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- Lee, Hyun Ju, et al.
(författare)
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Intricate role of water in proton transport through cytochrome c oxidase
- 2010
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 132:45, s. 16225-16239
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Tidskriftsartikel (refereegranskat)abstract
- Cytochrome c oxidase (CytcO), the final electron acceptor in the respiratory chain, catalyzes the reduction of O2 to H2O while simultaneously pumping protons across the inner mitochondrial or bacterial membrane to maintain a transmembrane electrochemical gradient that drives, for example, ATP synthesis. In this work mutations that were predicted to alter proton translocation and enzyme activity in preliminary computational studies are characterized with extensive experimental and computational analysis. The mutations were introduced in the D pathway, one of two proton-uptake pathways, in CytcO from Rhodobacter sphaeroides. Serine residues 200 and 201, which are hydrogen-bonded to crystallographically resolved water molecules halfway up the D pathway, were replaced by more bulky hydrophobic residues (Ser200Ile, Ser200Val/Ser201Val, and Ser200Val/Ser201Tyr) to query the effects of changing the local structure on enzyme activity as well as proton uptake, release, and intermediate transitions. In addition, the effects of these mutations on internal proton transfer were investigated by blocking proton uptake at the pathway entrance (Asp132Asn replacement in addition to the above-mentioned mutations). Even though the overall activities of all mutant CytcO's were lowered, both the Ser200Ile and Ser200Val/Ser201Val variants maintained the ability to pump protons. The lowered activities were shown to be due to slowed oxidation kinetics during the PR → F and F → O transitions (PR is the "peroxy" intermediate formed at the catalytic site upon reaction of the four-electron-reduced CytcO with O2, F is the oxoferryl intermediate, and O is the fully oxidized CytcO). Furthermore, the PR → F transition is shown to be essentially pH independent up to pH 12 (i.e., the apparent pKa of Glu286 is increased from 9.4 by at least 3 pKa units) in the Ser200Val/Ser201Val mutant. Explicit simulations of proton transport in the mutated enzymes revealed that the solvation dynamics can cause intriguing energetic consequences and hence provide mechanistic insights that would never be detected in static structures or simulations of the system with fixed protonation states (i.e., lacking explicit proton transport). The results are discussed in terms of the proton-pumping mechanism of CytcO.
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- Candelier, F., et al.
(författare)
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Inertial torque on a squirmer
- 2022
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 953
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Tidskriftsartikel (refereegranskat)abstract
- A small spheroid settling in a quiescent fluid experiences an inertial torque that aligns it so that it settles with its broad side first. Here we show that an active particle experiences such a torque too, as it settles in a fluid at rest. For a spherical squirmer, the torque is T '=-9/8m(f)(v(s)((0) )boolean AND v(g)((0))) where v(s)((0) )is the swimming velocity, v(g)((0)) is the settling velocity in the Stokes approximation and mf is the equivalent fluid mass. This torque aligns the swimming direction against gravity: swimming up is stable, swimming down is unstable.
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- Collins, D., et al.
(författare)
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Lord Kelvin's isotropic helicoid
- 2021
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Ingår i: Physical Review Fluids. - 2469-990X. ; 6:7
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Tidskriftsartikel (refereegranskat)abstract
- Nearly 150 years ago, Lord Kelvin proposed the isotropic helicoid, a particle with isotropic yet chiral interactions with a fluid so that translation couples to rotation. An implementation of his design fabricated with a three-dimensional printer is found experimentally to have no detectable translation-rotation coupling, although the particle point-group symmetry allows this coupling. We explain these results by demonstrating that in Stokes flow, the chiral coupling of such isotropic helicoids made out of nonchiral vanes is due only to hydrodynamic interactions between these vanes. Therefore it is small. In summary, Kelvin's predicted isotropic helicoid exists, but only as a weak breaking of a symmetry of noninteracting vanes in Stokes flow.
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