Functional Difference Between Deuterated and Protonated Macromolecules

Sugiyama, Takashi; Yoshioka, Tohru

doi:10.5772/36649

“…When H is replaced with D in a biological molecule, the C−D bond is about 10 times stronger than the C−H bond. 44,45 A Porod slope of 1.70 ± 0.01, which is insensitive within the experimental concentration range, confirmed an equilibrium intrinsic structure quality of a fully swollen coil at neutral pH (Table 2).…”

Section: Resultsmentioning

confidence: 53%

“…On the basis of quantum chemical calculation, it has been reported that isotopic substitution of H by D lowers the total energy of hydrophilic amino acids because of the decrease in zero-point vibration energy. When H is replaced with D in a biological molecule, the C–D bond is about 10 times stronger than the C–H bond. , A Porod slope of 1.70 ± 0.01, which is insensitive within the experimental concentration range, confirmed an equilibrium intrinsic structure quality of a fully swollen coil at neutral pH (Table ).…”

Section: Resultsmentioning

confidence: 81%

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

Balu

¹

,

Mata

²

,

Knott

³

et al. 2016

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In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles.

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“…The transport rate estimated from the initial linear part of the trace is lower by less than a factor of two compared to H 2 O. A slightly reduced rate in D 2 O has been reported for other membrane proteins ( Sugiyama and Yoshiok, 2012 ) and is explainable by slightly altered properties of the two solvents ( Némethy and Scheraga, 1964 ; Hummer et al, 2000 ). We could also inhibit CorA activity in D 2 O with Co[NH3] 6 3+ ( Figure 3A , green), supporting that the protein is indeed functional under the SANS conditions.…”

Section: Resultsmentioning

confidence: 61%

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

Johansen

¹

,

Bonaccorsi

²

,

Bengtsen

³

et al. 2022

eLife

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The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.

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“…The transport rate estimated from the initial linear part of the trace is lower by less than a factor of two compared to H2O. A slightly reduced rate in D2O has been reported for other membrane proteins 36 and is explainable by slightly altered properties of the two solvents 35,37 . We could also inhibit CorA activity in D2O with Co[NH3]6 3+ (Figure 3A, green), supporting that the protein is indeed functional under the SANS conditions.…”

Section: Cora Is Active and Preserves Its Tertiary Structure In D2omentioning

confidence: 60%

Mg²⁺-dependent conformational equilibria in CorA: an integrated view on transport regulation

Johansen

¹

,

Bonaccorsi

²

,

Bengtsen

³

et al. 2021

Preprint

1

3

0

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The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.

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Functional Difference Between Deuterated and Protonated Macromolecules

Cited by 3 publications

References 43 publications

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

Mg²⁺-dependent conformational equilibria in CorA: an integrated view on transport regulation

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Functional Difference Between Deuterated and Protonated Macromolecules

Cited by 3 publications

References 43 publications

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

Mg2+-dependent conformational equilibria in CorA: an integrated view on transport regulation

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Product

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Mg²⁺-dependent conformational equilibria in CorA: an integrated view on transport regulation