by Keyword: diffusion

Bodrenko, I, Ceccarelli, M, Acosta-Gutierrez, S, (2023). The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics Physical Chemistry Chemical Physics 25, 26497-26506

General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores. General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. In the diffusive transport process of molecules, electrostatic interactions can help to decrease the entropic free energy barrier.

JTD Keywords: Channel, Diffusion barrier, Electric-field, Molecular-dynamics, Outer-membrane permeability, Permeation, Porins, Simulations, Translocation, Transport

Milenkovic, Stefan, Wang, Jiajun, Acosta-Gutierrez, Silvia, Winterhalter, Mathias, Ceccarelli, Matteo, Bodrenko, Igor V., (2023). How the physical properties of bacterial porins match environmental conditions Physical Chemistry Chemical Physics 25, 12712-12722

Despite the high homology of OmpF and OmpC, the internally folded loop responds differently to temperature increase.

JTD Keywords: diffusion, mechanism, molecules, nanopores, permeability, proteins, rules, simulations, transport, Membrane

Avalos-Padilla Y, Georgiev VN, Ewins E, Robinson T, Orozco E, Lipowsky R, Dimova R, (2023). Stepwise remodeling and subcompartment formation in individual vesicles by three ESCRT-III proteins Iscience 26, 105765

The endosomal sorting complex required for transport (ESCRT) is a multi-protein machinery involved in several membrane remodeling processes. Different approaches have been used to resolve how ESCRT proteins scission membranes. However, the underlying mechanisms generating membrane deformations are still a matter of debate. Here, giant unilamellar vesicles, microfluidic technology, and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodeling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate bud size and generate intraluminal vesicles even in the absence of ATP. We demonstrate that the bud stability depends on the protein concentration and membrane tension. The approaches introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.© 2022 The Author(s).

JTD Keywords: bilayer, curvature, diffusion-coefficients, identification, membrane-scission, phase-diagram, reveals, sorting complex, structural basis, Biophysics, Biotechnology, Cell biology, Giant vesicles, Membranes

Jurado A, Ulldemolins A, Lluís H, Gasull X, Gavara N, Sunyer R, Otero J, Gozal D, Almendros I, Farré R, (2023). Fast cycling of intermittent hypoxia in a physiomimetic 3D environment: A novel tool for the study of the parenchymal effects of sleep apnea Frontiers In Pharmacology 13, 1081345

Background: Patients with obstructive sleep apnea (OSA) experience recurrent hypoxemic events with a frequency sometimes exceeding 60 events/h. These episodic events induce downstream transient hypoxia in the parenchymal tissue of all organs, thereby eliciting the pathological consequences of OSA. Whereas experimental models currently apply intermittent hypoxia to cells conventionally cultured in 2D plates, there is no well-characterized setting that will subject cells to well-controlled intermittent hypoxia in a 3D environment and enable the study of the effects of OSA on the cells of interest while preserving the underlying tissue environment.Aim: To design and characterize an experimental approach that exposes cells to high-frequency intermittent hypoxia mimicking OSA in 3D (hydrogels or tissue slices).Methods: Hydrogels made from lung extracellular matrix (L-ECM) or brain tissue slices (300-800-mu m thickness) were placed on a well whose bottom consisted of a permeable silicone membrane. The chamber beneath the membrane was subjected to a square wave of hypoxic/normoxic air. The oxygen concentration at different depths within the hydrogel/tissue slice was measured with an oxygen microsensor.Results: 3D-seeded cells could be subjected to well-controlled and realistic intermittent hypoxia patterns mimicking 60 apneas/h when cultured in L-ECM hydrogels & AP;500 mu m-thick or ex-vivo in brain slices 300-500 mu m-thick.Conclusion: This novel approach will facilitate the investigation of the effects of intermittent hypoxia simulating OSA in 3D-residing cells within the parenchyma of different tissues/organs.

JTD Keywords: 3d culture, cell culture, diffusion, disease model, hydrogels, hypoxia, model, oxygen diffusion, tissue slice, transport, 3d culture, Cell culture, Disease model, Hydrogels, Hypoxia, Obstructive sleep apnea, Oxygen, Oxygen diffusion, Tissue slice

Checa, Marti, Jin, Xin, Millan-Solsona, Ruben, Neumayer, Sabine M., Susner, Michael A., McGuire, Michael A., OHara, Andrew, Gomila, Gabriel, Maksymovych, Petro, Pantelides, Sokrates T., Collins, Liam, (2022). Revealing Fast Cu-Ion Transport and Enhanced Conductivity at the CuInP2S6?In4/3P2S6 Heterointerface Acs Nano 16, 15347-15357

Van der Waals layered ferroelectrics, such as CuInP2S6 (CIPS), offer a versatile platform for miniaturization of ferroelectric device technologies. Control of the targeted composition and kinetics of CIPS synthesis enables the formation of stable self-assembled heterostructures of ferroelectric CIPS and nonferroelectric In4/3P2S6 (IPS). Here, we use quantitative scanning probe microscopy methods combined with density functional theory (DFT) to explore in detail the nanoscale variability in dynamic functional properties of the CIPS-IPS heterostructure. We report evidence of fast ionic transport which mediates an appreciable out-of-plane electromechanical response of the CIPS surface in the paraelectric phase. Further, we map the nanoscale dielectric and ionic conductivity properties as we thermally stimulate the ferroelectric-paraelectric phase transition, recovering the local dielectric behavior during this phase transition. Finally, aided by DFT, we reveal a substantial and tunable conductivity enhancement at the CIPS/IPS interface, indicating the possibility of engineering its interfacial properties for next generation device applications.

JTD Keywords: copper indium thiophosphate, diffusion, elastic band method, ferroelectrics, ionic conductor, migration, nanoscale, phase transition, piezoresponse force microscopy, scanning dielectric microscopy, transition, Copper indium thiophosphate, Initio molecular-dynamics, Scanning dielectric microscopy

Tuveri, GM, Ceccarelli, M, Pira, A, Bodrenko, IV, (2022). The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway Antibiotics 11, 840

We investigated the diffusion of three cyclic boronates formulated as beta-lactamase inhibitors through the porin OmpF to evaluate their potential to cross OM via the porin pathway. The three nonbeta-lactam molecules diffuse through the porin eyelet region with the same mechanism observed for beta-lactam molecules and diazobicyclooctan derivatives, with the electric dipole moment aligned with the transversal electric field. In particular, the BOH group can interact with both the basic ladder and the acidic loop L3, which is characteristic of the size-constricted region of this class of porins. On one hand, we confirm that the transport of small molecules through enterobacter porins has a common general mechanism; on the other, the class of cyclic boronate molecules does not seem to have particular difficulties in diffusing through enterobacter porins, thus representing a good scaffold for new anti-infectives targeting Gram-negative bacteria research.

JTD Keywords: beta-lactamase inhibitors, cyclic boronates, diffusion current, metadynamics, molecular dynamics simulations, permeation, Antibiotics, Beta-lactamase inhibitors, Cyclic boronates, Diffusion, Diffusion current, Discovery, Electric-field, Metadynamics, Molecular dynamics simulations, Molecular-dynamics simulations, Nanopores, Permeability, Permeation, Porins, Rules, Translocation

Valles, Morgane, Pujals, Sílvia, Albertazzi, Lorenzo, Sánchez, Samuel, (2022). Enzyme Purification Improves the Enzyme Loading, Self-Propulsion, and Endurance Performance of Micromotors Acs Nano 16, 5615-5626

Enzyme-powered micro- and nanomotors make use of biocatalysis to self-propel in aqueous media and hold immense promise for active and targeted drug delivery. Most (if not all) of these micro- and nanomotors described to date are fabricated using a commercially available enzyme, despite claims that some commercial preparations may not have a sufficiently high degree of purity for downstream applications. In this study, the purity of a commercial urease, an enzyme frequently used to power the motion of micro- and nanomotors, was evaluated and found to be impure. After separating the hexameric urease from the protein impurities by size-exclusion chromatography, the hexameric urease was subsequently characterized and used to functionalize hollow silica microcapsules. Micromotors loaded with purified urease were found to be 2.5 times more motile than the same micromotors loaded with unpurified urease, reaching average speeds of 5.5 ?m/s. After comparing a number of parameters, such as enzyme distribution, protein loading, and motor reusability, between micromotors functionalized with purified vs unpurified urease, it was concluded that protein purification was essential for optimal performance of the enzyme-powered micromotor.

JTD Keywords: canavalin, catalysis, delivery, dls, enhanced diffusion, enzyme, lipase immobilization, micromotors, self-propulsion, super-resolution microscopy, urease, Mesoporous silica nanoparticles, Micromotors, Super-resolution microscopy

Kaurin, D, Bal, PK, Arroyo, M, (2022). Peeling dynamics of fluid membranes bridged by molecular bonds: moving or breaking Journal Of The Royal Society Interface 19, 20220183

Biological adhesion is a critical mechanical function of complex organisms. At the scale of cell-cell contacts, adhesion is remarkably tunable to enable both cohesion and malleability during development, homeostasis and disease. It is physically supported by transient and laterally mobile molecular bonds embedded in fluid membranes. Thus, unlike specific adhesion at solid-solid or solid-fluid interfaces, peeling at fluid-fluid interfaces can proceed by breaking bonds, by moving bonds or by a combination of both. How the additional degree of freedom provided by bond mobility changes the mechanics of peeling is not understood. To address this, we develop a theoretical model coupling diffusion, reactions and mechanics. Mobility and reaction rates determine distinct peeling regimes. In a diffusion-dominated Stefan-like regime, bond motion establishes self-stabilizing dynamics that increase the effective fracture energy. In a reaction-dominated regime, peeling proceeds by travelling fronts where marginal diffusion and unbinding control peeling speed. In a mixed reaction-diffusion regime, strengthening by bond motion competes with weakening by bond breaking in a force-dependent manner, defining the strength of the adhesion patch. In turn, patch strength depends on molecular properties such as bond stiffness, force sensitivity or crowding. We thus establish the physical rules enabling tunable cohesion in cellular tissues and in engineered biomimetic systems.

JTD Keywords: cell–cell adhesion, peeling, Adhesive contact, Cadherins, Cell-cell adhesion, Detachment, Detailed mechanics, Diffusion, Growth, Kinetics, Peeling, Red-blood-cells, Repulsion, Separation, Vesicle adhesion

Crespo, Anna, Pedraz, Lucas, Astola, Josep, Torrents, Eduard, (2016). Pseudomonas aeruginosa exhibits deficient biofilm formation in the absence of class II and III ribonucleotide reductases due to hindered anaerobic growth Frontiers in Microbiology 7, Article 688

Chronic lung infections by the ubiquitous and extremely adaptable opportunistic pathogen Pseudomonas aeruginosa correlate with the formation of a biofilm, where bacteria grow in association with an extracellular matrix and display a wide range of changes in gene expression and metabolism. This leads to increased resistance to physical stress and antibiotic therapies, while enhancing cell-to-cell communication. Oxygen diffusion through the complex biofilm structure generates an oxygen concentration gradient, leading to the appearance of anaerobic microenvironments. Ribonucleotide reductases (RNRs) are a family of highly sophisticated enzymes responsible for the synthesis of the deoxyribonucleotides, and they constitute the only de novo pathway for the formation of the building blocks needed for DNA synthesis and repair. P. aeruginosa is one of the few bacteria encoding all three known RNR classes (Ia, II, and III). Class Ia RNRs are oxygen dependent, class II are oxygen independent, and class III are oxygen sensitive. A tight control of RNR activity is essential for anaerobic growth and therefore for biofilm development. In this work we explored the role of the different RNR classes in biofilm formation under aerobic and anaerobic initial conditions and using static and continuous-flow biofilm models. We demonstrated the importance of class II and III RNR for proper cell division in biofilm development and maturation. We also determined that these classes are transcriptionally induced during biofilm formation and under anaerobic conditions. The molecular mechanism of their anaerobic regulation was also studied, finding that the Anr/Dnr system is responsible for class II RNR induction. These data can be integrated with previous knowledge about biofilms in a model where these structures are understood as a set of layers determined by oxygen concentration and contain cells with different RNR expression profiles, bringing us a step closer to the understanding of this complex growth pattern, essential for P. aeruginosa chronic infections.

JTD Keywords: Pseudomonas aeruginosa, Ribonucleotide Reductases, Vitamin B 12, Anaerobic metabolism, Biofilm formation, DNA Synthesis, Oxygen diffusion, nrd genes.

Malandrino, Andrea, Noailly, Jerome, Lacroix, Damien, (2011). The effect of sustained compression on oxygen metabolic transport in the intervertebral disc decreases with degenerative changes PLoS Computational Biology Plos Computational Biology , 7, (8), 1-12

Intervertebral disc metabolic transport is essential to the functional spine and provides the cells with the nutrients necessary to tissue maintenance. Disc degenerative changes alter the tissue mechanics, but interactions between mechanical loading and disc transport are still an open issue. A poromechanical finite element model of the human disc was coupled with oxygen and lactate transport models. Deformations and fluid flow were linked to transport predictions by including strain-dependent diffusion and advection. The two solute transport models were also coupled to account for cell metabolism. With this approach, the relevance of metabolic and mechano-transport couplings were assessed in the healthy disc under loading-recovery daily compression. Disc height, cell density and material degenerative changes were parametrically simulated to study their influence on the calculated solute concentrations. The effects of load frequency and amplitude were also studied in the healthy disc by considering short periods of cyclic compression. Results indicate that external loads influence the oxygen and lactate regional distributions within the disc when large volume changes modify diffusion distances and diffusivities, especially when healthy disc properties are simulated. Advection was negligible under both sustained and cyclic compression. Simulating degeneration, mechanical changes inhibited the mechanical effect on transport while disc height, fluid content, nucleus pressure and overall cell density reductions affected significantly transport predictions. For the healthy disc, nutrient concentration patterns depended mostly on the time of sustained compression and recovery. The relevant effect of cell density on the metabolic transport indicates the disturbance of cell number as a possible onset for disc degeneration via alteration of the metabolic balance. Results also suggest that healthy disc properties have a positive effect of loading on metabolic transport. Such relation, relevant to the maintenance of the tissue functional composition, would therefore link disc function with disc nutrition.

JTD Keywords: Bovine nucleus pulposus, Human anulus fibrosus, Finite-element, Fluid-flow, Hydraulic permeability, Confined compression, Coupled diffusion, Solute transport, Water-content, Lumbar spine

Kodippili, G. C., Spector, J., Kang, G. E., Liu, H., Wickrema, A., Ritchie, K., Low, P. S., (2010). Analysis of the kinetics of band 3 diffusion in human erythroblasts during assembly of the erythrocyte membrane skeleton British Journal of Haematology , 150, (5), 592-600

Summary During definitive erythropoiesis, erythroid precursors undergo differentiation through multiple nucleated states to an enucleated reticulocyte, which loses its residual RNA/organelles to become a mature erythrocyte. Over the course of these transformations, continuous changes in membrane proteins occur, including shifts in protein abundance, rates of expression, isoform prominence, states of phosphorylation, and stability. In an effort to understand when assembly of membrane proteins into an architecture characteristic of the mature erythrocyte occurs, we quantitated the lateral diffusion of the most abundant membrane protein, band 3 (AE1), during each stage of erythropoiesis using single particle tracking. Analysis of the lateral trajectories of individual band 3 molecules revealed a gradual reduction in mobility of the anion transporter as erythroblasts differentiated. Evidence for this progressive immobilization included a gradual decline in diffusion coefficients as determined at a video acquisition rate of 120 frames/s and a decrease in the percentage of compartment sizes >100 nm. Because complete acquisition of the properties of band 3 seen in mature erythrocytes is not observed until circulating erythrocytes are formed, we suggest that membrane maturation involves a gradual and cooperative assembly process that is not triggered by the synthesis of any single protein.

JTD Keywords: Band 3 diffusion, Erythrocyte, Progenitor cells, Single particle tracking, Streptavidin quantum dot