Tag Archive for: Quartz Crystal Microbalance with Dissipation

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Variant-Specific Interactions at the Plasma Membrane: Heparan Sulfate’s Impact on SARS-CoV-2 Binding Kinetics

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Authors: Dario Valter Conca, Fouzia Bano, Małgorzata Graul, Julius von Wirén, Lauriane Scherrer, Hudson Pace, Himanshu Sharma, Justas Svirelis, Konrad Thorsteinsson, Andreas Dahlin, and Marta Bally

Journal: Analytical Chemistry

Abstract: The spread of SARS-CoV-2 led to the emergence of several variants of concern (VOCs). The spike glycoprotein, responsible for engaging the viral receptor, exhibits the highest density of mutations, suggesting an ongoing evolution to optimize viral entry. This study characterizes the bond formed by virion mimics carrying the SARS-CoV-2 spike protein and the plasma membrane of host cells in the early stages of virus entry. Contrary to the traditional analysis of isolated ligand-receptor pairs, we utilized well-defined biomimetic models and biochemical and biophysical techniques to characterize the multivalent interaction of VOCs with the complex cell membrane. We observed an overall increase in the binding affinity for newer VOCs. By progressively reducing the system complexity, we identify heparan sulfate (HS) as a main driver of this variation, with a 10-fold increase in affinity for Omicron BA.1 over that of the original strain. These results demonstrate the essential role of coreceptors, particularly HS, in the modulation of SARS-CoV-2 infection and highlight the importance of multiscale biophysical and biochemical assays that account for membrane complexity to fully characterize and understand the role of molecular components and their synergy in viral attachment and entry.

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In silico maturation of DNA aptamer against the prostate-specific antigen (PSA) and kinetic analysis

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Authors: Chi-Ping Huang, Wen-Pin Hu, Wei Yang, Zheng-Jie Lee, Wen-Yih Chen

Journal: Biochemical and Biophysical Research Communications

Abstract: The detection of the prostate-specific antigen (PSA) serves as a critical marker for the diagnosis and follow-up of prostate cancer. DNA aptamers targeting PSA have been successfully screened using the systematic evolution of ligands by exponential enrichment (SELEX) technique, complemented by in silico maturation processes. In this study, we aim to optimize a truncated aptamer, denoted as TA87, through computational methods and to analyze potential aptamer candidates in the aptamer-PSA interactions. The PSA antibody, aptamer ΔPSap4#5, and an identified but unpublished aptamer, PSAG221, were evaluated in quartz crystal microbalance (QCM) experiments alongside aptamers derived from TA87. The Tanimoto similarity score and the ZDOCK program, coupled with the ZRANK scoring function, were adopted to assess the secondary structure of single-point mutants of TA87 and their binding interactions with PSA, respectively. Detailed analyses of the aptamer-protein complexes were conducted using molecular dynamics (MD) simulations. Mutations TA87M24 and TA87M49, along with PSAG221 and TA87, showed superior ZDOCK scores compared to ΔPSap4#5. MD simulations further suggested that PSAG221 aptamer might offer enhanced binding to PSA over ΔPSap4#5. The affinity constant (KD) values for the antibody, ΔPSap4#5, PSAG221, TA87, TA87M24, and TA87M49 with PSA were determined through QCM measurements to be 0.35, 0.33, 0.35, 0.56, 0.45, and 0.51 μM−1, respectively. The experimental results showed that the truncated aptamers, TA87, and the two mutations, TA87M24 and TA87M49, did not demonstrate superior PSA binding affinity. Aptamer PSAG221 demonstrated performance comparable to that of the antibody, although slightly inferior to ΔPSap4#5. The aptamer PSAG221 reported in this study could be an alternative probe for developing future PSA aptasensor platforms.

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Lipid packing frustration in the outer leaflet of the plasma membrane prevents scission of caveolae

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Authors: Elin Larsson, Aleksei Kabedev, Hudson Pace, Jakob Lindwall, Fouzia Bano, Robert G Parton, Christel A. S. Bergstrom, Ingela Parmryd, Marta Bally, Richard Lundmark

Journal: bioRxiv

Abstract: Lipid packing is a fundamental characteristic of bilayer membranes. It affects all membrane-associated processes ranging from curvature generation to membrane fission. Yet, we lack detailed, mechanistic understanding of how lipid packing directly affects these processes in cellular membranes. Here, we address this by focusing on caveolae, small Ω-shaped invaginations of the plasma membrane which serve as key regulators of cellular lipid sorting and mechano-responses. In addition to caveolae coat proteins, the lipid membrane is a core component of caveolae that critically impacts both the biogenesis, morphology and stability of such membrane invaginations. We show that the small compound Dyngo-4a inserts into the membrane, resulting in a dramatic dynamin-independent inhibition of caveola scission. Analysis of model membranes in combination with molecular dynamics simulations revealed that a substantial amount of Dyngo-4a was inserted and positioned at the level of cholesterol in the bilayer. Dyngo-4a-treatment resulted in decreased lipid packing in the outer leaflet of the plasma membrane preventing scission without affecting caveola morphology, caveolae- associated proteins, or the overall membrane stiffness. Artificially increasing plasma membrane cholesterol levels was found to counteract the block in caveola scission caused by Dyngo-4a-mediated lipid packing frustration. Therefore, we propose that the packing of cholesterol in the outer leaflet of the plasma membrane critically controls the confinement of caveolae to the plasma membrane.

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The Frequency‐Domain Lattice Boltzmann Method (FreqD‐LBM): A Versatile Tool to Predict the QCM Response Induced by Structured Samples

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Authors: Diethelm Johannsmann, Paul Häusner, Arne Langhoff, Christian Leppin, Ilya Reviakine, Viktor Vanoppen

Journal: Advanced Theory and Simulations

Abstract: The quartz crystal microbalance with dissipation monitoring (QCM-D) is routinely used to investigate structured samples. Here, a simulation technique is described, that predicts the shifts of frequency and half bandwidth, Δfn and ΔΓn, of a quartz resonator operating on different overtone orders, n, induced by structured samples in contact with the resonator surface in liquid. The technique, abbreviated as FreqD-LBM, solves the Stokes equation in the frequency domain. The solution provides the complex amplitude of the area-averaged tangential stress at the resonator surface, from which Δfn and ΔΓn are derived. Because the dynamical variables are complex amplitudes, the viscosity can be complex, as well. The technique naturally covers viscoelasticity. Limitations are linked to the grid resolution and to problems at large viscosity. Validation steps include viscoelastic films, rough surfaces, an oscillating cylinder in a viscous medium, and a free-floating sphere above the resonator. Application examples are soft adsorbed particles, stiff adsorbed particles, and a large, immobile spherical cap above the resonator, which allows to study the high-frequency properties of the material in the gap. FreqDLBM runs on an office PC and does not require expert knowledge of numerical techniques. It is accessible to an experimentalist.

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Kinetic selectivity in metal-organic framework chemical sensors

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Authors: Aleksander Matavž, Margot F. K. Verstreken, Leen Boullart, Max L. Tietze, Masaya Sugihara, Lars Heinke, and Rob Ameloot

Journal: ChemRxiv

Abstract: Selective detection of specific volatile organic compounds (VOCs) is crucial for health, safety, and environmental applications, but current sensors suffer from poor selectivity and struggle to measure specific VOCs in the presence of interfering compounds and water vapor. To address this issue, we introduce the kinetic selectivity achievable in nanoporous crystals, specifically metal-organic frameworks (MOFs), into the domain of chemical sensors. In well-selected MOFs, similar molecules can have diffusivities that differ by orders of magnitude. Measuring these diffusivity values is challenging since conventional methods based on rapid changes in atmosphere composition cannot be used in a sensing context. A novel temperature perturbation method was developed for thin-film capacitive sensors with a MOF dielectric layer to enable diffusivity measurements in a fixed atmosphere. Our approach enabled a single sensor to differentiate and quantify VOCs at ppm concentrations, even in mixtures containing high water vapor concentrations, outperforming a state-of-the-art ten-element sensor array.

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Chemical and Mechanical Properties of Drying Oils during Polymerization

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Author: Gwen dePolo

PhD Thesis: Northwestern University (September 2023)

 

Abstract

Drying oils have been used as a binding medium for oil paints since the 15th century. These oil paints transition from a liquid-like paste to a solid-like film as a result of crosslinks forming between the oil molecules. These reactions have been extensively studied chemically, but other material properties are not as well characterized for drying oils. Oil paints are typically used in complex composite structures where the mechanical properties matter just as much as the chemical properties. This thesis focuses on understanding the evolution of mechanical properties during drying oil polymerization.

 

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Methods for Calibrating the Electrochemical Quartz Crystal Microbalance: Frequency to Mass and Compensation for Viscous Load

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Authors: Claes-Olof A. Olsson, Anna Neus Igual-Muñoz and Stefano Mischler

Journal: Chemosensors (2023)

 

Abstract

The main output from an Electrochemical Quartz Crystal Microbalance is a frequency shift. This note describes how to separate the mass- and viscous load contributions to this shift by a calibration procedure. The mass calibration is made by electroplating from a copper sulfate solution in ethanol/water with 100% current efficiency. An estimate of viscous load is obtained by measuring the energy dissipation and is related to frequency change using the Kanazawa–Gordon equation. Two approaches are discussed: either by performing calibration experiments in a series of water–glycerol mixtures or by following oscillations in frequency and dissipation by collecting data during the stabilization phase of the experiment.

 

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Comparison of Thin-Film Capacitor Geometries for the Detection of Volatile Organic Compounds Using a ZIF-8 Affinity Layer

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Authors: Aleksander Matavž, Margot F. K. Verstreken, Jorid Smets, Max L. Tietze, and Rob Ameloot

Journal: ACS Sensors (2023)

 

Abstract

Their chemical diversity, uniform pore sizes, and large internal surface areas make metal–organic frameworks (MOFs) highly suitable for volatile organic compound (VOC) adsorption. This work compares two geometries of capacitive VOC sensors that use the MOF material ZIF-8 as an affinity layer. When using a permeable top electrode (thickness < 25 nm), the metal–insulator–metal (MIM) sandwich configuration exhibits superior sensitivity, an improved detection limit, and a smaller footprint than the conventional interdigitated electrode layout. Moreover, the transduction of VOC adsorption in ZIF-8 via MIM capacitors is more sensitive to polar VOCs and provides better selectivity at high loadings than gravimetric and optical transductions.

 

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Fouling of Reverse Osmosis Membrane with Effluent Organic Matter: Componential Role of Hydrophobicity

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Authors: Noa Stein, Revital Sharon-Gojman, Meagan S. Mauter, Roy Bernstein and Moshe Herzberg

Journal: ACS ES&T Water (2023)

 

Abstract

Organic matter dissolved in tertiary effluents (effluent organic matter, EfOM) is the predominant organic membrane foulant in tertiary wastewater reverse osmosis (RO) desalination, ultimately causing biofouling. The interrelated effects of EfOM fractions of different hydrophobicity and polarity on membrane performance were studied by (i) examining each fraction’s overall effect on membrane permeability; (ii) analyzing the intrinsic hydraulic resistance induced by each fraction; (iii) studying their adsorption on the active layer of an RO membrane using a quartz crystal microbalance with dissipation monitoring (QCM-D); (iv) assessing their “dry” molecular mass when adsorbed on polyamide using localized surface plasmon resonance (LSPR) sensing; (v) analyzing their hydrodynamic radii by dynamic light scattering (DLS); and (vi) characterization using excitation–emission matrix (EEM) analysis and parallel-factor (PARAFAC) modeling. Hydrophobic and transphilic neutral fractions (containing ∼12.5% total organic carbon) have the greatest effect on membrane flux reduction and the highest hydraulic resistance and adhere most strongly to polyamide surfaces, resulting in the highest adsorbed “dry” mass. Therefore, in terms of their effect on RO permeate flux reduction, these fractions are the most detrimental in the EfOM mix. EEM analysis and associated PARAFAC modeling indicate that the main components causing this effect are mixtures of protein-like compounds, together with humic-like substances. Novel LSPR-based analysis elucidated the role of the fractions most detrimental to membrane permeability through measurement of dry mass surface concentration on a polyamide mimetic sensor. This study provides valuable insights into the roles of different EfOM fractions in RO membrane fouling and enhances our understanding of fouling during tertiary wastewater desalination.

Fouling of Reverse Osmosis Membrane with Effluent Organic Matter: Componential Role of Hydrophobicity

 

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Trace Water Effects on Crystalline 1-Ethyl-3-methylimidazolium Acetate

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Authors: Ashlee Aiello, John R. Hoffman, Anthony P. Kotula, Lucas Q. Flagg, Ruipeng Li, and Jeremiah W. Woodcock

Journal: J. Phys. Chem. B (2023)

 

Abstract

Spontaneous room-temperature crystallization of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) was observed upon removal of trace water. Sample purity was confirmed using analytical nuclear magnetic resonance spectroscopy to ensure that trace water or other contaminants did not produce this observation. Raman spectroscopy and simultaneous quartz crystal microbalance/infrared spectroscopy measurements were used to study molecular reorganization during crystallization and decrystallization using trace water in the form of atmospheric moisture. These experimental results were supplemented with density functional theory calculations that indicate imidazolium cation ring stacking and side chain clustering with an exclusive arrangement of the acetate anion in the cation ring plane upon water removal. Crystal structure formation was confirmed using two-dimensional wide-angle X-ray scattering. This natural crystallization is attributed to the removal of trace water over extended periods of time and calls attention to the molecular-level role of water in the structure of hygroscopic ionic liquid systems.

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