Partial Specific Volume Of Protein Research Articles

Volume Changes Upon Unfolding of Globular Proteins: Computational and Experimental Studies

Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation. Increasing pressure, much like increasing temperature, perturbs the thermodynamic equilibrium between folded state and unfolded state. In thermodynamic terms stability is defined by Gibbs energy, G, that is function of both temperature and pressure and is related to the population of native, N, and unfolded, U, states aswhere Keq is equilibrium constant. The pressure dependence of G is defined by the volume changes between the unfolded and native states. What is the origin of the changes in volume of a protein upon unfolding? The presence of internal cavities and voids in the interior of the native proteins makes the volume of the native protein larger that the volume of the unfolded state. However, the hydration of internal protein groups that become exposed to the solvent upon unfolding should also contribute to the changes in volume. Based on model compound data, the hydration in expected to contribute negatively to the changes in the V specific volume of a protein upon unfolding. As a result it appears that the unfolding of proteins should be accompanied by a large decrease in their volumes. However, in most cases, only small decreases, or even small increases, in the partial specific volume of proteins upon unfolding are observed. To reconcile these observations, we have analyzed volume changes due to the internal cavities and volume using structural ensembles of proteins generated using various computational models including an all-atom explicit solvent molecular dynamics simulations. We show that previous calculations significantly over-estimated the volume changes due to the cavities and voids. Supported by a grant from the National Science Foundation CLP-1145407

Density Contrast Sedimentation Velocity for the Determination of Protein Partial-Specific Volumes

The partial-specific volume of proteins is an important thermodynamic parameter required for the interpretation of data in several biophysical disciplines. Building on recent advances in the use of density variation sedimentation velocity analytical ultracentrifugation for the determination of macromolecular partial-specific volumes, we have explored a direct global modeling approach describing the sedimentation boundaries in different solvents with a joint differential sedimentation coefficient distribution. This takes full advantage of the influence of different macromolecular buoyancy on both the spread and the velocity of the sedimentation boundary. It should lend itself well to the study of interacting macromolecules and/or heterogeneous samples in microgram quantities. Model applications to three protein samples studied in either H2O, or isotopically enriched H218O mixtures, indicate that partial-specific volumes can be determined with a statistical precision of better than 0.5%, provided signal/noise ratios of 50 - 100 can be achieved in the measurement of the macromolecular sedimentation velocity profiles. The approach is implemented in the global modeling software SEDPHAT.

Density contrast sedimentation velocity for the determination of protein partial-specific volumes.

The partial-specific volume of proteins is an important thermodynamic parameter required for the interpretation of data in several biophysical disciplines. Building on recent advances in the use of density variation sedimentation velocity analytical ultracentrifugation for the determination of macromolecular partial-specific volumes, we have explored a direct global modeling approach describing the sedimentation boundaries in different solvents with a joint differential sedimentation coefficient distribution. This takes full advantage of the influence of different macromolecular buoyancy on both the spread and the velocity of the sedimentation boundary. It should lend itself well to the study of interacting macromolecules and/or heterogeneous samples in microgram quantities. Model applications to three protein samples studied in either H2O, or isotopically enriched H2 18O mixtures, indicate that partial-specific volumes can be determined with a statistical precision of better than 0.5%, provided signal/noise ratios of 50–100 can be achieved in the measurement of the macromolecular sedimentation velocity profiles. The approach is implemented in the global modeling software SEDPHAT.

Global Structure Analysis of Acid-Unfolded Myoglobin with Consideration to Effects of Intermolecular Coulomb Repulsion on Solution X-ray Scattering

To obtain information on the global structure of protein in the acid-unfolded (AU) state, the structure of apomyoglobin (apoMb) was analyzed by using the solution X-ray scattering (SXS) method. SXS profiles were obtained over a wide range of protein concentrations, 1-18 mg mL-1, under strongly acidic conditions. From analysis of the SXS profile extrapolated to a zero protein concentration, the mean square radius, Rsq, of AU-apoMb at 20 mM HCl was estimated to be 4.81 +/- 0.31 nm. This estimate is more than 1.3 nm larger than those of 3.0-3.5 nm reported thus far. The difference originates from the fact that effects of Coulomb repulsive forces acting between AU-apoMb molecules have not been correctly taken into account in the conventional analysis. In fact, even at a low protein concentration of 1 mg mL-1 close to the limit of measurement in the present SXS method, the solution condition applicable to estimating accurately structural parameters of AU-apoMb is very limited. At HCl concentrations lower than 10 mM, the scattering intensity at a small scattering vector decreases remarkably through the effect of intermolecular repulsive forces and the forward scattering intensity is significantly lower than the estimate from the partial specific volume of protein. On the other hand, at HCl concentrations higher than 50 mM, some compact molten-globule-like structures emerge. As a result, the intermediate concentration of 20 mM HCl is the best choice of the solution condition for determining Rsq of AU-apoMb. The effect of intermolecular Coulomb repulsion on the SXS profile of AU-apoMb is at its maximum for forward scattering and decreases monotonously with an increase in the scattering angle to be virtually negligible at K approximately 0.63 nm(-1). Whereas urea-denatured apoMb shows a SXS profile typical of Gaussian chains, the intrinsic SXS profile of AU-apoMb differs significantly from those of Gaussian chains.

3P075 蛋白質の部分比容に対する水和水の寄与(蛋白質 C) 物性 : 安定性、折れたたみなど)

3P075 蛋白質の部分比容に対する水和水の寄与(蛋白質 C) 物性 : 安定性、折れたたみなど)

Calculation of the partial specific volumes of proteins in concentrated salt, sugar, and amino acid solutions.

A method for calculating the isopotential partial specific volumes of proteins in concentrated salt, sugar, and amino acid solutions has been developed. It is based on the finding that the preferential hydration of the protein in these solutions is relatively independent of the concentration of the additive and is proportional to the specific surface area of the proteins, i.e., to the ratio of the total accessible surface area to molecular weight. Agreement between the calculated and experimental values was satisfactory, indicating the reliability of the proposed method. These calculations show that the isopotential partial specific volume increases greatly with the concentration of the additive, in particular in the case of Na2SO4, (NH4)2SO4 and sucrose, and for smaller proteins.

4] Calculation of partial specific volumes of proteins in 8 M urea solution

4] Calculation of partial specific volumes of proteins in 8 M urea solution

Partial specific volume changes of proteins densimetric studies

The partial specific volume of proteins has been investigated as a function of protein concentration, temperature, pH, and a number of denaturing and non-denaturing solvent components. Protein concentration (5–100 mg·ml −1) is found to have no effect; increasing temperature (4–40°C), as well as addition of electrolytes, sugars, and polyols, leads to an approximately linear increase; upon ligand binding, as well as denaturation by heat, extremes of pH, guanidine. HCl, urea, or sodium dodecyl sulfate, a predominantly non-linear decrease is observed. The study demonstrates the importance of measuring rather than calculating the specific volume of proteins. This holds especially in multicomponent systems, where solvent conditions may cause drastic effects.

The calculation of partial specific volumes of proteins in 8 m urea solution

A method for calculating the number of urea and water molecules bound to proteins in 8 m urea solution in acidic pH is presented. The preferential interaction parameter of solvent components with proteins can be obtained by a proper combination of the calculated number of urea and water molecules bound to the protein. This in turn can give accurate values of the apparent partial specific volumes of proteins in 8 m urea solution. the method demands only a knowledge of the amino acid composition of the protein.

The calculation of partial specific volumes of proteins in guanidine hydrochloride

A method is presented for calculating the number of guanidine hydrochloride and water molecules bound to proteins in 6 m guanidine hydrochloride solution. By correct combination of these quantities, the preferential interaction parameter of solvent components with proteins can be calculated, and, in turn, accurate values of the apparent partial specific volumes of proteins in 6 m guanidine hydrochloride can be predicted. This method requires only the knowledge of the amino acid composition of the protein. Application of this method to literature data shows that the predicted values of the partial specific volumes of proteins render possible an accurate estimation of their subunit molecular weights from sedimentation equilibrium experiments in 6 m guanidine hydrochloride.

A dilatometric study of the denaturation of bovine serum albumin by guanidine hydrochloride

The denaturation of bovine serum albumin by guanidine hydrochloride was studied using the dilatometric method. From dilatometric measurements the differences between the partial specific volume of the protein in denaturant solutions and water, respectively, were determined. The differences reflect the extent of unfolding as well as the binding of the denaturant. From the differences and the known partial specific volume of the native protein, the partial specific volumes at individual denaturant concentrations were obtained.

5] The determination of the partial specific volume of proteins by the mechanical oscillator technique

Publisher Summary The partial specific volume of a solute is a characteristic parameter that can be used in investigations of protein associations and changes in conformation, as well as in studies on protein solvent interactions and various other intermolecular interactions. It provides information needed for the determination of particle mass by means of ultracentrifugation and small-angle X-ray scattering. The precision density measurement in the apparatus described in the chapter is based on the determination of the natural frequency of an electronically excited, mechanical oscillator, its effective mass being composed of its own unknown mass and the well-defined, but also unknown, volume of the sample under investigation. To assure that this volume be well defined, the oscillator is made of a hollow, U-shaped glass tube that can be filled with the liquid sample. The mode of vibration is that of a bending-type oscillator. The positions of its vibrating nodes, which in fact determine the limits of the volume of sample taking part in the motion, is kept stable by the abrupt change in the cross-section of the glass tubes.

Determination of hydration and partial specific volume of proteins with the spring balance

Determination of hydration and partial specific volume of proteins with the spring balance

The partial specific volume of muscle proteins

The partial specific volume, v , of the muscle proteins: rabbit myosin, rabbit tropomyosin and Pinna nobilis tropomyosin has been explored by the pycnometric method as a function of solvent composition and temperature. The values determined in neutral salt solutions fit the general pattern of agreement noted by McMeekin and Marshall between observed and calculated partial specific volumes of proteins. Since this agreement depends on neglecting electrostriction in calculating v , measurements were made in a non-aqueous organic solvent, xylene, and in solutions of different pH as well as in concentrated urea. The findings obtained are consistent with the view that electrostriction exists in these proteins but is presumably being masked by a compensating factor which may well be the “excluded volume” postulated by Linderstrøm-Lang. Significant variations of v with the temperature over the range 5–25° were observed for the 3 proteins studied, suggesting that the evaluation of molecular weights from sedimentation-diffusion data at temperatures below room temperature should also include v measurements at the same temperature.

Partial Specific Volumes of Proteins in Relation to Composition and Environment1

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPartial Specific Volumes of Proteins in Relation to Composition and Environment1P. A. CharlwoodCite this: J. Am. Chem. Soc. 1957, 79, 4, 776–781Publication Date (Print):February 1, 1957Publication History Published online1 May 2002Published inissue 1 February 1957https://doi.org/10.1021/ja01561a002RIGHTS & PERMISSIONSArticle Views277Altmetric-Citations126LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (713 KB) Get e-Alerts Get e-Alerts