Erratum: Dissipative Effects in Odd Viscous Stokes Flow around a Single Sphere [Phys. Rev. Lett. 132, 218303 (2024)].

This corrects the article DOI: 10.1103/PhysRevLett.132.

Dissipative Effects in Odd Viscous Stokes Flow around a Single Sphere.

Odd viscosity (OV) is a transport coefficient in, for example, fluids of self-spinning (active) particles or electrons in an external magnetic field. The key feature of OV is that it does not contribute to dissipation in two spatial dimensions. In contrast, we explicitly show that in the three-dimensional case, OV can contribute indirectly to dissipation by modifying the fluid flow.

Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs.

Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes.

Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells.

First coarse grain then scale: How to estimate diffusion coefficients of confined molecules.

An approach for approximating position and orientation dependent translational and rotational diffusion coefficients of rigid molecules of any shape suspended in a viscous fluid under geometric confinement is proposed. It is an extension of the previously developed scheme for evaluating near-wall diffusion of macromolecules, now applied to any geometry of boundaries. The method relies on shape based coarse-graining combined with scaling of mobility matrix components by factors derived based on energy dissipation arguments for Stokes flows.

Synthesis and Photochemical Properties of Fluorescent Metabolites Generated from Fluorinated Benzoylmenadiones in Living Cells.

This work describes the reactivity and properties of fluorinated derivatives ( and ) of plasmodione () and its metabolite, the plasmodione oxide (). Introduction of a fluorine atom on the 2-methyl group markedly alters the redox properties of the 1,4-naphthoquinone electrophore, making the compound highly oxidizing and particularly photoreactive. A fruitful set of analytical methods (electrochemistry, absorption and emission spectrophotometry, and HRMS-ESI) have been used to highlight the products resulting from UV photoirradiation in the absence or presence of selected nucleophiles.

Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules.

We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid.

Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast.

Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin-associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export.

A Class of Valuable (Pro-)Activity-Based Protein Profiling Probes: Application to the Redox-Active Antiplasmodial Agent, Plasmodione.

Plasmodione () is a potent antimalarial redox-active drug acting at low nM range concentrations on different malaria parasite stages. In this study, in order to determine the precise protein interactome in parasites, we developed a class of (pro-)activity-based protein profiling probes (ABPP) as precursors of photoreactive benzophenone-like probes based on the skeleton of metabolites () generated in a cascade of redox reactions. Under UV-photoirradiation, we clearly demonstrate that benzylic oxidation of 3-benzylmenadione produces the 3-benzoylmenadione probe , allowing investigation of the proof-of-concept of the ABPP strategy with 3-benzoylmenadiones -.

Ferredoxin-NADP Reductase-Catalyzed Redox Cycling of Plasmodione Generates Both Predicted Key Drug Metabolites: Implication for Antimalarial Drug Development.

Plasmodione (PD) is a potent antimalarial redox-active 3-benzyl-menadione acting at low nanomolar range concentrations on different malaria parasite stages. The specific bioactivation of PD was proposed to occur via a cascade of redox reactions starting from one-electron reduction and then benzylic oxidation, leading to the generation of several key metabolites including corresponding benzylic alcohol (PD-bzol, for PD benzhydrol) and 3-benzoylmenadione (PDO, for PD oxide). In this study, we showed that the benzylic oxidation of PD is closely related to the formation of a benzylic semiquinone radical, which can be produced under two conditions: UV photoirradiation or catalysis by apicoplast ferredoxin-NADP reductase (FNR) redox cycling in the presence of oxygen and the parent PD.

Generalized Rotne-Prager-Yamakawa approximation for Brownian dynamics in shear flow in bounded, unbounded, and periodic domains.

Inclusion of hydrodynamic interactions is essential for a quantitatively accurate Brownian dynamics simulation of colloidal suspensions or polymer solutions. We use the generalized Rotne-Prager-Yamakawa (GRPY) approximation, which takes into account all long-ranged terms in the hydrodynamic interactions, to derive the complete set of hydrodynamic matrices in different geometries: unbounded space, periodic boundary conditions of Lees-Edwards type, and vicinity of a free surface. The construction is carried out both for non-overlapping as well as for overlapping particles.

The Biogenesis of Mitochondrial Outer Membrane Proteins Show Variable Dependence on Import Factors.

Biogenesis of mitochondrial outer membrane proteins involves their integration into the lipid bilayer. Among these proteins are those that form a single-span topology, but our understanding of their biogenesis is scarce. In this study, we found that the MIM complex is required for the membrane insertion of some single-span proteins.

GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.

Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping.

Pex19 is involved in importing dually targeted tail-anchored proteins to both mitochondria and peroxisomes.

Tail-anchored (TA) proteins are embedded into their corresponding membrane via a single transmembrane segment at their C-terminus whereas the majority of the protein is facing the cytosol. So far, cellular factors that mediate the integration of such proteins into the mitochondrial outer membrane were not found. Using budding yeast as a model system, we identified the cytosolic Hsp70 chaperone Ssa1 and the peroxisome import factor Pex19 as import mediators for a subset of mitochondrial TA proteins.

Near-wall diffusion tensor of an axisymmetric colloidal particle.

Hydrodynamic interactions with confining boundaries often lead to drastic changes in the diffusive behaviour of microparticles in suspensions. For axially symmetric particles, earlier numerical studies have suggested a simple form of the near-wall diffusion matrix which depends on the distance and orientation of the particle with respect to the wall, which is usually calculated numerically. In this work, we derive explicit analytical formulae for the dominant correction to the bulk diffusion tensor of an axially symmetric colloidal particle due to the presence of a nearby no-slip wall.

Near-wall dynamics of concentrated hard-sphere suspensions: comparison of evanescent wave DLS experiments, virial approximation and simulations.

In this article we report on a study of the near-wall dynamics of suspended colloidal hard spheres over a broad range of volume fractions. We present a thorough comparison of experimental data with predictions based on a virial approximation and simulation results. We find that the virial approach describes the experimental data reasonably well up to a volume fraction of ϕ≈ 0.

Brownian motion of a particle with arbitrary shape.

Brownian motion of a particle with an arbitrary shape is investigated theoretically. Analytical expressions for the time-dependent cross-correlations of the Brownian translational and rotational displacements are derived from the Smoluchowski equation. The role of the particle mobility center is determined and discussed.

Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism.

Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key step in lipid biosynthesis that is carried out by multienzyme complexes to extend fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high redundancy of carboxyltransferase genes and biotin carboxylase genes, creating multiple combinations of protein/protein complexes of unknown overall composition and functional readout. By combining pull-down assays with mass spectrometry, we identified nine binary protein/protein interactions and four validated holo acyl-coenzyme A carboxylase complexes.

Translational and rotational near-wall diffusion of spherical colloids studied by evanescent wave scattering.

In this article we extend recent experimental developments [Rogers et al., Phys. Rev.

Hydrodynamic radius approximation for spherical particles suspended in a viscous fluid: influence of particle internal structure and boundary.

Systems of spherical particles moving in Stokes flow are studied for different particle internal structures and boundaries, including the Navier-slip model. It is shown that their hydrodynamic interactions are well described by treating them as solid spheres of smaller hydrodynamic radii, which can be determined from measured single-particle diffusion or intrinsic viscosity coefficients. Effective dynamics of suspensions made of such particles is quite accurately described by mobility coefficients of the solid particles with the hydrodynamic radii, averaged with the unchanged direct interactions between the particles.

Transport properties of suspensions-critical assessment of Beenakker-Mazur method.

The Beenakker-Mazur method of calculation of transport coefficients for suspensions has been analyzed. The analysis relies on calculation of the hydrodynamic function and the effective viscosity with higher accuracy and comparison of these characteristics to the original Beennakker-Mazur results. Comparison to numerical simulations is also given.

Fibrinogen conformations and charge in electrolyte solutions derived from DLS and dynamic viscosity measurements.

Hydrodynamic properties of fibrinogen molecules were theoretically calculated. Their shape was approximated by the bead model, considering the presence of flexible side chains of various length and orientation relative to the main body of the molecule. Using the bead model, and the precise many-multipole method of solving the Stokes equations, the mobility coefficients for the fibrinogen molecule were calculated for arbitrary orientations of the arms whose length was varied between 12 and 18 nm.

One-particle correlation function in evanescent wave dynamic light scattering.

In order to interpret measured intensity autocorrelation functions obtained in evanescent wave scattering, their initial decay rates have been analyzed recently [P. Holmqvist, J. K.

Diffusion, sedimentation, and rheology of concentrated suspensions of core-shell particles.

Short-time dynamic properties of concentrated suspensions of colloidal core-shell particles are studied using a precise force multipole method which accounts for many-particle hydrodynamic interactions. A core-shell particle is composed of a rigid, spherical dry core of radius a surrounded by a uniformly permeable shell of outer radius b and hydrodynamic penetration depth κ(-1). The solvent flow inside the permeable shell is described by the Brinkman-Debye-Bueche equation, and outside the particles by the Stokes equation.