Protein-Rich Rafts in Hybrid Polymer/Lipid Giant Unilamellar Vesicles

Considerable attention has been dedicated to lipid rafts due to their importance in numerous cell functions such as membrane trafficking, polarization, and signaling. Next to studies in living cells, artificial micrometer-sized vesicles with a minimal set of components are established as a major tool to understand the phase separation dynamics and their intimate interplay with membrane proteins. In parallel, mixtures of phospholipids and certain amphiphilic polymers simultaneously offer an interface for proteins and mimic this segregation behavior, presenting a tangible synthetic alternative for fundamental studies and bottom-up design of cellular mimics. However, the simultaneous insertion of complex and sensitive membrane proteins is experimentally challenging and thus far has been largely limited to natural lipids. Here, we present the co-reconstitution of the proton pump bo3 oxidase and the proton consumer ATP synthase in hybrid polymer/lipid giant unilamellar vesicles (GUVs) via fusion/electroformation. Variations of the current method allow for tailored reconstitution protocols and control of the vesicle size. In particular, mixing of protein-free and protein-functionalized nanosized vesicles in the electroformation film results in larger GUVs, while separate reconstitution of the respiratory enzymes enables higher ATP synthesis rates. Furthermore, protein labeling provides a synthetic mechanism for phase separation and protein sequestration, mimicking lipid- and protein-mediated domain formation in nature. The latter means opens further possibilities for re-enacting phenomena like supercomplex assembly or symmetry breaking and enriches the toolbox of bottom-up synthetic biology.

Gibbs-Helmholtz Graph Neural Network for the Prediction of Activity Coefficients of Polymer Solutions at Infinite Dilution

Machine learning models have gained prominence for predicting pure-component properties, yet their application to mixture property prediction remains relatively limited. However, the significance of mixtures in our daily lives is undeniable, particularly in industries such as polymer processing. This study presents a modification of the Gibbs-Helmholtz graph neural network (GH-GNN) model for predicting weight-based activity coefficients at infinite dilution (Ωij∞) in polymer solutions. We evaluate various polymer representations ranging from monomer, repeating unit, periodic unit, and oligomer and observe that, in data-scarce scenarios of polymer-solvent mixtures, polymer representation specifics have a reduced impact compared to data-rich environments. Leveraging transfer learning, we harness richer activity coefficient data from small-size systems, enhancing model accuracy and reducing prediction variability. The modified GH-GNN model achieves remarkable prediction results in mixture interpolation and solvent extrapolation tasks having an overall mean absolute error of 0.15, showcasing the potential of graph-neural-network-based models for property prediction of polymer solutions. Comparative analysis with the established models UNIFAC-ZM and Entropic-FV suggests a promising avenue for future research on the use of data-driven models for the prediction of the thermodynamic properties of polymer solutions.

Electrochemical evaluation of the de-/re-activation of oxygen evolving Ir oxide

Understanding the influence of dynamic and stationary polarization on the deactivation of state-of-the-art IrOx catalysts is imperative for the design and operation of robust and efficient proton exchange membrane water...

Fusion-Induced Growth of Biomimetic Polymersomes: Behavior of Poly(dimethylsiloxane)-Poly(ethylene oxide) Vesicles in Saline Solutions Under High Agitation

Giant unilamellar vesicles serve as membrane models and primitive mockups of natural cells. With respect to the latter use, amphiphilic polymers can be used to replace phospholipids in order to introduce certain favorable properties, ultimately allowing for the creation of truly synthetic cells. These new properties also enable the employment of new preparation procedures that are incompatible with the natural amphiphiles. Whereas the growth of lipid compartments to micrometer dimensions has been well established, growth of their synthetic analogs remains underexplored. Here, the influence of experimental parameters like salt type/concentration and magnitude of agitation on the fusion of nanometer-sized vesicles made of poly(dimethylsiloxane)-poly(ethylene oxide) graft copolymer (PDMS-g-PEO) is investigated in detail. To this end, dynamic light scattering, microscopy, and membrane mixing assays are employed, and the process at different time and length scales is analyzed. This optimized method is used as an easy tool to obtain giant vesicles, equipped with membrane and cytosolic biomachinery, in the presence of salts at physiological concentrations.

En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes

A variety of artificial cells springs from the functionalization of liposomes with proteins. However, these models suffer from low durability without repair and replenishment mechanisms, which can be partly addressed by replacing the lipids with polymers. Yet natural membranes are also dynamically remodeled in multiple cellular processes. Here, we show that synthetic amphiphile membranes also undergo fusion, mediated by the protein machinery for synaptic secretion. We integrated fusogenic SNAREs in polymer and hybrid vesicles and observed efficient membrane and content mixing. We determined bending rigidity and pore edge tension as key parameters for fusion and described its plausible progression through cryo-EM snapshots. These findings demonstrate that dynamic membrane phenomena can be reconstituted in synthetic materials, thereby providing new tools for the assembly of synthetic protocells.

Light-Powered Reactivation of Flagella and Contraction of Microtubule Networks: Toward Building an Artificial Cell

Artificial systems capable of self-sustained movement with self-sufficient energy are of high interest with respect to the development of many challenging applications, including medical treatments, but also technical applications. The bottom-up assembly of such systems in the context of synthetic biology is still a challenging task. In this work, we demonstrate the biocompatibility and efficiency of an artificial light-driven energy module and a motility functional unit by integrating light-switchable photosynthetic vesicles with demembranated flagella. The flagellar propulsion is coupled to the beating frequency, and dynamic ATP synthesis in response to illumination allows us to control beating frequency of flagella in a light-dependent manner. In addition, we verified the functionality of light-powered synthetic vesicles in in vitro motility assays by encapsulating microtubules assembled with force-generating kinesin-1 motors and the energy module to investigate the dynamics of a contractile filamentous network in cell-like compartments by optical stimulation. Integration of this photosynthetic system with various biological building blocks such as cytoskeletal filaments and molecular motors may contribute to the bottom-up synthesis of artificial cells that are able to undergo motor-driven morphological deformations and exhibit directional motion in a light-controllable fashion.

Bottom-Up Synthesis of Artificial Cells: Recent Highlights and Future Challenges

The bottom-up approach in synthetic biology aims to create molecular ensembles that reproduce the organization and functions of living organisms and strives to integrate them in a modular and hierarchical fashion toward the basic unit of life-the cell-and beyond. This young field stands on the shoulders of fundamental research in molecular biology and biochemistry, next to synthetic chemistry, and, augmented by an engineering framework, has seen tremendous progress in recent years thanks to multiple technological and scientific advancements. In this timely review of the research over the past decade, we focus on three essential features of living cells: the ability to self-reproduce via recursive cycles of growth and division, the harnessing of energy to drive cellular processes, and the assembly of metabolic pathways. In addition, we cover the increasing efforts to establish multicellular systems via different communication strategies and critically evaluate the potential applications.

Scale up of Transmembrane NADH Oxidation in Synthetic Giant Vesicles

The transfer of electrons across and along biological membranes drives the cellular energetics. In the context of artificial cells, it can be mimicked by minimal means, while using synthetic alternatives of the phospholipid bilayer and the electron-transducing proteins. Furthermore, the scaling up to biologically relevant and optically accessible dimensions may provide further insight and allow assessment of individual events but has been rarely attempted so far. Here, we visualized the mediated transmembrane oxidation of encapsulated NADH in giant unilamellar vesicles via confocal laser scanning and time-correlated single photon counting wide-field microscopy. To this end, we first augmented phospholipid membranes with an amphiphilic copolymer in order to check its influence on the oxidation kinetics spectrophotometrically. Then, we scaled up the compartments and followed the process microscopically.

On the role of microkinetic network structure in the interplay between oxygen evolution reaction and catalyst dissolution

Understanding the pathways of oxygen evolution reaction (OER) and the mechanisms of catalyst degradation is of essential importance for developing efficient and stable OER catalysts. Experimentally, a close coupling between OER and catalyst dissolution on metal oxides is reported. In this work, it is analysed how the microkinetic network structure of a generic electrocatalytic cycle, in which a common intermediate causes catalyst dissolution, governs the interplay between electrocatalytic activity and stability. Model discrimination is possible based on the analysis of incorporated microkinetic network structures and the comparison to experimental data. The derived concept is used to analyse the coupling of OER and catalyst dissolution on rutile and reactively sputtered Iridium oxides. For rutile Iridium oxide, the characteristic activity and stability behaviour can be well described by a mono-nuclear, adsorbate evolution mechanism and the chemical type of both competing dissolution and rate-determining OER-step. For the reactively sputtered Iridium oxide surface, experimentally observed characteristics can be captured by the assumption of an additional path via a low oxidation state intermediate, which explains the observed characteristic increase in OER over dissolution selectivity with potential by the competition between electrochemical re-oxidation and chemical dissolution.

Light-Driven ATP Regeneration in Diblock/Grafted Hybrid Vesicles

Light-driven ATP regeneration systems combining ATP synthase and bacteriorhodopsin have been proposed as an energy supply in the field of synthetic biology. Energy is required to power biochemical reactions within artificially created reaction compartments like protocells, which are typically based on either lipid or polymer membranes. The insertion of membrane proteins into different hybrid membranes is delicate, and studies comparing these systems with liposomes are needed. Here we present a detailed study of membrane protein functionality in different hybrid compartments made of graft polymer PDMS-g-PEO and diblock copolymer PBd-PEO. Activity of more than 90 % in lipid/polymer-based hybrid vesicles could prove an excellent biocompatibility. A significant enhancement of long-term stability (80 % remaining activity after 42 days) could be demonstrated in polymer/polymer-based hybrids.

Constructing artificial respiratory chain in polymer compartments: Insights into the interplay between bo3 oxidase and the membrane

Cytochrome bo3 ubiquinol oxidase is a transmembrane protein, which oxidizes ubiquinone and reduces oxygen, while pumping protons. Apart from its combination with F1Fo-ATPase to assemble a minimal ATP regeneration module, the utility of the proton pump can be extended to other applications in the context of synthetic cells such as transport, signaling, and control of enzymatic reactions. In parallel, polymers have been speculated to be phospholipid mimics with respect to their ability to self-assemble in compartments with increased stability. However, their usability as interfaces for complex membrane proteins has remained questionable. In the present work, we optimized a fusion/electroformation approach to reconstitute bo3 oxidase in giant unilamellar vesicles made of PDMS-g-PEO and/or phosphatidylcholine (PC). This enabled optical access, while microfluidic trapping allowed for online analysis of individual vesicles. The tight polymer membranes and the inward oriented enzyme caused 1 pH unit difference in 30 min, with an initial rate of 0.35 pH·min-1 To understand the interplay in these composite systems, we studied the relevant mechanical and rheological membrane properties. Remarkably, the proton permeability of polymer/lipid hybrids decreased after protein insertion, while the latter also led to a 20% increase of the polymer diffusion coefficient in polymersomes. In addition, PDMS-g-PEO increased the activity lifetime and the resistance to free radicals. These advantageous properties may open diverse applications, ranging from cell-free biotechnology to biomedicine. Furthermore, the presented study serves as a comprehensive road map for studying the interactions between membrane proteins and synthetic membranes, which will be fundamental for the successful engineering of such hybrid systems.

Symmetry Breaking and Emergence of Directional Flows in Minimal Actomyosin Cortices

Cortical actomyosin flows, among other mechanisms, scale up spontaneous symmetry breaking and thus play pivotal roles in cell differentiation, division, and motility. According to many model systems, myosin motor-induced local contractions of initially isotropic actomyosin cortices are nucleation points for generating cortical flows. However, the positive feedback mechanisms by which spontaneous contractions can be amplified towards large-scale directed flows remain mostly speculative. To investigate such a process on spherical surfaces, we reconstituted and confined initially isotropic minimal actomyosin cortices to the interfaces of emulsion droplets. The presence of ATP leads to myosin-induced local contractions that self-organize and amplify into directed large-scale actomyosin flows. By combining our experiments with theory, we found that the feedback mechanism leading to a coordinated directional motion of actomyosin clusters can be described as asymmetric cluster vibrations, caused by intrinsic non-isotropic ATP consumption with spatial confinement. We identified fingerprints of vibrational states as the basis of directed motions by tracking individual actomyosin clusters. These vibrations may represent a generic key driver of directed actomyosin flows under spatial confinement in vitro and in living systems.

Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

BACKGROUND

The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, this work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the recently published nuclear genome and its validation with experimental observations and literature data.

RESULTS

The reconstruction resulted in a network model with 221 reactions and 212 metabolites within three compartments: cytosol, chloroplast and mitochondrion. The network was implemented in the MATLAB toolbox CellNetAnalyzer and checked for feasibility. Furthermore, a flux balance analysis was carried out for different light and nutrient uptake rates. The comparison of the experimental knowledge with the model prediction revealed that the results of the stoichiometric network analysis are plausible and in good agreement with the observed behavior. Accordingly, our model provides an excellent tool for investigating the carbon core metabolism of D. salina.

CONCLUSIONS

The reconstructed metabolic network of D. salina presented in this work is able to predict the biological behavior under light and nutrient stress and will lead to an improved process understanding for the optimized production of high-value products in microalgae.

Transformation of remnant algal biomass to 5-HMF and levulinic acid: influence of a biphasic solvent system

The primary commercial product from the green microalgae Dunaliella salina is β-carotene. After extracting the lipophilic fraction containing this red-orange pigment, an algal residue remains. As the carotenogenesis is induced by light stress with simultaneous nitrogen depletion, the protein content is low and the remnant is comprised largely of storage carbohydrates. In this work, we transformed the defatted remnant directly to the platform chemicals, 5-hydroxy methyl furfural (5-HMF) and levulinic acid (LA), without previous purification or any pretreatment. The batch experiments were carried out in an autoclave under biphasic solvent conditions at 453 K for 1 h using acidic ZSM-5 zeolite as a heterogeneous catalyst. Mixtures of methyl isobutyl ketone (MIBK/H₂O) or tetrahydrofuran (THF/H₂O/NaCl) with water were used to create the biphasic reactor conditions. The biphasic reaction mixtures helped to increase the 5-HMF yield and simultaneously mitigated the formation of insoluble humins. The carbon yields of 5-HMF and of LA in the MIBK/H₂O biphasic system without NaCl were 13.9% and 3.7%, respectively. The highest carbon yield of 5-HMF (34.4%) was achieved by adding NaCl to the reaction mixture containing THF/H₂O. The experimentally measured partition ratios of 5-HMF between the two liquid phases were compared to the predictions calculated by the computational method COSMO-RS, which is a quantum chemistry-based method to predict the thermodynamic equilibria of liquid mixtures and the solubilities. The COSMO-RS predicted partition ratios of 5-HMF were in line with the experimentally measured ones.

Defatted algal remnant is transformed to 5-HMF and LA.

A Guide to Concentration Alternating Frequency Response Analysis of Fuel Cells

An experimental setup capable of generating a periodic concentration input perturbation of oxygen was used to perform concentration-alternating frequency response analysis (cFRA) on proton-exchange membrane (PEM) fuel cells. During cFRA experiments, the modulated concentration feed was sent to the cathode of the cell at different frequencies. The electric response, which can be cell potential or current depending on the control applied on the cell, was registered in order to formulate a frequency response transfer function. Unlike traditional electrochemical impedance spectroscopy (EIS), the novel cFRA methodology makes it possible to separate the contribution of different mass transport phenomena from the kinetic charge transfer processes in the frequency response spectra of the cell. Moreover, cFRA is able to differentiate between varying humidification states of the cathode. In this protocol, the focus is on the detailed description of the procedure to perform cFRA experiments. The most critical steps of the measurements and future improvements to the technique are discussed.

Compartments for Synthetic Cells: Osmotically Assisted Separation of Oil from Double Emulsions in a Microfluidic Chip

Liposomes are used in synthetic biology as cell-like compartments and their microfluidic production through double emulsions allows for efficient encapsulation of various components. However, residual oil in the membrane remains a critical bottleneck for creating pristine phospholipid bilayers. It has been discovered that osmotically driven shrinking leads to detachment of the oil drop. Separation inside a microfluidic chip has been realized to automate the procedure, which allows for controlled continuous production of monodisperse liposomes.

Polymer-Based Module for NAD+ Regeneration with Visible Light

The regeneration of enzymatic cofactors by cell-free synthetic modules is a key step towards producing a purely synthetic cell. Herein, we demonstrate the regeneration of the enzyme cofactor NAD⁺ by photo-oxidation of NADH under visible-light irradiation by using metal-free conjugated polymer nanoparticles. Encapsulation of the light-active nanoparticles in the lumen of polymeric vesicles produced a fully organic module able to regenerate NAD⁺ in an enzyme-free system. The polymer compartment conferred physical and chemical autonomy to the module, allowing the regeneration of NAD⁺ to occur efficiently, even in harsh chemical environments. Moreover, we show that regeneration of NAD⁺ by the photocatalyst nanoparticles can oxidize a model substrate, in conjunction with the enzyme glycerol dehydrogenase. To ensure the longevity of the enzyme, we immobilized it within a protective silica matrix; this yielded enzymatic silica nanoparticles with enhanced long-term performance and compatibility with the NAD⁺ -regeneration system.