Increase in apparent compressibility of cytochrome c upon oxidation

Effects of Corneal Hydration on Brillouin Microscopy In Vivo

Purpose

To investigate how corneal hydration affects the Brillouin frequency of corneal stroma.

Methods

From a simple analytical model considering the volume fraction of water in corneal stroma, we derived the dependence of Brillouin frequency on hydration and hydration-induced corneal thickness variation. The Brillouin frequencies of fresh ex vivo porcine corneas were measured as their hydration was varied in dextran solution and water. Healthy volunteers (8 eyes) were scanned in vivo repeatedly over the course of 9 hours, and the diurnal variations of Brillouin frequency and central corneal thickness (CCT) were measured.

Results

The measured dependence of Brillouin frequency on hydration, both ex vivo and in vivo, agreed well with the theoretical prediction. The Brillouin frequencies of human corneas scanned immediately after waking were on average ∼25 MHz lower than their daytime average values. For stabilized corneas, the typical variation of Brillouin frequency was ± 7.2 MHz. With respect to CCT increase or swelling, the Brillouin frequency decreased with a slope of −1.06 MHz/μm in vivo.

Conclusions

The ex vivo and in vivo data agree with our theoretical model and support that the effect of corneal hydration on Brillouin frequency comes predominantly from the dependence of the tissue compressibility on the water. Corneal hydration correlates negatively with the Brillouin frequency. During daytime activities, the influence of physiological hydration changes in human corneas is < ± 10 MHz. The sensitivity to hydration may potentially be useful in detecting abnormal hydration change in patients with endothelial disorders.

Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins

Hydrogen-deuterium exchange (HDX) experiments are widely used in studies of protein dynamics. To predict the propensity of amide hydrogens for exchange with deuterium, several models have been reported in which computations of amide-hydrogen protection factors are carried out using molecular dynamics (MD) simulations. Given significant variation in the criteria used in different models, the robustness and broader applicability of these models to other proteins, especially homologous proteins showing distinct amide-exchange patterns, remains unknown. The sensitivity of the predictions when MD simulations are conducted with different force-fields is yet to tested and quantified. Using MD simulations and experimental HDX data on three homologous signaling proteins, we report detailed studies quantifying the performance of seven previously reported models (M1-M7) of two general types: empirical and fractional-population models. We find that the empirical models show inconsistent predictions but predictions of the fractional population models are robust. Contrary to previously reported work, we find that the solvent-accessible surface area of amide hydrogens is a useful metric when combined with a new metric defining the distances of amide hydrogens from the first polar atoms in proteins. On the basis of this, we report two new models, one empirical (M8) and one population-based (M9). We find strong protection of amide hydrogens from solvent exchange both within the stable helical motifs and also in the interhelical loops. We further observe that the exchange-competent states of amide hydrogens occur on the sub 100 ps time-scale via localized fluctuations, and such states among amides of a given protein do not appear to show any cooperativity or allosteric coupling.

Structural analysis of diheme cytochrome c by hydrogen-deuterium exchange mass spectrometry and homology modeling

A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen–deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic predictions. Here a unique diheme cytochrome c (DHCC) protein from Heliobacterium modesticaldum is studied with both HDX and homology modeling to bring some definition of the structure of the protein and its role. Specifically, HDX data were used to guide the homology modeling to yield a more functionally relevant structural model of DHCC.

Coupled motion in proteins revealed by pressure perturbation

The cooperative nature of protein substructure and internal motion is a critical aspect of their functional competence about which little is known experimentally. NMR relaxation is used here to monitor the effects of high pressure on fast internal motion in the protein ubiquitin. In contrast to the main chain, the motions of the methyl-bearing side chains have a large and variable pressure dependence. Within the core, this pressure sensitivity correlates with the magnitude of motion at ambient pressure. Spatial clustering of the dynamic response to applied hydrostatic pressure is also seen, indicating localized cooperativity of motion on the sub-nanosecond time scale and suggesting regions of variable compressibility. These and other features indicate that the native ensemble contains a significant fraction of members with characteristics ascribed to the recently postulated "dry molten globule". The accompanying variable side-chain conformational entropy helps complete our view of the thermodynamic architecture underlying protein stability, folding, and function.

Use of metal oxide nanoparticle band gap to develop a predictive paradigm for oxidative stress and acute pulmonary inflammation

We demonstrate for 24 metal oxide (MOx) nanoparticles that it is possible to use conduction band energy levels to delineate their toxicological potential at cellular and whole animal levels. Among the materials, the overlap of conduction band energy (E(c)) levels with the cellular redox potential (-4.12 to -4.84 eV) was strongly correlated to the ability of Co(3)O(4), Cr(2)O(3), Ni(2)O(3), Mn(2)O(3), and CoO nanoparticles to induce oxygen radicals, oxidative stress, and inflammation. This outcome is premised on permissible electron transfers from the biological redox couples that maintain the cellular redox equilibrium to the conduction band of the semiconductor particles. Both single-parameter cytotoxic as well as multi-parameter oxidative stress assays in cells showed excellent correlation to the generation of acute neutrophilic inflammation and cytokine responses in the lungs of C57 BL/6 mice. Co(3)O(4), Ni(2)O(3), Mn(2)O(3), and CoO nanoparticles could also oxidize cytochrome c as a representative redox couple involved in redox homeostasis. While CuO and ZnO generated oxidative stress and acute pulmonary inflammation that is not predicted by E(c) levels, the adverse biological effects of these materials could be explained by their solubility, as demonstrated by ICP-MS analysis. These results demonstrate that it is possible to predict the toxicity of a large series of MOx nanoparticles in the lung premised on semiconductor properties and an integrated in vitro/in vivo hazard ranking model premised on oxidative stress. This establishes a robust platform for modeling of MOx structure-activity relationships based on band gap energy levels and particle dissolution. This predictive toxicological paradigm is also of considerable importance for regulatory decision-making about this important class of engineered nanomaterials.

Cytochrome c folding / unfolding: a unifying picture

Recent NMR structural and dynamical data on partially folded forms of mono-heme cytochrome c provide a unifying picture of the behavior of the protein far from the native conditions and suggest useful hints to explain the redox dependent stability of the protein. A fragile hinge in the structure of mitochondrial cytochrome c is identified, which may not have correspondents in smaller type-1 cytochromes. Former spectroscopic and kinetic data are here discussed in terms of this new view.

Evidence of protein collective motions on the picosecond timescale

We investigate the presence of structural collective motions on a picosecond timescale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time domain spectroscopy and molecular dynamics simulations. The THz response dramatically increases with oxidation, with the largest increase for lowest hydrations, and highest frequencies. For both oxidation states the THz response rapidly increases with hydration saturating above ∼25% (g H(2)O/g protein). Quasiharmonic vibrational modes and dipole-dipole correlation functions were calculated from molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence, providing strong evidence of the existence of these motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of buried internal water molecules. This source for the observed oxidation dependence is consistent with the lack of an oxidation dependence in nuclear resonant vibrational spectroscopy measurements.

Resilience of the iron environment in heme proteins

Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.

The influence of correlated protein-water volume fluctuations on the apparent compressibility of proteins determined by ultrasonic velocimetry

The elasticity of proteins, expressed by the compressibility, is potentially one of the most important properties of proteins because of the close relationship with its functionality. The compressibility of solutions can be determined by measurements of sound velocity and density. These quantities are related by the Newton-Laplace equation. In order to interpret the apparent compressibility of solutes in highly dilute solutions, it is required to consider the relation between compressibility and sound velocity of the solution using an appropriate reference system. The classical approach usually gives too small values for the apparent compressibility when compared with other methods. We show that the difference can partially be explained if the correlated volume fluctuations of the solvent are taken into consideration. A special attention is given to the compressibility of proteins. Finally, the present paper is not intended to replace established approaches, but it wants to create awareness that the classical mixing rules refer to ideal gasses assuming uncorrelated volume fluctuations and that a considerable part of the hydration effects could be explained by correlated volume fluctuations.

Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation

Molecular dynamics simulation has been performed on five native proteins in water to evaluate their intrinsic isothermal compressibilities beta(T,int). To identify physical factors contributing to protein compressibility, a general method is presented for analyzing the compressibility of mechanically inhomogeneous systems. The value of beta(T,int) varies with protein species considerably: beta-lactoglobulin (14.15 x 10(-2) GPa(-1)) is more than twice as compressible as ribonuclease A (6.77 x 10(-2) GPa(-1)). Beta-lactoglobulin and myoglobin (13.95 x 10(-2) GPa(-1)) have similar values of beta(T,int), but the mechanisms responsible for them are significantly different. The volume fluctuations of internal cavities and the magnitudes of the crosscorrelation between them are the key factors determining beta(T,int) of proteins. Though the volume fractions of internal cavity for the five studied proteins are nearly equal to one another, the mean cavity compressibilities beta(T,cav) vary considerably with protein species and range from 0.35 to 0.69 GPa(-1), which are much smaller than those of normal organic liquids such as methanol, ethanol, and benzene and close to that of glycerol (0.55 GPa(-1)), a strongly associated liquid.

Decomposition of protein experimental compressibility into intrinsic and hydration shell contributions

The experimental determination of protein compressibility reflects both the protein intrinsic compressibility and the difference between the compressibility of water in the protein hydration shell and bulk water. We use molecular dynamics simulations to explore the dependence of the isothermal compressibility of the hydration shell surrounding globular proteins on differential contributions from charged, polar, and apolar protein-water interfaces. The compressibility of water in the protein hydration shell is accounted for by a linear combination of contributions from charged, polar, and apolar solvent-accessible surfaces. The results provide a formula for the deconvolution of experimental data into intrinsic and hydration contributions when a protein of known structure is investigated. The physical basis for the model is the variation in water density shown by the surface-specific radial distribution functions of water molecules around globular proteins. The compressibility of water hydrating charged atoms is lower than bulk water compressibility, the compressibility of water hydrating apolar atoms is somewhat larger than bulk water compressibility, and the compressibility of water around polar atoms is about the same as the compressibility of bulk water. We also assess whether hydration water compressibility determined from small compound data can be used to estimate the compressibility of hydration water surrounding proteins. The results, based on an analysis from four dipeptide solutions, indicate that small compound data cannot be used directly to estimate the compressibility of hydration water surrounding proteins.

Redox-Coupled Dynamics and Folding in Cytochrome c

Cytochrome c functions as an electron carrier in the mitochondrial electron-transport chain using the Fe(II)-Fe(III) redox couple of a covalently attached heme prosthetic group, and it has served as a paradigm for both biological redox activity and protein folding. On the basis of a wide variety of biophysical techniques, it has been suggested that the protein is more flexible in the oxidized state than in the reduced state, which has led to speculation that it is the dynamics of the protein that has been evolved to control the cofactor's redox properties. To test this hypothesis, we incorporated carbon-deuterium bonds throughout cytochrome c and characterized their absorption frequencies and line widths using IR spectroscopy. The absorption frequencies of several residues on the proximal side of the heme show redox-dependent changes, but none show changes in line width, implying that the flexibility of the oxidized and reduced proteins is not different. However, the spectra demonstrate that folded protein is in equilibrium with a surprisingly large amount of locally unfolded protein, which increases with oxidation for residues localized to the proximal side of the heme. The data suggest that while the oxidized protein is not more flexible than the reduced protein, it is more locally unfolded. Local unfolding of cytochrome c might be one mechanism whereby the protein evolved to control electron transfer.

The redox couple of the cytochrome c cyanide complex: the contribution of heme iron ligation to the structural stability, chemical reactivity, and physiological behavior of horse cytochrome c

Contrary to most heme proteins, ferrous cytochrome c does not bind ligands such as cyanide and CO. In order to quantify this observation, the redox potential of the ferric/ferrous cytochrome c-cyanide redox couple was determined for the first time by cyclic voltammetry. Its E0' was -240 mV versus SHE, equivalent to -23.2 kJ/mol. The entropy of reaction for the reduction of the cyanide complex was also determined. From a thermodynamic cycle that included this new value for the cyt c cyanide complex E0', the binding constant of cyanide to the reduced protein was estimated to be 4.7 x 10(-3) L M(-1) or 13.4 kJ/mol (3.2 kcal/mol), which is 48.1 kJ/mol (11.5 kcal/mol) less favorable than the binding of cyanide to ferricytochrome c. For coordination of cyanide to ferrocytochrome c, the entropy change was earlier experimentally evaluated as 92.4 J mol(-1) K(-1) (22.1 e.u.) at 25 K, and the enthalpy change for the same net reaction was calculated to be 41.0 kJ/mol (9.8 kcal/mol). By taking these results into account, it was discovered that the major obstacle to cyanide coordination to ferrocytochrome c is enthalpic, due to the greater compactness of the reduced molecule or, alternatively, to a lower rate of conformational fluctuation caused by solvation, electrostatic, and structural factors. The biophysical consequences of the large difference in the stabilities of the closed crevice structures are discussed.

Large oxidation dependence observed in terahertz dielectric response for cytochrome c

Far infrared dielectric response is used to characterize the collective mode density of states for cytochrome c as a function of oxidation state and hydration using terahertz time domain spectroscopy. A strong absorbance and refractive index increase was observed with the oxidation. A simple phenomenological fitting using a continuous distribution of oscillators reproduces the frequency dependence of the complex dielectric response as well as demonstrates quantitative agreement with a uniform increase in either mode density or polarizability with oxidation in the 5-80 cm(-1) frequency range. Hydration dependence measurements find that a difference in the equilibrium water content for ferri and ferro cytochrome c is not sufficient to account for the large change in terahertz response. The large dielectric increase at terahertz frequencies with oxidation suggests either a significant global softening of the potential and/or a significant increase in polarizability with oxidation.

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.

The cytochrome c fold can be attained from a compact apo state by occupancy of a nascent heme binding site

NMR techniques and 8-anilino-1-napthalenesulphonate (ANS) binding studies have been used to characterize the apo state of a variant of cytochrome c(552) from Hydrogenobacter thermophilus. In this variant the two cysteines that form covalent thioether linkages to the heme group have been replaced by alanine residues (C11A/C14A). CD studies show that the apo state contains approximately 14% helical secondary structure, and measurements of hydrodynamic radii using pulse field gradient NMR methods show that it is compact (R(h), 16.6 A). The apo state binds 1 mol of ANS/mol of protein, and a linear reduction in fluorescence enhancement is observed on adding aliquots of hemin to a solution of apo C11A/C14A cytochrome c(552) with ANS bound. These results suggest that the bound ANS is located in the heme binding pocket, which would therefore be at least partially formed in the apo state. Consistent with these characteristics, the formation of the holo state of the variant cytochrome c(552) from the apo state on the addition of heme has been demonstrated using NMR techniques. The properties of the apo state of C11A/C14A cytochrome c(552) reported here contrast strongly with those of mitochondrial cytochrome c whose apo state resembles a random coil under similar conditions.

Protein compressibility, dynamics, and pressure

The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure.

Structure of the soluble domain of cytochrome c(552) from Paracoccus denitrificans in the oxidized and reduced states

The crystal structure of the soluble domain of the membrane bound cytochrome c(552) (cytochrome c(552)') from Paracoccus denitrificans was determined using the multiwavelength anomalous diffraction technique and refined at 1.5 A resolution for the oxidized and at 1. 4 A for the reduced state. This is the first high-resolution crystal structure of a cytochrome c at low ionic strength in both redox states. The atomic model allowed for a detailed assessment of the structural properties including the secondary structure, the heme geometry and interactions, and the redox-coupled structural changes. In general, the structure has the same features as that of known eukaryotic cytochromes c. However, the surface properties are very different. Cytochrome c(552)' has a large strongly negatively charged surface part and a smaller positively charged area around the solvent-exposed heme atoms. One of the internal water molecules conserved in all structures of eukaryotic cytochromes c is also present in this bacterial cytochrome c. It contributes to the interactions between the side-chain of Arg36 and the heme propionate connected to pyrrole ring A. Reduction of the oxidized crystals does not influence the conformation of cytochrome c(552)' in contrast to eukaryotic cytochromes c. The oxidized cytochrome c(552)', especially the region of amino acid residues 40 to 56, appears to be more flexible than the reduced one.

High-resolution multiwavelength surface plasmon resonance spectroscopy for probing conformational and electronic changes in redox proteins

To date, surface plasmon resonance (SPR) spectroscopy identifies molecules via specific bindings with their ligands immobilized on a surface. We demonstrate here that a high-resolution multiwavelength SPR technique can measure the electronic states of the molecules and thus allow direct identification of the molecules. Using this new capability, we have studied the electronic and conformational differences between the oxidized and reduced states of cytochrome c immobilized on a modified gold electrode. When the wavelength of the incident light is far away from the optical absorption bands of the protein, a approximately 0.008 degree decrease in the resonance angle, due to a conformational change, occurs as the protein is switched from the oxidized to reduced states. When the wavelength is tuned to the absorption bands, the resonance angle oscillates at the wavelengths of the absorption peaks, which provides electronic signatures of the protein.

Polyol-induced molten globule of cytochrome c: an evidence for stabilization by hydrophobic interaction

To address the contribution of hydrophobic interaction to the stability of molten globule (MG) of proteins, the effects of various polyols (ethylene glycol, glycerol, erythritol, xylitol, sorbitol, and inositol) on the structure of acid-unfolded horse cytochrome c were examined at pH 2, by means of circular dichroism (CD), partial specific volume, adiabatic compressibility, and differential scanning calorimetry (DSC). Addition of polyols induced the characteristic CD spectra of MG, the effect being enhanced with an increase in their concentration and chain length (the number of OH groups) of polyols except for ethylene glycol. The free energy change of MG formation by sorbitol was comparable with those for the salt-induced MG formation but the heat capacity change was negligibly small. The partial specific volume did not change within the experimental error but the adiabatic compressibility largely increased by MG formation. The sorbitol-induced MG showed a highly cooperative DSC thermogram with a large heat capacity change in comparison with the salt-induced one. These results demonstrate that polyols can stabilize the MG state of this protein through the enhanced hydrophobic interaction overcoming the electrostatic repulsion between charged residues. The stabilizing mechanism and structure of MG state induced by polyols were discussed in terms of the preferential solvent interactions and osmotic pressure of the medium, in comparison with the salt-induced one.

A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states

Molecular dynamics calculations have been performed over long trajectories with the inclusion of explicit solvent molecules on the reduced and the oxidized states of yeast iso-1-cytochrome c. The resulting structures have been analyzed and compared both in terms of structural properties and dynamical behavior. The structure of the buried water molecules around the heme has been also analyzed for the two oxidation states and compared with the experimental observations on the X-ray and the solution NMR structures. From the overall analysis we learn that, as also observed experimentally through NMR, no significant differences are present between the structures of the two oxidation states beside the arrangement of a few side chains. Also the internal mobility is similar for the two oxidation states, even if interesting differences are observed for some residues, as for Tyr67, a residue present at the heme site. The location and the mobility of the ordered water molecules, observed in solution by NMR, are completely reproduced in the molecular dynamics simulations, which have been able to predict the different displacements of the catalytically relevant water molecule WAT166, similar to those observed in solution for the two oxidation states, at variance with that observed in the starting crystallographic structures. The relevance of these findings with respect to the prediction of structural and dynamical properties is discussed.

Combined pressure/heat-induced inactivation of butyrylcholinesterase

The combined effects of pressure and temperature on the activity of butyrylcholinesterase (BuChE) were investigated in the pressure range from 10(-3) to 5 kbar and temperature range from -10 degrees C to 70 degrees C. Inactivation of the enzyme showed a complex dependence on pressure and temperature. Under moderate pressures (1-3 kbar) at temperatures 40-65 degrees C BuChE was resistant to heat inactivation; under other conditions of pressure and temperature, the action of both parameters was synergistic and caused inactivation. Results allowed to construct a pressure-temperature kinetic phase diagram for the enzyme inactivation. The elliptic diagram for the irreversible transition active-->inactive BuChE as a function of both pressure and temperature has a positive angular coefficient. This indicates that pressure acts as a stabilizer of BuChE against heat denaturation.

Control of the redox potential in c-type cytochromes: importance of the entropic contribution

The enthalpic and entropic components of the redox free energy variation of cytochrome c553 from Desulfovibrio vulgaris Hildenborough and its mutant Y64V, flavocytochrome b2 from Saccharomyces cerevisiae, and the different hemes of cytochromes c3 from Desulfovibrio vulgaris Miyazaki and Desulfovibrio desulfuricans Norway have been determined in 0.1 M Tris-HCl pH 7.0 (7.6 for cytochromes c3) at 25 degrees C by using nonisothermal potentiometric titrations. The set of available experimental data demonstrates that the entropic component plays an important role in the control of the redox potential in c-type and b-type cytochromes. The variation of the entropic component within the class of cytochromes characterized by a positive value of E degrees ' is proposed to be mainly determined by the variation of the exposure of the heme propionates to the solvent. In the case of tetraheme cytochromes c3, the thermodynamic characteristics vary largely among the hemes belonging to the same molecule, which reflects the environmental peculiarities of each heme and also the heme-heme redox interactions. This study substantiates the existence of compensatory effects between large and opposite contributions to E degree ' predicted by all the current theoretical models which are based on electrostatic free energy calculations.

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.

Side-chain entropy and packing in proteins

What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.

Adiabatic compressibility of myosin subfragment-1 and heavy meromyosin with or without nucleotide

The partial specific adiabatic compressibilities of myosin subfragment-1 (S1) and heavy meromyosin (HMM) of skeletal muscle in solution were determined by measuring the density and the sound velocity of the solution. The partial specific volumes of S1 and HMM were 0.713 and 0.711 cm3/g, respectively. The partial specific adiabatic compressibilities of S1 and HMM were 4.2 x 10(-12) and 2.9 x 10(-12) cm2/dyn, respectively. These values are in the same range as the most of globular proteins so far studied. The result indicates that the flexibility of S1 region almost equals to that of HMM. After binding to ADP.orthovanadate, S1 and HMM became softer than their complexes with ADP. The bulk moduli of S1 and HMM were of the order of (4-6) x 10(10) dyn/cm2, which are very comparable with the bulk modulus of muscle fiber.

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.

The low-temperature heat capacity of solid proteins

Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low-frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T less than 30 K. The experimental b's of proteins are 1.6-1.8, and the theoretical, 1.1-1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100-200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.

Redox-dependent changes in beta-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra

The redox-dependent changes in secondary structure of cytochromes c from horse, cow, and dog hearts in water at 20 degrees C have been determined by amide I infrared spectroscopy. Second derivative amide I spectra were obtained by use of a procedure that includes a convenient method for the effective subtraction of the spectrum of water vapor in the system. The band at 1657 cm-1 representing the helix structure was unaffected by a change in redox state whereas changes in bands due to turns at 1680, 1672, and 1666 cm-1, unordered structure at 1650 cm-1, and beta-structures at 1632 and 1627 cm-1 occurred. About one-fourth of the beta-extended chain spectral region and one-fifth of the beta-turn region (involving a total of approximately 9-13 residues) were sensitive to the oxidation state of heme iron. No significant changes in the secondary structure of either the reduced or oxidized protein due to changes in ionic strength were detected. The localized structural rearrangements triggered by the changes in oxidation state of heme iron are consistent with differences in the binding of heme iron to a histidine imidazole nitrogen and a methionine sulfur atom from the beta-extended chain. The demonstrated ability to obtain highly reproducible second derivative amide I infrared spectra confirms the unique utility of such spectral measurements for localization of subtle changes in secondary structure within a protein, especially for changes among the multiple turns and beta-structures.

Reduction of thioredoxin significantly decreases its partial specific volume and adiabatic compressibility

The partial specific volume and adiabatic compressibility were determined at several temperatures for oxidized and reduced Escherichia coli thioredoxin. Oxidized thioredoxin had a partial specific volume of 0.785-0.809 mL/g at the observed upper limit for all proteins whereas the partial specific volume of reduced thioredoxin was 0.745-0.755 mL/g, a value in the range found for a majority of proteins. The adiabatic compressibility of oxidized thioredoxin was also much larger (9.8-18 x 10(-12) cm2 dyne-1) than that of the reduced protein (3.8-7.3 x 10(-12)). Apart from the region immediately around the small disulfide loop, the structures of the oxidized (X-ray, crystal) and reduced protein (nuclear magnetic resonance, solution) are reported to be very similar. It would appear that alterations in the solvent layer in contact with the protein surface must play a major role in producing these large changes in the apparent specific volumes and compressibilities in this system. Some activities of thioredoxin require the reduced structure but are not electron transfer reactions. The large changes in physical parameters reported here suggest the possibility of a reversible metabolic control function for the SS bond.

Differences in thermal stability between reduced and oxidized cytochrome b562 from Escherichia coli

The thermal stabilities of ferri- and ferrocytochrome b562 were examined. Thermally induced spectral changes, monitored by absorption and second-derivative spectroscopies, followed the dissociation of the heme moiety and the increased solvation of tyrosine residue(s) located in close proximity to the heme binding site. All observed thermal transitions were independent of the rate of temperature increase (0.5-2 degrees C/min), and the denatured protein exhibited partial to near-complete reversibility upon return to ambient temperature. The extent of renaturation of cytochrome b562 is dependent on the amount of time the unfolded conformer is exposed to temperatures above the transition temperature, Tm. All thermally induced spectra changes fit a simple two-state model, and the thermal transition was assumed to be reversible. The thermal transition for ferrocytochrome b562 yielded Tm and van't Hoff enthalpy (delta HvH) values of 81.0 degrees C and 137 kcal/mol, respectively. In contrast, Tm and delta HvH values obtained for the ferricytochrome were 66.7 degrees C and 110 kcal/mol, respectively. The estimated increase in the stabilization free energy at the Tm of ferricytochrome b562 following the one-electron reduction to the ferrous form, where delta delta G = delta Tm delta Sm [delta Sm = 324 cal/(K.mol), delta Tm = 14.3 degrees C] [Becktel, W. J., & Schellman, J. A. (1987) Biopolymers 26, 1859-1877], is 4.6 kcal/mol.

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.

Salt-dependent structure change and ion binding in cytochrome c studied by two-dimensional proton NMR

To search for salt-dependent structure changes that might help to explain physicochemical differences observed in previous solution studies, two-dimensional proton NMR spectra of reduced and oxidized cytochrome c were recorded at relatively high and low salt concentrations. The results rule out substantial ionic strength dependent structure change in either redox form over the salt concentrations tested (5 mM phosphate to 5 mM phosphate plus 200 mM NaCl, at pH 7). Chemical shift changes were found for several residues within a limited segment of the oxidized protein, most prominently in the sequence Lys-86, Lys-87, Lys-88, Thr-89. A salt-dependent binding of phosphate anion(s) at this site, as observed earlier by others, is indicated. The binding of one or two phosphates at the cytochrome c surface can explain earlier small-angle X-ray scattering observations of an increase in the calculated radius of gyration of the oxidized protein at the same low-salt condition used here. Other observations, by ultraviolet resonance Raman and 1D NMR spectroscopies, of salt-dependent changes could not be corroborated, but may depend on the still lower salt used and the absence of phosphate. The results obtained support the view that the absence of sizeable redox-dependent structure change observed in X-ray and NMR studies at varying salt conditions is characteristic of the protein at all salt conditions above the low millimolar range. Physicochemical differences between oxidized and reduced cytochrome c apparently represent differences in stability without patent structure change.

Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences (delta delta) for structure change, we removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor parameters were determined from the delta delta values of a large set (64) of C alpha H protons at well-defined spatial positions in the oxidized horse protein. The g-tensor calculation, when repeated using only 12 available C alpha H proton resonances for cytochrome c from tuna, proved to be remarkably stable. The largest principal value of the g tensor (gz) falls precisely along the ligand bond between the heme iron and methionine-80 sulfur, while gx and gy closely match the natural heme axes defined by the pyrrole nitrogens. The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution (delta pc) to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, delta delta-delta pc, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, which are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. Smaller chemical shift discrepancies point to a concerted change, involving residues 39-43 and 50-60 (bottom of the protein), and to other changes in the immediate vicinity of the heme ligands. Also, the three internal water molecules are implicated in redox sensitivity. The residues found to change are in good but not perfect agreement with prior X-ray diffraction observations of subangstrom redox-related displacements in the tuna protein. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impression is one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.