Partial Molar Volume Change Research Articles

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics method

A multibaric-multithermal molecular dynamics (MD) simulation of a 10-residue protein, chignolin, was performed. All-atom model with the Amber parm99SB force field was used for the protein and the TIP3P model was used for the explicit water molecules. This MD simulation covered wide ranges of temperature between 260 and 560 K and pressure between 0.1 and 600 MPa and sampled many conformations without getting trapped in local-minimum free-energy states. Folding events to the native β-hairpin structure occurred five times and unfolding events were observed four times. As the temperature and/or pressure increases, fraction of folded chignolin decreases. The partial molar enthalpy change ΔH and partial molar volume change ΔV of unfolding were calculated as ΔH = 24.1 ± 4.9 kJ/mol and ΔV = -5.6 ± 1.5 cm(3)/mol, respectively. These values agree well with recent experimental results. Illustrating typical local-minimum free-energy conformations, folding and unfolding pathways were revealed. When chignolin unfolds from the β-hairpin structure, only the C terminus or both C and N termini open first. It may undergo an α-helix or 3(10)-helix structure and finally unfolds to the extended structure. Difference of the mechanism between temperature denaturation and pressure denaturation is also discussed. Temperature denaturation is caused by making the protein transferred to a higher entropy state and making it move around more with larger space. The reason for pressure denaturation is that water molecules approach the hydrophobic residues, which are not well hydrated at the folded state, and some hydrophobic contacts are broken.

Measurement of the change in partial molar volume during electrode reaction by gravity electrode—II. Examination of the accuracy of the measurement

The reliability of the measurement of the change in partial molar volume between product and reactant ions measured by gravity electrode (GE) was examined by the thermodynamic measurement of pycnometer (PM). Since the PM method requires an experimental equation of the apparent molar volume to calculate the partial molar volumes of the individual ions, the most suitable experimental equation must be first determined. As a test reaction for the experiment, oxidation of ferrocyanide (FERO) ion to ferricyanide (FERI) ion was adopted. After fitting several experimental equations to the data of the apparent molar volumes by the PM method, the calculated changes in the partial molar volume were compared with the data of the GM method. Then, it is concluded that the polynomial with a degree of 3 of the logarithm of the molality of the FERO ion suggests the most suitable equation. As a result, the reliability of the GE method was also experimentally validated.

Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume: Time-Resolved Surficial Kirkwood-Buff Approach

The influence of hydrostatic pressure on the partial molar volume (PMV) of the protein apomyoglobin (AMb) was investigated by all-atom molecular dynamics (MD) simulations. Using the time-resolved Kirkwood-Buff (KB) approach, the dynamic behavior of the PMV was identified. The simulated time average value of the PMV and its reduction by 3000 bar pressurization correlated with experimental data. In addition, with the aid of the surficial KB integral method, we obtained the spatial distributions of the components of PMV to elucidate the detailed mechanism of the PMV reduction. New R-dependent PMV profiles identified the regions that increase or decrease the PMV under the high pressure condition. The results indicate that besides the hydration in the vicinity of the protein surface, the outer space of the first hydration layer also significantly influences the total PMV change. These results provide a direct and detailed picture of pressure induced PMV reduction.

Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory

CO escaping pathways of Myoglobin were investigated in terms of 3D distribution function which was calculated by the 3D-RISM theory. The partial molar volume changes through the CO escaping pathways show excellent agreement with those from the experiment.

A Comprehensive Model for Packing and Hydration for Amyloid Fibrils of β2-Microglobulin

Volume can provide informative structural descriptions of macromolecules such as proteins in solution because a final volumetric outcome accompanies the exquisite equipoise of packing effects between residues, and residues and waters inside and outside proteins. Here we performed systematic investigations on the volumetric nature of the amyloidogenic conformations of beta2-microglobulin (beta2-m) and its amyloidogenic core peptide, K3, using a high precision densitometer. The transition from the acid-denatured beta2-m to the mature amyloid fibrils was accompanied by a positive change in the partial specific volume, which was larger than that observed for the transition from the acid-denatured beta2-m to the native structure. The data imply that the mature amyloid fibrils are more voluminous than the native structure because of a sparse packing density of side chains. In contrast, the formation of the mature amyloid-like fibrils of the K3 from the random coil was followed by a considerable decrease in the partial specific volume, suggesting a highly compact core structure. Interestingly, the immature amyloid-like fibrils of beta2-m exhibited a volume intermediate between those of the mature fibrils of beta2-m and K3, because of the core structure at their center and the relatively noncompact region around the core with much hydration. These volumetric differences would result from the nature of main-chain-dominated fibrillogenesis. We suggest comprehensive models for these three types of fibrils illustrating packing and hydrational states.

Uncovering the physical origin of the difference between aliphatic chain and aromatic ring in the “hydrophobic” effects on partial molar volume

The partial molar volume changes in the transfer of several hydrophobic molecules, which are composed of aromatic rings and an aliphatic chain of different lengths, from carbon tetrachloride to water (DeltaV(hyd)) are calculated using the three-dimensional interaction site model theory of molecular solvation. The theory reproduces recent experimental observations: the addition of a methyl group decreases DeltaV(hyd); in contrast, the addition of an aromatic ring increases DeltaV(hyd). The discrepancy is found to originate from the difference between chain and ring structures rather than that between aliphaticity and aromaticity. Furthermore, a general rule of the variation in DeltaV(hyd) due to the addition of a hydrocarbon is found through the theoretical analysis. An outward addition at the trans position, which is to form chain structure, decreases DeltaV(hyd), while an inward addition at the cis position, which is to form ring structure, increases DeltaV(hyd). This is explained in terms of solvent packing rather than the so-called hydrophobic hydration. The present findings argue against the traditional idea that the hydrophobic hydration can be represented by the observed values of DeltaV(hyd).

Theoretical study of the partial molar volume change associated with the pressure‐induced structural transition of ubiquitin

The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.

Influence of Hydrostatic Pressure and Cosolutes on RNA Tertiary Structure

RNAs fold into complex three-dimensional structures that are critical to their various biological functions. These structures often form independently of the RNA secondary structure, and the three-dimensional fold is stabilized by specific tertiary interactions between various motifs. However, the detailed molecular mechanisms that drive formation of these RNA tertiary interactions are not well understood. The most commonly used variables for probing the thermodynamics or kinetics of RNA−RNA interactions are temperature, metal ion concentration, and chemical denaturant concentration. In this study, the effects of hydrostatic pressure and nondenaturing cosolutes were examined. The commonly occurring GAAA tetraloop−receptor RNA tertiary motif was used as a model system, with formation of this interaction assayed by fluorescence resonance energy transfer. The results showed that the GAAA tetraloop−receptor interaction is slightly destabilized by hydrostatic pressure, and analysis of the pressure data yielded the change in partial molar volume for this RNA−RNA interaction. Polyethylene glycol and dextran cosolutes were both shown to favor formation of the tertiary structure, whereas sucrose and glycerol had little effect on the folding of the RNA. These results demonstrate that hydrostatic pressure and nondenaturing cosolute concentration can be useful variables for investigating tertiary or intermolecular RNA−RNA interactions.

Theoretical Study of the Cosolvent Effect on the Partial Molar Volume Change of Staphylococcal Nuclease Associated with Pressure Denaturation

We explain the molecular mechanism of the effect of urea and glycerol cosolvents on the partial molar volume (PMV) change associated with the pressure denaturation of staphylococcal nuclease (SNase) protein recently observed in experiments. Native and denatured conformations of SNase are produced by using molecular dynamics simulations in water, and the PMV is obtained from the integral equation theory of molecular liquids called 3D-RISM, which is based on statistical mechanics. The PMV of the native SNase in water predicted by 3D-RISM theory is in good agreement with experiment. The PMV changes associated with pressure denaturation in water and in water-urea and water-glycerol mixtures are qualitatively reproduced. By analyzing the results obtained, we found two interesting cosolvent effects on the PMV: (1) both urea and glycerol cosolvents increase the PMVs of both native and denatured SNase compared to those in water and (2) both urea and glycerol cosolvents increase the PMV of denatured SNase more than that of native SNase. We also showed that these two observations can be explained in terms of the thermal volume, which is related to the packing effect of solvent molecules.

Theoretical Study of Volume Changes Accompanying Xenon−Lysozyme Binding: Implications for the Molecular Mechanism of Pressure Reversal of Anesthesia

The change in partial molar volume (PMV) accompanying the xenon-lysozyme binding was investigated for elucidating the molecular mechanism of the pressure reversal of general anesthesia, using the three-dimensional reference interaction site model theory of molecular solvation. An increase of the PMV from xenon binding to the substrate binding site of lysozyme was found, and the binding is suppressed by pressure, while the internal site binding did not change the PMV. The PMV change was analyzed by decomposing it into several contributions from geometry and hydration. We also analyzed the hydration change due to the binding. From the results, we draw a molecular picture of the PMV change accompanying xenon-lysozyme binding, which gives a possible mechanism of pressure reversal of anesthesia.

Reply to “Comment on ‘Hydrophobic effects on partial molar volume’ ” [J. Chem. Phys. 123, 167103 (2005)

In the Comment on our paper [J. Chem. Phys. 123, 167103 (2005), preceding paper], Graziano argues based on the scaled particle theory that the partial molar volume change in the transfer of a hydrophobic solute from “hypothetical nonpolar water” to water can be explained simply by the difference in the effective size of solvent molecules. Opposing to the argument, we clarify using the reference interaction site model theory that the attractive interactions represented by the hydrogen bonding play an essential role for the volume change, and that the explanation given by Graziano replaces the real physics by a fake model based on an “effective” molecular diameter. We also make a general argument against the use of hard-sphere models when one considers the properties of hydration.

Effect of ω-Hydrogenation on the Adsorption of Fluorononanols at the Hexane/Water Interface: Pressure Effect on the Adsorption of Fluorononanols

The interfacial tension gamma of the hexane solution of 1H,1H-perfluorononanol (FDFC(9)OH) and its omega-hydrogenated analogue, 1H,1H,9H-perfluorononanol (HDFC(9)OH), against water was measured as a function of pressure and concentration at 298.15 K in order to clarify the effect of omega-dipole on the orientation of fluorononanol molecules from the viewpoint of volume. The adsorbed films of both alcohols exhibit two kinds of phase transitions among three different states: the gaseous, expanded, and condensed states. The partial molar volume changes of adsorption - in the expanded and condensed states were evaluated and compared between the two systems. The - values of both alcohols are negative, and thus the alcohol molecules have smaller volume in the adsorbed film than in the bulk solution. Furthermore, the value was obtained through the evaluation of by the density measurement of the bulk hexane solution. It was found that the value of HDFC(9)OH is smaller than that of FDFC(9)OH in the condensed state. On the basis of three matters concerning the molecular structure of alcohols, the occupied area at the interface, and the orientation of FDFC(9)OH in the adsorbed film deduced from the earlier results of X-ray reflectivity measurement, the mean tilt angle of HDFC(9)OH from the interface normal in the condensed film was estimated to be 15 degrees . The thermodynamic estimation demonstrated here is highly valuable one to provide structure information on an adsorbed film.

Hydrophobic effects on partial molar volume

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.

Protein volume changes on cosolvent denaturation

A thermodynamic relationship is obtained which links the effect of a cosolvent on the denaturation equilibrium of a protein to the effect of the cosolvent on the change in partial molar volume (pmv) of a protein on denaturation. The relationship uses the concept of preferential interactions and is exact for an infinitely dilute protein. Analysis of the literature data on protein volume changes suggests that many of the observed volume changes are thermodynamically inconsistent with the corresponding free energy changes, especially at low cosolvent concentrations. It is argued that the most reasonable explanation for this involves cosolvent induced changes in the degree of protein–protein association.

The Kirkwood–Buff theory and the effect of cosolvents on biochemical reactions

Cosolvents added to aqueous solutions of biomolecules profoundly affect protein stability, as well as biochemical equilibria. Some cosolvents, such as urea and guanidine hydrochloride, denature proteins, whereas others, such as osmolytes and crowders, stabilize the native structures of proteins. The way cosolvents interact with biomolecules is crucial information required to understand the cosolvent effect at a molecular level. We present a statistical mechanical framework based upon Kirkwood-Buff theory, which enables one to extract this picture from experimental data. The combination of two experimental results, namely, the cosolvent-induced equilibrium shift and the partial molar volume change upon the reaction, supplimented by the structural change, is shown to yield the number of water and cosolvent molecules bound or released during a reaction. Previously, denaturation experiments (e.g., m-value analysis) were analyzed by empirical and stoichiometric solvent-binding models, while the effects of osmolytes and crowders were analyzed by the approximate molecular crowding approach for low cosolvent concentration. Here we synthesize these previous approaches in a rigorous statistical mechanical treatment, which is applicable at any cosolvent concentration. The usefulness and accuracy of previous approaches was also evaluated.

Effect of hydrostatic pressure on conformational changes of canine milk lysozyme between the native, molten globule, and unfolded states

The effect of pressure on the unfolding of the native (N) and molten globule (MG) state of canine milk lysozyme (CML) was examined using ultraviolet (UV) spectroscopy at pH 4.5 and 2.0, respectively. It appeared that the thermally induced unfolding was promoted by the increase of pressure from atmospheric to 100 MPa, which indicates that both the N and MG states of CML unfolded with the decrease of the partial molar volume change (Δ V). The volume changes needed for unfolding were estimated from the free energy change vs. pressure plots, and these volume changes became less negative from 20 to 60 °C. The Δ V values at 25 °C were obtained for the N–MG (−46 cm 3/mol) and MG-unfolded-state (U) transition (−40 cm 3/mol). With regards to the MG–U transition, this value is contrastive to that of bovine α-lactalbumin (BLA) (0.9 cm 3/mol), which is homologous to CML. Previous studies revealed that the MG state of CML was significantly more stable, and closer to the N state in structure, than that of BLA. In contrast to the swollen hydrophobic core of the MG state of BLA, our results suggest that the MG state of CML possesses a tightly packed hydrophobic core into which water molecules cannot penetrate.

FT-IR studies of acetylacetonates in supercritical CO2 using a capillary cell at pressures up to 3.1 kbar.

The keto-enol equilibria of the beta-diketones acetylacetone, trifluoroacetylacetone, and hexafluoroacetylacetone were determined using Fourier transform infrared spectroscopy in a novel high-pressure capillary cell. Acetylacetone and its fluorinated analogues were studied as neat liquid and as supercritical CO2 solutions at pressures up to 3.1 kbar. The keto form was found to be favored at high pressure and low temperature. The change in partial molar volume and enthalpy between the keto and enol forms was determined for the acetylacetone and trifluoroacetylacetone. Under all conditions studied, only the enol form of hexafluoroacetylacetone was observed. Based on the thermodynamic data obtained, there appears to be no advantage gained in conducting metal extractions at high pressures and low temperatures using acetylacetone or trifluoroacetylacetone.

Effect of Pressure on the Excited-State Proton Transfer of 3-Hydroxyflavone

We have investigated the effect of pressure on excited-state intramolecular proton transfer (ESIPT) in 3-hydroxyflavone dissolved in four polymeric matrixespoly(methyl methacrylate) (PMMA), poly(vinyl acetate) (PVAc), poly(acrylic acid) (PAA), and cellulose acetate (CAC). We have also determined the change in normalized equilibrium constant (K*) and the change in partial molar volume (ΔV) as a function of pressure. In all matrixes, with an increase of pressure, the fluorescence intensity of the phototautomer decreases. In PMMA, PVAC, and CAC, the equilibrium constant (K) and change of partial molar volume (ΔV) are sensitive to pressure below 30 kbar. The results imply that ESIPT of 3-hydroxyflavone is effectively suppressed by pressure. The anomalous proton-transfer behavior of 3-hydroxyflavone in PAA can be explained by protonation of the carbonyl oxygen.

The volumetric properties of aqueous solutions of glycylglycine and [formula omitted] -serine at elevated temperatures and pressures

Relative densities ρ–ρ0have been measured over an extended concentration range for aqueous solutions of glycylglycine andl-serine in the temperature range 298⩽ (T/K)⩽ 423 and the pressure range 0.10⩽ (p/MPa)⩽ 30.00. Apparent molar volumesVm,φ have been calculated from measured densities and have been used to estimate partial molar volumes at infinite dilution V0. Values of V0obtained for aqueous solutions ofl-serine in water have been combined with previously reported V0values for aqueous solutions of glycine, to obtain estimates of serine side chain contributions to partial molar volumes over an extended temperature and pressure range. The reported volumetric data of glycylglycine have been used to calculate the partial molar volume change associated with the formation of a peptide bond.

A quantitative study of the volume changes resulting from pressure-induced unfolding of m-phenylene ethynylene foldamers in solid PMMA and PtBMA

We have measured the change of the equilibrium constant with pressure for four foldamers of m-phenylene ethynylene. From the change in ln K over short pressure intervals, we have extracted the change in partial molar volume vs pressure in polymethylmethacrylate (PMMA) and polytertbutylmethacrylate (PtBMA). For a given foldamer the ratio of Δ V ′ in the two media is larger for shorter oligomers. The effect of replacing hydrogen by CH 3 in the foldamer is greater in PMMA than in PtBMA. In a given medium, the Δ V ′ per monomer unit is essentially independent of the chain length.