Relaxational contributions to protein compressibility from ultrasonic data

Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations

The pressure tolerance of monomeric α-actin proteins from the deep-sea fish Coryphaenoides armatus and C. yaquinae was compared to that of non-deep-sea fish C. acrolepis, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from C. armatus and C. yaquinae have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to C. acrolepis, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.

Compressibility changes accompanying conformational transitions of apomyoglobin

We used high-precision density and ultrasonic velocity measurements to characterize the native (N), molten globule (MG), and unfolded (U) conformations of apomyoglobin. The molten globule states that were studied in this work include the MG(pH4)(NaCl) state observed at pH 4 and 20 mM NaCl, the MG(pH4)(NaTCA) state observed at pH 4 and 20 mM sodium trichloracetate (NaTCA), the MG(pH2)(NaCl) state observed at pH 2 and 200 mM NaCl, and the MG(pH2)(NaTCA) state observed at pH 2 and 20 mM NaTCA. We used our densimetric and acoustic data to evaluate changes in adiabatic compressibility associated with the acid- or salt-induced N-to-MG, MG-to-U, MG-to-MG, and U-to-MG transitions of the protein. The N-to-MG(pH4)(NaCl) and N-to-MG(pH4)(NaTCA) transitions are accompanied by decreases in compressibility of -(3.0 +/- 0.6) x 10(-6) and -(2.0 +/- 0.6) x 10(-6) cm3 g(-1)bar(-1), respectively. The N-to-MG(pH2)(NaCl) and N-to-MG(pH2)(NaTCA) transitions are associated with compressibility changes of -(4.9 +/- 1.1) x 10(-6) and (0.7 +/- 0.9) x 10(-6) cm3 g(-1) bar(-1), respectively. We interpret these data in terms of the degree of unfolding of the various molten globule forms of apomyoglobin. In general, our compressibility data reveal significant disparities between the various equilibrium molten globule states of apomyoglobin while also quantitatively characterizing each of these states. Volumetric insights provided by our data facilitate gaining a better understanding of the folding pathways, intermediates, and kinetics of apomyoglobin folding.

Volumetric properties of proteins

Structural and thermodynamic characterizations of a variety of intra- and intermolecular interactions stabilizing/destabilizing protein systems represent a major part of multidisciplinary efforts aimed at solving the problems of protein folding and binding. To this end, volumetric techniques have been successfully used to gain insights into protein hydration and intraglobular packing. Despite the fact that the use of volumetric measurements in protein-related studies dates back to the 1950s, such measurements still represent a relatively untapped yet potentially informative means for tackling the problems of protein folding and binding. This notion has been further emphasized by recent advances in the development of highly sensitive volumetric instrumentation that has led to intensifying volumetric investigations of protein systems. This paper reviews the volumetric properties of proteins and their low-molecular-weight analogs, in particular, discussing the recent progress in the use of volumetric data for studying conformational transitions of proteins as well as protein-ligand, protein-protein, and protein-nucleic acid interactions.

High pressure simulations of biomolecules

Pressure is a thermodynamic variable which is particularly suitable for exploration of the properties of biological macromolecules. For proteins, in particular, denaturation induced by pressure is different from that induced by temperature or denaturants. The response of proteins to pressure changes can provide information on properties of their native and non-native states. This review focuses on molecular dynamics studies of the effect of pressure on detailed atomic models of proteins. It also reports on other theoretical approaches, such as Monte Carlo simulations, which have been used to study simplified models. Another purpose of this review is to try to point out potential future studies that may be both interesting and feasible, with constantly increasing computing power.

Compressibility of protein transitions

We review the results of compressibility studies on proteins and low molecular weight compounds that model the hydration properties of these biopolymers. In particular, we present an analysis of compressibility changes accompanying conformational transitions of globular proteins. This analysis, in conjunction with experimental compressibility data on protein transitions, were used to define the changes in the hydration properties and intrinsic packing associated with native-to-molten globule, native-to-partially unfolded, and native-to-fully unfolded transitions of globular proteins. In addition, we discuss the molecular origins of predominantly positive changes in compressibility observed for pressure-induced denaturation transitions of globular proteins. Throughout this review, we emphasize the importance of compressibility data for characterizing protein transitions, while also describing how such data can be interpreted to gain insight into role that hydration and intrinsic packing play in modulating the stability of and recognition between proteins and other biologically important compounds.

Characterization of pH-induced transitions of beta-lactoglobulin: ultrasonic, densimetric, and spectroscopic studies

Depending on solution conditions, beta-lactoglobulin can exist in one of its six pH-dependent structural states. We have characterized the acid and basic-induced conformational transitions between these structural states over the pH range of pH 1 to pH 13. To this end, we have employed high-precision ultrasonic and densimetric measurements coupled with fluorescence and CD spectroscopic data. Our combined spectroscopic and volumetric results have revealed five pH-induced transitions of beta-lactoglobulin between pH 1 and pH 13. The first transition starts at pH 2 and is not completed even at pH 1, our lowest experimental pH. This transition is followed by the dimer-to-monomer transition of beta-lactoglobulin between pH 2.5 and pH 4. The dimer-to-monomer transition is accompanied by decreases in volume, v degrees (-0.008(+/-0.003) cm3 x g(-1)), and adiabatic compressibility, k degrees (S) (-(0.7(+/-0.4))x10(-6) cm3 x g(-1) x bar(-1)). We interpret the observed changes in volume and compressibility associated with the dimer-to-monomer transition of beta-lactoglobulin, in conjunction with X-ray crystallographic data, as suggesting a 7 % increase in protein hydration, with the hydration changes being localized in the area of contact between the two monomeric subunits. The so-called N-to-Q transition of beta-lactoglobulin occurs between pH 4.5 and pH 6 and is accompanied by increases in volume, v degrees (0.004(+/-0.003) cm3 x g(-1)), and compressibility, k degrees (S) ((0.7(+/-0.4))x10(-6) cm3 x g(-1) x bar(-1)). The Tanford transition of beta-lactoglobulin is centered at pH 7.5 and is accompanied by a decrease in volume, v degrees (-0.006(+/-0.003) cm3 x g(-1)), and an increase in compressibility, k degrees (S) ((1.5(+/-0.5))x10(-6) cm3 x g(-1) x bar(-1)). Based on these volumetric results, we propose that the Tanford transition is accompanied by a 5 to 10 % increase in the protein hydration and a loosening of the interior packing of beta-lactoglobulin as reflected in a 12 % increase in its intrinsic compressibility. Finally, above pH 9, the protein undergoes irreversible base-induced unfolding which is accompanied by decreases in v degrees (-0.014(+/-0.003) cm3 x g(-1)) and k degrees (S) (-(7.0(+/-0.5))x10(-6) cm3 x g(-1) x bar(-1)). Combining these results with our CD spectroscopic data, we propose that, in the base-induced unfolded state of beta-lactoglobulin, only 80 % of the surface area of the fully unfolded conformation is exposed to the solvent. Thus, in so far as solvent exposure is concerned, the base-induced unfolded states of beta-lactoglobulin retains some order, with 20 % of its amino acid residues remaining solvent inaccessible.

Acid- and base-induced conformational transitions of equinatoxin II

We have investigated the acid- and base-induced conformational transitions of equinatoxin II (EqTxII), a pore-forming protein, by a combination of CD-spectroscopy, ultrasonic velocimetry, high precision densimetry, viscometry, gel electrophoresis, and hemolytic activity assays. Between pH 7 and 2, EqTxII does not exhibit any significant structural changes. Below pH 2, EqTxII undergoes a native-to-partially unfolded transition with a concomitant loss of its rigid tertiary structure and the formation of a non-native secondary structure containing additional alpha-helix. The acid-induced denatured state of EqTxII exhibits a higher intrinsic viscosity and a lower adiabatic compressibility than the native state. Above 50 degrees C, the acid-induced denatured state of EqTxII reversibly denatures to a more unfolded state as judged by the far UV CD spectrum of the protein. At alkaline pH, EqTxII undergoes two base-induced conformational transitions. The first transition occurs between pH 7 and 10 and results in a partial disruption of tertiary structure, while the secondary structure remains largely preserved. The second transition occurs between pH II and 13 and results in the complete loss of tertiary structure and the formation of a non-native, more alpha-helical secondary structure. The acid- and base-induced partially unfolded states of EqTxII form water-soluble oligomers at low salt, while at high salt (> 350 mM NaCl), the acid-induced denatured state precipitates. The hemolytic activity assay shows that the acid- and base-induced denatured states of EqTxII exhibit significantly reduced activity compared to the native state.

Correlation between drug release kinetics from proteineous matrices and protein folding: elasticity and compressibility study

Naproxen sodium (NS) release mechanism from proteineous matrices based on egg albumin (EA) and bovine serum albumin (BSA) was investigated by several physico-chemical methods. The gel strength, modulus of elasticity and erosion properties of the matrices were studied and correlated with drug release kinetics. The results revealed that NS release rate from EA and BSA matrices was markedly different, indicating the significant role of protein nature and conformation on matrix behavior. Unexpectedly it was found that incorporation of NS to EA matrix increased gel strength and modulus of elasticity and decreased matrix erosion. This effect was dependent on NS concentration in the matrix. In contrast to EA, BSA behaved as a non-gelling matrix and was unable to retard drug release because of its high solubility. The influence of NS on protein folding and compressibility in protein solutions was studied using densitometric and ultrasonic techniques. Adiabatic compressibility measurements revealed that NS caused unfolding of EA, an effect which led to a decrease in EA intrinsic compressibility and the exposure of atomic side groups buried in protein interior. Unfolding of EA led to an increase of modulus of elasticity in solution (measured by ultrasonic velocimetry technique) which is in correlation with the modulus of elasticity measurements of gelled tablets (measured by Instron). In concentrated EA solutions, the results showed a large increase in EA compressibility and ultrasonic absorption in the presence of NS indicating a strong aggregation of the denatured state of EA. Regarding BSA, the results suggested that NS affected the packing of the protein interior, transforming it to a molten globule intermediate state, an effect that led to an increase in BSA compressibility. At high BSA concentrations, aggregation of the molten globule state was observed as indicated by an increase of BSA compressibility and ultrasonic absorption values.

Volumetric and spectroscopic characterizations of the native and acid-induced denatured states of staphylococcal nuclease

We have characterized the acid-induced denaturation of staphylococcal nuclease (SNase) at different urea concentrations by a combination of ultrasonic velocimetry, high precision densimetry, and CD spectroscopy. Our CD spectroscopic results suggest that, at low salt and acidic pH, the protein is unfolded with disrupted secondary and tertiary structures. Furthermore, as judged by far UV CD spectra, the protein is further unfolded at acidic pH upon the addition of urea up to the concentration of 1.5 M. The midpoint of the transition shifts to more neutral pH values and the cooperativity of the transition decreases as the acid-induced denaturation of SNase occurs at higher urea concentrations. We find that the change in volume, Deltav, accompanying the acid-induced denaturation of SNase increases from -0.013 cm(3) g(-1) (-218 cm(3) mol(-1)) in the absence of urea to 0.011 cm(3) g(-1) (185 cm(3) mol(-1)) at 1.5 M urea. At all urea concentrations, the partial specific adiabatic compressibility, k(o)(s), of the protein decreases upon its unfolding with the values of Deltak(o)(s) equal to -6.3x10(-6) (-0.106 cm(3) mol(-1) bar(-1)), -4.5x10(-6) (-0.076 cm(3) mol(-1) bar(-1)), -4.6x10(-6) (-0.077 cm(3) mol(-1) bar(-1)), and -3.8x10(-6) (-0.064 cm(3) mol(-1) bar(-1)) cm(3) g(-1) bar(-1) at urea concentrations of 0, 0.5, 1.0, and 1.5 M, respectively. In general, our volumetric results suggest that the acid-induced denatured state of SNase is only partially unfolded with the solvent-exposed surface area equal to 70-80 % of that expected for the fully extended conformation.

The volume and compressibility changes of lysozyme associated with guanidinium chloride and pressure-assisted unfolding

The apparent specific volumes and isentropic compressibilities of hen egg white lysozyme were measured in aqueous guanidinium chloride solutions at 25 degrees C by means of a vibrational densimeter and a sing-around ultrasonic velocimeter. Little transition attributable to a protein unfolding was detected in the partial specific volume, while the partial specific isentropic compressibility decreased slightly around the transition region. The pressure-assisted unfolding was also investigated in aqueous guanidinium chloride solutions by means of ultraviolet spectroscopy. Assuming a two-state transition model, it was found that the free energy change of unfolding depends almost linearly on pressure and the unfolding reaction is accompanied by a small decrease in volume. The compressibility behavior is in conflict with the notion that a protein structure is almost completely unfolded by guanidinium chloride and most of the amino acid residues in the protein interior are exposed to solvent. These results support the current view that globular proteins have some residual structures even in the unfolded state induced by a strong denaturant.

Hydration of diglycyl tripeptides with non-polar side chains: a volumetric study

We have determined the apparent molar volumes and the apparent molar adiabatic compressibilities at 25 degrees C of 10 X-Gly-Gly and Gly-Gly-X tripeptides in which X represents a residue with a non-polar side chain. We also have determined the changes in volume and compressibility which accompany neutralization of the amino and carboxyl termini in these tripeptides. The mutual influence of the non-polar side chain of the X residue and the terminal amino and carboxyl groups on the hydration of each other depends on the chemical nature of the side chain and the state of ionization of the termini. We interpret our data in terms of the hydration of the component aliphatic, aromatic, and charged atomic groups, as well as the mutual interactions between these groups.

Properties of the protein matrix revealed by the free energy of cavity formation

BACKGROUND

The classical picture of the hydrophobic stabilization of proteins invokes a resemblance between the protein interior and nonpolar solvents, but the extent to which this is the case has often been questioned. The protein interior is believed to be at least as tightly packed as organic crystals, and was shown to have very low compressibility. There is also evidence that these properties are not uniform throughout the protein, and conflicting views exist on the nature of sidechain packing and on its influence on the properties of the protein.

RESULTS

In order to probe the physical properties of the protein, the free energy associated with the formation of empty cavities has been evaluated for two proteins: barnase and T4 lysozyme. To this end, the likelihood of encountering such cavities was computed from room temperature molecular dynamics trajectories of these proteins in water. The free energy was evaluated in each protein taken as a whole and in submolecular regions. The computed free energies yielded information on the manner in which empty space is distributed in the system, while the latter undergoes thermal motion, a property hitherto not analyzed in heterogeneous media such as proteins. Our results showed that the free energy of cavity formation is higher in proteins than in both water and hexane, providing direct evidence that the native protein medium differs in fundamental ways from the two liquids. Furthermore, although the packing density was found to be higher in nonpolar regions of the protein than in polar ones, the free energy cost of forming atomic size cavities is significantly lower in nonpolar regions, implying that these regions contain larger chunks of empty space, thereby increasing the likelihood of containing atomic size packing defects. These larger empty spaces occur preferentially where buried hydrophobic sidechains belonging to secondary structures meet one another. These particular locations also appear to be more compressible than other parts of the core or surface of the protein.

CONCLUSIONS

The cavity free energy calculations described here provide a much more detailed physical picture of the protein matrix than volume and packing calculations. According to this picture, the packing of hydrophobic sidechains is tight in the interior of the protein, but far from uniform. In particular, the packing is tighter in regions where the backbone forms less regular hydrogen-bonding interactions than at interfaces between secondary structure elements, where such interactions are fully developed. This may have important implications on the role of sidechain packing in protein folding and stability.

Compressibility and specific volume of actin decrease upon G to F transformation

We measured the densities as well as the sound velocities in solutions of G-actin, F-actin and the reconstituted thin filament. Using the data obtained, we determined their partial specific volumes and partial specific adiabatic compressibilities. The objectives were to investigate the volume change of actin upon polymerization and to detect the conformational change associated with the ca2+-binding to the reconstituted thin filament. The partial specific volume and the partial specific adiabatic compressibility of G-actin were 0.749 cm3/g and 9.3 x 10(-12) cm2/dyne, respectively. The results suggest that G-actin is a rather soft protein compared with other globular proteins. The partial specific volumes of F-actin were in a range of 0.63 -0.66 cm3/g depending on the solvent conditions. The partial specific adiabatic compressibilities of F-actin were negative (-(7-13) x 10(-12) cm3/dyne). These data indicate that the amount of hydration may increase by several times upon polymerization assuming that the size of the cavity remains constant. We detected little difference between the partial specific adiabatic compressibility of the reconstituted thin filament in a Ca2+-bound state and that in a Ca2+-unbound state. This suggests that the Ca2+ binding affected not the subunit itself but the inter-subunit junction.

Hydration and partial compressibility of biological compounds

We review the results of compressibility studies on proteins, nucleic acids, and systematically altered low molecular weight compounds that model the constituents of these biopolymers. The model compound data allow one to define the compressibility properties of water surrounding charged, polar, and nonpolar groups. These results, in conjunction with compressibility data on proteins and nucleic acids, were used to define the properties of water that is perturbed by the presence of these biopolymers in aqueous solutions. Throughout this review, we emphasize the importance of compressibility data for characterizing the hydration properties of solutes (particularly, proteins, nucleic acids, and their constituents), while describing how such data can be interpreted to gain insight into role that hydration can play in modulating the stability of and recognition between biologically important compounds.

Adiabatic compressibility of molten globules

We report the measurement of the adiabatic compressibility beta for "molten globule" states of cytochrome b562 and cytochrome c. Precise density and sound velocity measurements allow determination of beta in aqueous solution. Surprisingly, the molten globule apocytochrome b562 shows a beta comparable to the native holocytochrome b562. We estimated the maximum difference in the hydration contribution to the compressibility of apocytochrome b562 relative to holocytochrome b562 to be only -2.6 x 10(-11) Pa-1. Our results suggest that the intrinsic compressibility and the overall volume fluctuations in the molten globule state differ only slightly from those in the native protein. With cytochrome c we investigated the changes in beta for the transitions from the native to the acid molten globule and expanded premolten globule states. The molten globule at pH 2.2 was found to be somewhat "softer" than the native protein at neutral pH. In contrast, a decrease in beta of the premolten globule indicates an increased penetration of water into the macromolecule. In both of these intermediates the differences in adiabatic compressibility relative to the native state are small in comparison to the range of adiabatic compressibility observed for different native globular proteins.

Hydrational and intrinsic compressibilities of globular proteins

Partial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 +/- 3) X 10(-6) bar(-1) for the isothermal compressibility coefficient of the protein interior at 25 degrees C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x-ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 X 10(-6) bar(-1), which is 20% less than that of pure water.

Flexibility of globular proteins in water as revealed by compressibility

In order to elucidate the flexibility-structure-function relationships of proteins, the adiabatic compressibility of about 30 globular proteins, including food proteins, was determined by means of sound velocity and density measurements in aqueous solutions. Most proteins studied showed positive compressibility, indicating the large internal flexibility of the molecules. The volume fluctuation was in the range of 30-200 ml/mol, which corresponded to about 0.3% of the total protein volume. From the statistical analyses of the compressibility data, it was found that the flexibility of proteins is closely related to structural factors such as hydrophobicity, helix element, and amino acid composition, and to functional properties such as digestibility and foaming capacity. These results indicate that the dynamics of protein structure should be taken into account in predicting precisely the functions and properties of a protein from its primary or tertiary structure.

Volumetric properties of proteins and their analogs in diluted water solutions. 1. Partial volumes of amino acids at 15-55 degrees C

The apparent volumes of 14 amino acids in aqueous solutions at a concentration of 3 mg/ml were measured densitometrically within the temperature range 15-55 degrees C. The accuracy of measurements was +/- 0.3%. The decrease in volume of polar and charged atomic groups as well as the temperature dependences of the partial volumes was analysed. The differences in behaviour between charged, polar and nonpolar atomic groups were considered.

Protein and protein-bound water dynamics studied by Rayleigh scattering of Mössbauer radiation (RSMR)

In all contemporary models of enzyme catalysis, the functional activity of enzymes is directly associated with the dynamic properties of proteins (see Blumenfeld, 1977; Chernavaskaya & Chernavskii, 1977; Volkenstein, 1975; Austinet al.1975; Shaitan & Rubin, 1985; Ansariet al.1985). This has recently led to a much greater interest in the dynamical properties of proteins.

Interaction between external medium and haem pocket in myoglobin probed by low-temperature optical spectroscopy

The visible absorption spectra of carbonmonoxymyoglobin in the temperature range 300 to 20 K are reported and compared with the analogous spectra of carbonomonoxyhaemoglobin. The temperature dependence of the zeroth, first and second moment of the observed bands is analysed to obtain information on the local dynamics in the proximity of the haem. Contrary to haemoglobin, the first moment of the observed bands in myoglobin is markedly affected by the solvent composition and its value saturates at temperatures at which the solvent undergoes the glass transition. These data indicate that solvent properties influence the haem pocket stereodynamics in myoglobin; moreover, the different behaviour between myoglobin and haemoglobin suggests that the process should involve the surfaces that are buried in the haemoglobin tetramer and exposed to the solvent in myoglobin, and/or the different protein compressibility.

Compressibility-structure relationship of globular proteins

The adiabatic compressibility, -beta s, of 11 globular proteins in water was determined by means of sound velocity measurements at 25 degrees C. All the proteins studied except for subtilisin showed positive -beta s values, indicating the large internal compressibility of the protein molecules. The intrinsic compressibility of proteins free from the hydration effect appeared to be comparable to that of normal ice. The compressibility data for 25 proteins, including 14 reported previously [Gekko, K., & Noguchi, H. (1979) J. Phys. Chem. 83, 2706-2714], were statistically analyzed to examine the correlation of the compressibility with some structural parameters and the amino acid compositions of proteins. It was found that -beta s increases with increasing partial specific volume and hydrophobicity of proteins. The helix element also seemed to be a dynamic domain to increase -beta s. Four amino acid residues (Leu, Glu, Phe, and His) greatly increased -beta s, and another four (Asn, Gly, Ser, and Thr) decreased it. Some empirical equations were derived for the estimation of the -beta s values of unknown proteins on the basis of their amino acid compositions. The volume fluctuations of proteins revealed by the compressibility data were in the range of 30-200 mL/mol, which corresponded to about 0.3% of the total protein volume. The conformational fluctuation seemed to enhance the thermal stability of proteins.