Exploring volume, compressibility and hydration changes of folded proteins upon compression

Voloshin, V. P.; Medvedev, N. N.; Smolin, Nikolai; Geiger, Alfons; Winter, Roland

doi:10.1039/c5cp00251f

Cited by 23 publications

(13 citation statements)

References 61 publications

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“…is the intrinsic partial molar volume of the solute, which corresponds to the spatial architecture of protein interior [59], a domain where water cannot penetrate, V vdW is the van der Waals partial molar volume of the solute and V void is the partial molar volume of voids into the solute due to imperfect atom packing; V T is the partial molar thermal volume that represents an "empty volume" around the solute molecules resulting from thermally induced mutual molecular vibrations and reorientations of the solute and the solvent [63,68,69]. It is related to the fact that the "cavity" of the solute molecule that is created by inserting the molecule into the solvent should be larger than its molecular volume, and this extra volume should be sensitive to temperature [38,69]. For molecules of arbitrary shapes, the thermal volume can be approximated as a layer of constant thickness ∆ to the surface of the molecule [64]; and, V l the interaction volume is equal to…”

Section: Microscopic Description Of Macroscopic Volumetric Datamentioning

confidence: 99%

Flexibility and Hydration of Amphiphilic Hyperbranched Arabinogalactan-Protein from Plant Exudate: A Volumetric Perspective

Tamayo

Nigen

Apolinar-Valiente

et al. 2018

Colloids and Interfaces

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Plant Acacia gum exudates are composed by glycosylated hydroxyproline-rich proteins, which have a high proportion of heavily branched neutral and charged sugars in the polysaccharide moiety. These hyperbranched arabinogalactan-proteins (AGP) display a complexity arising from its composition, architecture, and conformation, but also from its polydispersity and capacity to form supramolecular assemblies. Flexibility and hydration partly determined colloidal and interfacial properties of AGPs. In the present article, these parameters were estimated based on measurements of density and sound velocity and the determination of volumetric parameters, e.g., partial specific volume (v s •) and coefficient of partial specific adiabatic compressibility coefficient (β s •). Measurements were done with Acacia senegal, Acacia seyal, and fractions from the former separated according to their hydrophobicity by Hydrophobic Interaction Chromatography, i.e., HIC-F1, HIC-F2, and HIC-F3. Both gums presented close values of v s • and β s •. However, data on fractions suggested a less hydrated and more flexible structure of HIC-F3, in contrast to a less flexible and more hydrated structure of HIC-F2, and especially HIC-F1. The differences between the macromolecular fractions of A. senegal are significantly related to the fraction composition, protein/polysaccharide ratio, and type of amino acids and sugars, with a polysaccharide moiety mainly contributing to the global hydrophilicity and a protein part mainly contributing to the global hydrophobicity. These properties form the basis of hydration ability and flexibility of hyperbranched AGP from Acacia gums.

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Section: Microscopic Description Of Macroscopic Volumetric Datamentioning

confidence: 99%

Flexibility and Hydration of Amphiphilic Hyperbranched Arabinogalactan-Protein from Plant Exudate: A Volumetric Perspective

Tamayo

Nigen

Apolinar-Valiente

et al. 2018

Colloids and Interfaces

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“…86,88 Recently, this method was used to calculate the volumetric characteristics of proteins in aqueous solutions. 89,90 An important characteristic of lipid bilayers is the profile of free volume along the axis perpendicular to the plane of the membrane. This profile can be calculated in several ways, e.g., by placing sample points in the system, either randomly or along a grid.…”

Section: Calculation Of the Free Volume Characteristics Free Volume mentioning

confidence: 99%

Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics

et al. 2017

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The effect of four general anesthetics, namely chloroform, halothane, diethyl ether, and enflurane on the free volume fraction and lateral pressure profiles in a fully hydrated dipalmitoylphosphatidylcholime (DPPC) membrane is investigated by means of computer simulation. In order to find changes that can be related to the molecular mechanism of anesthesia as well as its pressure reversal, the simulations are performed both at atmospheric and high (1000 bar) pressures. The obtained results show that the additional free volume occurring in the membrane is localized around the anesthetic molecules themselves. Correspondingly, the fraction of the free volume is increased in the outer of the two membrane regions (i.e., at the outer edge of the hydrocarbon phase) where anesthetic molecules prefer to stay in every case. As a consequence, the presence of anesthetics decreases the lateral pressure in the nearby region of the lipid chain ester groups, in which the anesthetic molecules themselves do not penetrate. Both of these changes, occurring upon introducing anesthetics in the membrane, are clearly reverted by the increase of the global pressure. These findings are in accordance both with the more than 60 years old "critical volume hypothesis" of Mullins, and with the more recent "lateral pressure hypothesis" of Cantor. Our results suggest that if anesthesia is indeed caused by conformational changes of certain membrane-bound proteins, induced by changes in the lateral pressure profile, as proposed by Cantor, the relevant conformational changes are expected to occur in the membrane region where the ester groups are located.

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“…The current view is that the volume reduction that accompanies pressure-modulated transitions in proteins, including formation of the denatured state, is dominated by the elimination of voids or cavities in the protein's interior (14, 21-24) via hydration, although other factors contribute (15,(25)(26)(27)(28). In the equilibrium between two folded conformations, G ↔ E for example, an alternative "structure-relaxation" mechanism may play a role in the pressure response.…”

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Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure

Lerch

López

Yang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Application of hydrostatic pressure shifts protein conformational equilibria in a direction to reduce the volume of the system. A current view is that the volume reduction is dominated by elimination of voids or cavities in the protein interior via cavity hydration, although an alternative mechanism wherein cavities are filled with protein side chains resulting from a structure relaxation has been suggested [López CJ, Yang Z, Altenbach C, Hubbell WL (2013) Proc Natl Acad Sci USA 110(46):E4306-E4315]. In the present study, mechanisms for elimination of cavities under high pressure are investigated in the L99A cavity mutant of T4 lysozyme and derivatives thereof using site-directed spin labeling, pressure-resolved double electronelectron resonance, and high-pressure circular dichroism spectroscopy. In the L99A mutant, the ground state is in equilibrium with an excited state of only ∼3% of the population in which the cavity is filled by a protein side chain [Bouvignies et al. (2011) Nature 477(7362):111-114]. The results of the present study show that in L99A the native ground state is the dominant conformation to pressures of 3 kbar, with cavity hydration apparently taking place in the range of 2-3 kbar. However, in the presence of additional mutations that lower the free energy of the excited state, pressure strongly populates the excited state, thereby eliminating the cavity with a native side chain rather than solvent. Thus, both cavity hydration and structure relaxation are mechanisms for cavity elimination under pressure, and which is dominant is determined by details of the energy landscape.DEER | EPR | conformational exchange | protein structural dynamics P roteins in solution exist in conformational equilibria that cannot be appreciated from structures observed in crystal lattices (1-5). The members of a folded conformational ensemble may have distinct functions and hence are of interest in elucidating mechanisms of protein action (5-7). The free-energy differences between the conformations can range from zero to a few kilocalories per mole; the higher free-energy states are referred to as "invisible" or "excited" (E) states owing to their low equilibrium populations. The structural transition between the native ground state (G) and the E state may involve rigid body motion of the peptide backbone (5, 8) or local unfolding (9).For a complete understanding of molecular mechanisms underlying function, characterization of functionally relevant conformational substates is required. However, in the case of E states, low populations and short lifetimes present a challenge for biophysical characterization. The elegant high-resolution NMR studies from Akasaka (10, 11) and coworkers suggest that application of hydrostatic pressure on the order of a few kilobars may solve this problem by reversibly populating functional E states, making them amenable for study by spectroscopic methods. For example, high-pressure NMR has been used to identify and characterize E states crucial to ligand binding in ubiquitin (12) and d...

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Exploring volume, compressibility and hydration changes of folded proteins upon compression

Cited by 23 publications

References 61 publications

Flexibility and Hydration of Amphiphilic Hyperbranched Arabinogalactan-Protein from Plant Exudate: A Volumetric Perspective

Flexibility and Hydration of Amphiphilic Hyperbranched Arabinogalactan-Protein from Plant Exudate: A Volumetric Perspective

Lateral Pressure Profile and Free Volume Properties in Phospholipid Membranes Containing Anesthetics

Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure

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