Contrast Variation

Hirai, Mitsuhiro

doi:10.1002/9780470933886.ch13

Cited by 9 publications

(12 citation statements)

References 50 publications

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“…In the case of neutron scattering, various types of the contrast-variation method are available to determine the structure of a particle in solution (38). We used the inverse-contrast variation method (29) to observe the effect of glycerol on the protein structure.…”

Section: Effect Of Glycerol On Protein Structure Observed By Neutron Scatteringmentioning

confidence: 99%

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition

Hirai

Ajito

Sugiyama

et al. 2018

Biophysical Journal

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The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (β ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross β-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.

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Section: Effect Of Glycerol On Protein Structure Observed By Neutron Scatteringmentioning

confidence: 99%

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition

Hirai

Ajito

Sugiyama

et al. 2018

Biophysical Journal

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“…One of the most attractive properties in neutron scattering is its ability to discern hydrogen from deuterium through differences in neutron scattering lengths 11 . Deuterium labeling of biomolecules is more advantageous than other labeling techniques, such as site-directed mutagenesis, fluorescence, or chemical labeling, because of its low structural and dynamic perturbations.…”

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confidence: 99%

New insight into the dynamical system of αB-crystallin oligomers

Inoue

Takata

Fujii

et al. 2016

Sci Rep

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α-Crystallin possesses a dynamic quaternary structure mediated by its subunit dynamics. Elucidation of a mechanism of subunit dynamics in homo-oligomers of αB-crystallin was tackled through deuteration-assisted small-angle neutron scattering (DA-SANS) and electrospray ionization (ESI) native mass spectrometry (nMS). The existence of subunit exchange was confirmed with DA-SANS, and monomers liberated from the oligomers were observed with nMS. With increasing temperature, an increase in both the exchange rate and monomer population was observed despite the absence of oligomer collapse. It is proposed that transiently liberated subunits, namely, “traveling subunits,” play a role in subunit exchange. Moreover, we propose that protein function is regulated by these traveling subunits.

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“…The R g value of a particle in solution determined by X-ray scattering is given by eq 2. 17,18 The R g value depends on the scattering density distribution of a particle and the difference between the average scattering densities (ρ ̅ , proportional to the average electron densities) of the solute particle and the solvent, Δρ ̅ , the so-called contrast.…”

Section: Resultsmentioning

confidence: 99%

“…The R g value of a particle in solution determined by X-ray scattering is given by eq . , The R g value depends on the scattering density distribution of a particle and the difference between the average scattering densities (ρ̅, proportional to the average electron densities) of the solute particle and the solvent, Δρ̅, the so-called contrast. In eq , the R g0 is an invariant for the change of contrast and does not depend on the internal scattering density distribution of the particle; it denotes the so-called geometrical radius of gyration. The α factor is a physical quantity obtained by integrating the scattering density distribution inside the particle with the weight of the square of the radial distance from the geometrical center of gravity of the particle.…”

Section: Resultsmentioning

confidence: 99%

Structure of Ultrafine Bubbles and Their Effects on Protein and Lipid Membrane Structures Studied by Small- and Wide-Angle X-ray Scattering

et al. 2019

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Ultrafine bubbles (UFBs) are defined as small gas-filled bubbles with a diameter smaller than 1 μm. UFBs are stable for several weeks in aqueous solutions due to their small size. Although the mechanism of the stability of UFBs remains under intensive investigation, industrial applications of UFBs have recently arisen in various fields such as agricultural and fishery industries and medical therapy. The relevance of ions (protons and hydroxide anions) in UFB solutions has been discussed; however, the mechanism underlying the behavior of UFBs is still ambiguous and there is little direct evidence of the effect of UFBs on biological materials. This study deals with gaseous UFBs in aqueous solutions. Using small- and wide-angle X-ray scattering, we have investigated the structures of UFBs (air-UFBs, O2-UFBs, and N2-UFBs) and their effect on protein and lipid membrane structures. X-ray scattering and modeling data suggest that UFBs present a dynamic diffusive boundary (interface) due to the continuous release and absorption of gas. UFBs were found to not affect the structures of proteins at all hierarchal structure levels (from quaternary to tertiary, to internal, to secondary), whereas they did influence the packing and fluctuation of the hydrocarbon chains in the liposomes but not their shapes.

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Contrast Variation

Cited by 9 publications

References 50 publications

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition

Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition

New insight into the dynamical system of αB-crystallin oligomers

Structure of Ultrafine Bubbles and Their Effects on Protein and Lipid Membrane Structures Studied by Small- and Wide-Angle X-ray Scattering

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