturation comprising the loss of the water entropy and the gain in the protein conformational entropy. The minimum and maximum values of the conformational-entropy gain (i.e., the range within which the exact value lies) are estimated via two routes. The range of the water-entropy loss is then determined from the entropy change experimentally obtained [Pastore et al., J. Am. Chem. Soc. 129, 5374 (2007)]. We calculate the water-entropy loss upon the transition from the native structure to a variety of unfolded structures. We then select the unfolded structures for which the water-entropy loss falls within the determined range. The selection is performed at cold and heat denaturation temperatures of yeast frataxin. The structures characterizing cold and heat denaturations are thus obtained. It is found that the average values of the radius of gyration, excluded volume, and water-accessible surface area for the cold-denatured structures are almost the same as those for the heat-denatured ones. We theoretically estimate the cold denaturation temperature of yeast frataxin from the experimental data for the enthalpy, entropy, and heat-capacity changes upon denaturation. The finding is that the temperature is considerably higher than 273 K. These results are in qualitatively good accord with the experimental observations.

Hydrophobicity at low temperatures and cold denaturation of a protein

We elucidate the microscopic mechanism of the weakening of the hydrophobicity at low temperatures by investigating cold denaturation of a protein. We employ an elaborate statistical-mechanical theory combined with a realistic water model. At low temperatures, the ordered structure with enhanced hydrogen bonds of water molecules is formed near nonpolar groups, leading to entropic loss and energy gain which are both quite large. However, they are canceled out and make no contribution to the free-energy change. We argue that a different factor, which is responsible for the weakening of the hydrophobicity at low temperatures, induces cold denaturation.