Brownian Motion at Lipid Membranes: A Comparison of Hydrodynamic Models Describing and Experiments Quantifying Diffusion within Lipid Bilayers

Nanocatalytic performance of pectinase immobilized over in situ prepared magnetic nanoparticles

Immobilization of enzymes is one of the protein engineering methods used to improve their thermal and long-term stabilities. Immobilized pectinase has become an essential biocatalyst for optimization in the food processing industry. Herein, nanostructured magnetic nanoparticles were prepared in situ for use as supports to immobilize pectinase. The structural, morphological, optical and magnetic features and the chemical compositions of the nanoparticles were characterized. Nanoparticle agglomeration and low porosity were observed due to the synthetic conditions. These nanoparticles exhibited superparamagnetic behavior, which is desirable for biotechnological applications. The maximum retention rate for the enzyme was observed at pH 4.5 with a value of 1179.3 U/mgNP (units per milligram of nanoparticle), which was equivalent to a 65.6% efficiency. The free and immobilized pectinase were affected by the pH and temperature. The long-term instability caused 40% and 32% decreases in the specific activities of the free and immobilized pectinase, respectively. The effects of immobilization were analyzed with kinetic and thermodynamic studies. These results indicated a significant affinity for the substrate, a decreased reaction rate, and improved thermal stability of the immobilized pectinase. The reusability of the immobilized pectinase was preserved effectively during cycling, with only a 21.2% decrease in activity observed from the first to the last use. Therefore, alternative magnetic nanoparticles are presented for immobilizing and maintaining the thermostability of pectinase.

A cell free biomembrane platform for multimodal study of influenza virus hemagglutinin and for evaluation of entry-inhibitors against hemagglutinin

Seasonal periodic pandemics and epidemics caused by Influenza A viruses (IAVs) are associated with high morbidity and mortality worldwide. They are frequent and unpredictable in severity so there is a need for biophysical platforms that can be used to provide both mechanistic insights into influenza virulence and its potential treatment by anti-IAV agents. Host membrane viral association through the glycoprotein hemagglutinin (HA) of IAVs is one of the primary steps in infection. HA is thus a potential target for drug discovery and development against influenza. Deconvolution of the multivalent interactions of HA at the interfaces of the host cell membrane can help unravel therapeutic targets. In this contribution, we reported the effect of a multivalent HA glycoprotein association on various glycosphingolipid receptors (GD1a, GM3, GM1) doped asymmetrically into an artificial host membrane spanned across an aqueous filled microcavity array. The extent of HA association and its impact on membrane resistance, capacitance, and diffusivity was measured using highly sensitive electrochemical impedance spectroscopy (EIS) and fluorescence lifetime correlation spectroscopy (FLCS). Furthermore, we investigated the inhibition of the influenza HA glycoprotein association with the host mimetic surface by natural and synthetic sialic acid-based inhibitors (sialic acid, Siaα2,3-GalOMe, FB127, 3-sialyl lactose) using electrochemical impedance spectroscopy and observe that while all inhibit, they do not prevent host binding. Overall, the work demonstrates the platform provides a label-free screening platform for the biophysical evaluation of new inhibitors in the development of potential therapeutics for IAV infection prevention and treatment.

Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes

Numerous key biological processes rely on the concept of multivalency, where ligands achieve stable binding only upon engaging multiple receptors. These processes, like viral entry or immune synapse formation, occur on the diffusive cellular membrane. One crucial, yet underexplored aspect of multivalent binding is the mobility of coupled receptors. Here, we discuss the consequences of mobility in multivalent processes from four perspectives: (I) The facilitation of receptor recruitment by the multivalent ligand due to their diffusivity prior to binding. (II) The effects of receptor preassembly, which allows their local accumulation. (III) The consequences of changes in mobility upon the formation of receptor/ligand complex. (IV) The changes in the diffusivity of lipid environment surrounding engaged receptors. We demonstrate how understanding mobility is essential for fully unravelling the principles of multivalent membrane processes, leading to further development in studies on receptor interactions, and guide the design of new generations of multivalent ligands.

A vesicle microrheometer for high-throughput viscosity measurements of lipid and polymer membranes

Viscosity is a key property of cell membranes that controls mobility of embedded proteins and membrane remodeling. Measuring it is challenging because existing approaches involve complex experimental designs and/or models, and the applicability of some methods is limited to specific systems and membrane compositions. As a result there is scarcity of systematic data, and the reported values for membrane viscosity vary by orders of magnitude for the same system. Here, we show how viscosity of membranes can be easily obtained from the transient deformation of giant unilamellar vesicles. The approach enables a noninvasive, probe-independent, and high-throughput measurement of the viscosity of membranes made of lipids or polymers with a wide range of compositions and phase state. Using this novel method, we have collected a significant amount of data that provides insights into the relation between membrane viscosity, composition, and structure.

Subdiffusive-Brownian crossover in membrane proteins: a generalized Langevin equation-based approach

In this work, we propose a generalized Langevin equation-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (noninstantaneous) component modeled through a Dirac δ function and a three-parameter Mittag-Leffler type function, respectively. By imposing a specific relationship between the parameters of the three-parameter Mittag-Leffler function, the different dynamical regimes-namely ballistic, subdiffusive, and Brownian, as well as the crossover from one regime to another-are retrieved. Within this approach, the transition time from the ballistic to the subdiffusive regime and the spectrum of relaxation times underlying the transition from the subdiffusive to the Brownian regime are given. The reliability of the model is tested by comparing the mean-square displacement derived in the framework of this model and the mean-square displacement of a protein diffusing in a membrane calculated through molecular dynamics simulations.

Physicochemical tools for studying virus interactions with targeted cell membranes in a molecular and spatiotemporally resolved context

The objective of this critical review is to provide an overview of how emerging bioanalytical techniques are expanding our understanding of the complex physicochemical nature of virus interactions with host cell surfaces. Herein, selected model viruses representing both non-enveloped (simian virus 40 and human norovirus) and enveloped (influenza A virus, human herpes simplex virus, and human immunodeficiency virus type 1) viruses are highlighted. The technologies covered utilize a wide range of cell membrane mimics, from supported lipid bilayers (SLBs) containing a single purified host membrane component to SLBs derived from the plasma membrane of a target cell, which can be compared with live-cell experiments to better understand the role of individual interaction pairs in virus attachment and entry. These platforms are used to quantify binding strengths, residence times, diffusion characteristics, and binding kinetics down to the single virus particle and single receptor, and even to provide assessments of multivalent interactions. The technologies covered herein are surface plasmon resonance (SPR), quartz crystal microbalance with dissipation (QCM-D), dynamic force spectroscopy (DFS), total internal reflection fluorescence (TIRF) microscopy combined with equilibrium fluctuation analysis (EFA) and single particle tracking (SPT), and finally confocal microscopy using multi-labeling techniques to visualize entry of individual virus particles in live cells. Considering the growing scientific and societal needs for untangling, and interfering with, the complex mechanisms of virus binding and entry, we hope that this review will stimulate the community to implement these emerging tools and strategies in conjunction with more traditional methods. The gained knowledge will not only contribute to a better understanding of the virus biology, but may also facilitate the design of effective inhibitors to block virus entry.

Patterning Microtubule Network Organization Reshapes Cell-Like Compartments

Eukaryotic cells contain a cytoskeletal network comprised of dynamic microtubule filaments whose spatial organization is highly plastic. Specialized microtubule architectures are optimized for different cell types and remodel with the oscillatory cell cycle. These spatially distinct microtubule networks are thought to arise from the activity and localization of microtubule regulators and motors and are further shaped by physical forces from the cell boundary. Given complexities and redundancies of a living cell, it is challenging to disentangle the separate biochemical and physical contributions to microtubule network organization. Therefore, we sought to develop a minimal cell-like system to manipulate and spatially pattern the organization of cytoskeletal components in real-time, providing an opportunity to build distinct spatial structures and to determine how they are shaped by or reshape cell boundaries. We constructed a system for induced spatial patterning of protein components within cell-sized emulsion compartments and used it to drive microtubule network organization in real-time. We controlled dynamic protein relocalization using small molecules and light and slowed lateral diffusion within the lipid monolayer to create stable micropatterns with focused illumination. By fusing microtubule interacting proteins to optochemical dimerization domains, we directed the spatial organization of microtubule networks. Cortical patterning of polymerizing microtubules leads to symmetry breaking and forces that dramatically reshape the compartment. Our system has applications in cell biology to characterize the contributions of biochemical components and physical boundary conditions to microtubule network organization. Additionally, active shape control has uses in protocell engineering and for augmenting the functionalities of synthetic cells.

Virology from the perspective of theoretical colloid and interface science

Viral infections occur at very different length and time scales and include various processes, which can often be described using the models developed and/or employed in colloid and interface science. Bearing in mind the currently active COVID-19, I discuss herein the models aimed at viral transmission via respiratory droplets and the contact of virions with the epithelium. In a more general context, I outline the models focused on penetration of virions via the cellular membrane, initial stage of viral genome replication, and formation of viral capsids in cells. In addition, the models related to a new generation of drug delivery vehicles, for example, lipid nanoparticles with size about 100-200 nm, are discussed as well. Despite the high current interest in all these processes, their understanding is still limited, and this area is open for new theoretical studies.

Mucin-Inspired, High Molecular Weight Virus Binding Inhibitors Show Biphasic Binding Behavior to Influenza A Viruses

Multivalent binding inhibitors are a promising new class of antivirals that prevent virus infections by inhibiting virus binding to cell membranes. The design of these inhibitors is challenging as many properties, for example, inhibitor size and functionalization with virus attachment factors, strongly influence the inhibition efficiency. Here, virus binding inhibitors are synthesized, the size and functionalization of which are inspired by mucins, which are naturally occurring glycosylated proteins with high molecular weight (MDa range) and interact efficiently with various viruses. Hyperbranched polyglycerols (hPGs) with molecular weights ranging between 10 and 2600 kDa are synthesized, thereby hitting the size of mucins and allowing for determining the impact of inhibitor size on the inhibition efficiency. The hPGs are functionalized with sialic acids and sulfates, as suggested from the structure of mucins, and their inhibition efficiency is determined by probing the inhibition of influenza A virus (IAV) binding to membranes using various methods. The largest, mucin-sized inhibitor shows potent inhibition at pm concentrations, while the inhibition efficiency decreases with decreasing the molecular weight. Interestingly, the concentration-dependent IAV inhibition shows a biphasic behavior, which is attributed to differences in the binding affinity of the inhibitors to the two IAV envelope proteins, neuraminidase, and hemagglutinin.

Getting around the cell: physical transport in the intracellular world

Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.

Ordered Lipid Domains Assemble via Concerted Recruitment of Constituents from Both Membrane Leaflets

Lipid rafts serve as anchoring platforms for membrane proteins. Thus far they escaped direct observation by light microscopy due to their small size. Here we used differently colored dyes as reporters for the registration of both ordered and disordered lipids from the two leaves of a freestanding bilayer. Photoswitchable lipids dissolved or reformed the domains. Measurements of domain mobility indicated the presence of 120 nm wide ordered and 40 nm wide disordered domains. These sizes are in line with the predicted roles of line tension and membrane undulation as driving forces for alignment.

Analysis and refinement of 2D single-particle tracking experiments

In recent decades, single particle tracking (SPT) has been developed into a sophisticated analytical approach involving complex instruments and data analysis schemes to extract information from time-resolved particle trajectories. Very often, mobility-related properties are extracted from these particle trajectories, as they often contain information about local interactions experienced by the particles while moving through the sample. This tutorial aims to provide a comprehensive overview about the accuracies that can be achieved when extracting mobility-related properties from 2D particle trajectories and how these accuracies depend on experimental parameters. Proper interpretation of SPT data requires an assessment of whether the obtained accuracies are sufficient to resolve the effect under investigation. This is demonstrated by calculating mean square displacement curves that show an apparent super- or subdiffusive behavior due to poor measurement statistics instead of the presence of true anomalous diffusion. Furthermore, the refinement of parameters involved in the design or analysis of SPT experiments is discussed and an approach is proposed in which square displacement distributions are inspected to evaluate the quality of SPT data and to extract information about the maximum distance over which particles should be tracked during the linking process.

Mobility-Based Quantification of Multivalent Virus-Receptor Interactions: New Insights Into Influenza A Virus Binding Mode

Viruses, such as influenza A, typically bind to the plasma membrane of their host by engaging multiple membrane receptors in parallel, thereby forming so-called multivalent interactions that are created by the collective action of multiple weak ligand-receptor bonds. The overall interaction strength can be modulated by changing the number of engaged receptors. This feature is used by viruses to achieve a sufficiently firm attachment to the host's plasma membrane but also allows progeny viruses to leave the plasma membrane after completing the virus replication cycle. Design of strategies to prevent infection, for example, by disturbing these attachment and detachment processes upon application of antivirals, requires quantification of the underlying multivalent interaction in absence and presence of antivirals. This is still an unresolved problem, as there is currently no approach available that allows for determining the valency (i.e., of the number of receptors bound to a particular virus) on the level of single viruses under equilibrium conditions. Herein, we track the motion of single influenza A/X31 viruses (IAVs; interacting with the ganglioside GD1a incorporated in a supported lipid bilayer) using total internal reflection fluorescence microscopy and show that IAV residence time distributions can be deconvoluted from valency effects by taking the IAV mobility into account. The so-derived off-rate distributions, expressed in dependence of an average, apparent valency, show the expected decrease in off-rate with increasing valency but also show an unexpected peak structure, which can be linked to a competition in the opposing functionalities of the two influenza A virus spike proteins, hemagglutinin (HA), and neuraminidase (NA). By application of the antiviral zanamivir that inhibits the activity of NA, we provide direct evidence, how the HA/NA balance modulates this virus-receptor interaction, allowing us to assess the inhibition concentration of zanamivir based on its effect on the multivalent interaction.

Lipid lateral self-diffusion drop at liquid-gel phase transition

A drop of lipid lateral self-diffusion coefficient at the liquid-gel phase transition in lipid membranes is calculated. So far this drop was missing theoretical description. Our microscopic model captures so-called subdiffusion regime, which takes place on 1 ps-100 ns timescale and reveals a jump of self-diffusion coefficient. Calculation of the jump is based on our recent study of liquid-gel phase transition. Subdiffusive regime is described within the free volume theory. Calculated values of self-diffusion coefficient are in agreement with quasielastic neutron scattering measurements. Self-diffusion coefficient is found to be composed of two factors: one is related to an area per lipid change at the phase transition, and the other one is due to an order of magnitude change in the stiffness of entropic repulsive potential.