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European Biophysics Journal

Springer Science and Business Media LLC

All preprints, ranked by how well they match European Biophysics Journal's content profile, based on 12 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Biophysics of the Coronavirus-Membrane Interaction: Role of Nonequilibrium Binding Energy

Udema, I. I.

2025-06-12 biophysics 10.1101/2025.06.10.658990 medRxiv
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Scientists seemed not to have explored mechanical kinetic energy, a path function for the determination of nonequilibrium binding energy (NEBE). The study explored mechanical kinetic energy, a path function in particles that requires nonequilibrium binding energy (NEBE) to counteract it. It aimed to show that there was a minimally sufficient NEBE to counteract mechanical kinetic energy, using literature data to evaluate derived equations and computations. As is typical, diffusivities increase with temperature; however, near binding, the binding limitations cause the diffusivities (1.519 [->] 2.784 exp. (- 15) m2/s for D variant; 1.415[->]2.577 exp. (- 15) m2/s for G variant) to be lower than when they are far from binding (4.36 [->]7.99 exp. (- 15) m2/s for D variant; 4.151[->]7.611 exp. (- 15) m2/s for G variant). With breath emission equal to 1.29 exp. (7)/m3, the NEBEs were 656.020 and 663.212 kcal/mol for Delta and Omicron variants of SARS-CoV-2, respectively; and with 27.9 exp. (7)/m3, the corresponding values were 568.921 and 633 kcal/mol; with a breath emission rate equal to 9.31 exp. (+6)/hr., the NEBEs for the Omicron variant in 1 hr. and in 1 min. were 651.703 and 683.353 kcal/mol, respectively; with 201 exp. (+6)/hr., the corresponding values were 444.157 and 663.212 kcal/mol. The G variant of SARS-CoV-2 showed higher NEBEs (952[->]671 kcal/mol) than D variants (834[->]588 kcal/mol), corresponding to 293.15[->]318.15 K. The decreasing trend in maximum NEBE [Formula] with rising temperature implies that the binding affinity of the virus may be attenuated at higher temperatures. It is, therefore, medically plausible to administer airborne, parenteral, oral, etc., drugs at temperatures above body temperatures that are tolerable and in a controlled fashion. Future studies should be directed to a definite determination of the size and molar mass of variants of SARS-CoV-2.

2
Unifying framework for the diffusion of microscopic particles in mucus

Cobarrubia, A.; Tall, J.; Crispin-Smith, A.; Luque, A.

2020-07-26 biophysics 10.1101/2020.07.25.221416 medRxiv
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Mucus is a fluid that protects animals against pathogens while promoting interactions with commensal microbes. Changes in the diffusivity of particles in mucus alter viruses infectivity, the efficiency of bacterial pathogens to invade a host, and the effectivity of drug delivery. Multiple physicochemical properties modulate the diffusion of microscopic particles in mucus, but their combined effect is unclear. Here, we analyzed the impact of particle size, charge, chemistry, anomalous diffusion exponent, and mucus composition in the diffusivity of particles from 106 published experiments. We used a time window sampling of one second to define a consistent, effective diffusion across experiments. The effective diffusion spanned seven orders of magnitude from 10-5 to 102 {micro}m2/s. The anomalous exponent was the strongest predictor among all variables tested. It displayed an exponential relationship with the effective diffusion that explained 90% of the empirical data variance. We showed that the relationship and dominance of the anomalous diffusion exponent resulted from a general mathematical relationship obtained from first-principles for any subdiffusion mechanism. Our derivation demonstrated that the generalized diffusion coefficient is not a measurable physical quantity and must be replaced by the length and time scales associated with the underlying mobility mechanisms. This led us to a fundamental reformulation of the classic subdiffusion equation, which calls for a reinterpretation of anomalous diffusion in physical systems. We also discussed how our results impact the characterization of microscopic particle diffusion in mucus and other hydrogels.

3
An automated interface for sedimentation velocity analysis in SEDFIT

Schuck, P.; To, S. C.; Zhao, H.

2023-05-14 biophysics 10.1101/2023.05.14.540690 medRxiv
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Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.

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The effect of surfactants and film-forming polymers on pulmonary surfactant function measured in vitro is dose-rate dependent

Sengupta, S.; Barlow, H. J.; Baltazar, M.; Sorli, J. B.

2024-10-21 biophysics 10.1101/2024.10.18.618437 medRxiv
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Surfactants and film-forming polymers are common ingredients in consumer spray products such as cleaning products, hair care products, and anti-perspirants. Spraying eases application by creating aerosolised droplets of the product that can distribute evenly over the treated surface. However, these aerosols can potentially be inhaled during their normal application. Droplets that reach the alveoli can interact with the pulmonary surfactant; a complex mixture of phospholipids and proteins that regulates the surface tension at the air-liquid interface. This interaction could elevate the minimum surface tension at maximum compression and change the surface rheology of the pulmonary surfactant at the interface. We tested four surfactants and seven polymers for their ability to inhibit pulmonary surfactant function in vitro and investigated if the inhibition is dose-rate dependent i.e., the product of the concentration (mg/mL) and aerosolisation rate (mL/min). We found that independent of chemical class (surfactant or polymer) there was a clear dose-rate dependent inhibition of pulmonary surfactant function and that different chemicals inhibited function at different dose-rates. We compared the points of departure of inhibitory chemicals to a polymer with known dose-rate dependent lung toxicity. When assessing the risk of chemicals that might be inhaled, it is essential to ensure normal use would not inhibit pulmonary surfactant function leading to immediate effects on the lungs. Lay summarySpray products create a cloud of tiny droplets in the air when they are used. This cloud can be inhaled, and if it reaches the deepest parts of the lungs, it can interact with the thin layer of liquid, called pulmonary surfactant, that covers the cells. It protects the lung tissue during the constant movement of breathing. Droplets can sometimes disrupt the pulmonary surfactant function, making breathing difficult. Chemicals that are used in spray products must be tested to assess if they are harmful if inhaled. In this project we studied the effect of chemicals that are commonly found in spray products on the functioning of the pulmonary surfactant in vitro. The results can be combined with other in vitro methods to test if chemicals are harmful to inhale without testing on animals.

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Rigorous equations for isothermal titration calorimetry: theoretical and practical consequences

Dumas, P.

2021-11-06 biophysics 10.1101/512780 medRxiv
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The author has withdrawn his manuscript because: The withdrawn preprint was about methodological aspects in Isothermal Titration Calorimetry (ITC) used to obtain thermodynamic information about reactions like A + B {rightleftarrows} C where A is initially in the cell and B injected from a syringe. The preprint considered the two possible methods in ITC: 1/ the Multiple Injection Method (MIM) making use of short-time injections separated by sufficient time to allow the reaction to reach equilibrium before a new injection. 2/ the Single Injection Method (SIM) making use of a slow continuous injection. The first result mentioned is about a new equation linking the rate of heat evolution with the injected volume (equations 9 and 10). With this equation and with the hypothesis that there is always perfect mixing of the cell content it was concluded that an ideal titration curve (i.e. not affected by any external influence) for a simple reaction like A + B {rightleftarrows} C cannot change sign (section 3.2). This conclusion turns out to be incorrect when taking in consideration real conditions with imperfect mixing, particularly with MIM using injections often of very short duration, which prevents from reaching perfect mixing. The major problem is that this erroneous conclusion was accompanied with comparisons of the results from well-established programs, which led to the conclusion that these were in error on this point (section 3.6). I therefore felt necessary to withdraw this preprint to avoid casting doubts unduly on these programs used extensively. Note that many other aspects in this preprint remain correct (section 3.8). A new version of this work, limited to SIM and considering imperfect mixing, will be submitted for publication under the title: "Isothermal titration calorimetry in the single-injection mode with imperfect mixing". If you have any questions, please contact me at dumasp@igbmc.fr or at p.dumas@unistra.fr Sorry for the inconvenience. Philippe Dumas November 6, 2021

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In a pathophysiologic state due to SARS-CoV-2, viscosity and cholesterol are two-edged swords.

Udema, I. I.

2025-02-19 biophysics 10.1101/2025.02.17.638432 medRxiv
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Much attention has been paid to the genetic composition and molecular biology of viral particles, infection, and micro-anatomical impacts that culminate in fatalities; vaccines have been in continuous development and production; less attention is paid to the fundamental issues of thermodynamics and activation energy characterization of viral RNA replication and cell death. The study aimed at deriving equations that can be fitted to both theoretically and empirically derived data for the quantitation of other thermodynamic parameters and its cognate dimensionless equilibrium constant; some of the derived equations addressed the issue of viscosity and the concentration of cholesterol in particular as they affect translational velocity needed for the delivery of biomolecules to the site of need. The instantaneous velocities before terminal velocity are: [~] 0.046674 m/s (cytosol); 0.141837 m/s (water). The terminal velocities were approximately equal to 3.548614 nm/s for the cytosol and 99.590626 nm/s for the water; these values were computed using literature values of translational diffusion coefficients (Di) of glucose in cytoplasm and in water. The value in water is higher than in the cytosol because of higher cytosolic viscosity than aqueous viscosity. These support the view that cholesterol and viscosity have a dual-edged effect on the pathophysiologic state orchestrated by SARS-CoV-2; higher viscosities in the membrane and in the cytoplasm enhance binding and infection and can diminish the progress of infection, respectively. Higher feasibility and rates were observed at lower thermodynamic temperatures than at higher ones, according to the outcome of the analysis of the viral binding free energy and activation energy, respectively. The dimensionless constant values were higher at the earlier time of the infection and decreased with time, exhibiting a power law relationship. It is advised, among others, that pharmaceuticals (including airborne surfactants) and drugs in solution be given at temperatures above body temperature. Swab testing should be performed on a regular basis to detect significant infections early. Future in vitro and in vivo studies on viral infection might focus on various time periods at different temperatures, above and below body temperature. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/638432v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1262294org.highwire.dtl.DTLVardef@a836a0org.highwire.dtl.DTLVardef@19a5f6forg.highwire.dtl.DTLVardef@1ef86c6_HPS_FORMAT_FIGEXP M_FIG C_FIG With vaccine and/or drug the viral infection can regress; without treatment there could be infection and progression into disease state; discontinuation of treatment can cause a reinfection.

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Modeling Oyster Reef Reproductive Sustainability: Analyzing Gamete Viability, Hydrodynamics, and Reef Structure to Facilitate Restoration of Crassostrea virginica

Weissberg, J.; Pagano, V.

2021-01-13 biophysics 10.1101/2021.01.12.426464 medRxiv
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The eastern oyster is a keystone species and ecosystem engineer. However, restoration efforts of wild oysters are often unsuccessful, in that they do not produce a robust population of oysters that are able to successfully reproduce. Furthermore, the dynamics of wild oyster fertilization is not yet well understood. Through conducting an experiment predicated on quantifying the influence of elementary aspects of fertilization kinetics--sperm concentration, gamete age, and success rate--we found that, as stochastic as the mating process may seem, there are correlations which fundamentally serve as the framework for assessing long-term sustainability, reef structure, and hydrodynamic parameters in relation to fertilization. We then focused on mathematically defining a procedure which simulated a concentration distribution of a single sperm and egg release where there existed conditions necessary for breeding to take place. We found a very significant impact of both gamete age and sperm concentration on fertilization rate (p < 0.0001). Our hydrodynamic model demonstrates that distance can also drastically influence broadcast spawning. This could be used as a foundation for developing a flexible model for wild oyster fertilization based on placement, initial seawater conditions, and size of the starting population. The results of this research could be implemented into a more user-friendly program which would accept multiple variables as inputs and output the probability of fertilization given arbitrary values. By accounting for environmental deviations, this generalization would increase its compatibility with the public and actualize the projects intended purpose: enhance the planning of oyster reef restoration projects.

8
Specific interaction of Penetratin with cell surface partners measured with biomembrane force probe

Soule, P.; Illien, F.; Kulifaj, S.; Joliot, A.; Gourier, C.; Sagan, S.; Cribier, S.; Rodriguez, N.

2020-07-22 biophysics 10.1101/2020.07.21.215111 medRxiv
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Penetratin is a Cell Penetrating Peptide able to cross the cell plasma membrane possibly bound to a cargo molecule to be delivered into the cell. The mechanism of its entry is poorly known. A key to a molecular description of this mechanism is to identify the partners of Penetratin at the cell surface during its adhesion and internalization. We used the Biomembrane Force Probe to identify the partners during the first second of adhesion of Penetratin on the cell plasma membrane. We evidenced that heparan sulfates are the first partners after contact as well as unknown partners hidden by sialic acids. Experiments of binding of Penetratin on vesicles bearing charged or sulfated lipids showed no adhesion pointing that a negatively charged partner is not enough and there is a specificity for certain chemical groups bearing the charges. A model of the measured forces of interaction enabled to determine the adhesion energy of a Penetratin with heparan sulfates on a cell to be in the range 18 to 22 kBT.

9
Simulating Colloid Motion in Spinning Suspension: Internal Dynamics in Orbital Shaker

Zhao, N.; Zheng, D.

2024-02-21 biophysics 10.1101/2024.02.19.581033 medRxiv
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Colloid suspensions in the form of mammalian or bacterial cell mixtures in orbital shakers are commonly encountered in biomedical research. An understanding of particle motion in these conditions would provide insight into bulk colloid behavior and distribution under short and long timeframes. Such data can be used to supplement and clarify existing concepts of biological phenomena encountered in the laboratory setting. It can also aid biomedical researchers in experiment design and data interpretation. We present a MATLAB based simulation of colloid motion under rotary agitation. Our simulation setup is modular and therefore designed to act as a scaffold that can be customized to simulate different mammalian, bacterial, or particle properties in liquid suspension.

10
Student-focused development of a next-generation centrifuge force microscope

Tompkins, K. J.; Berscheid, E. T.; Venkatesh, N.; Andrew, A. J.; Beckman, A. P.; Esler, M. A.; Evans, A. C.; Everett, B. A.; Houtti, M.; Koo, H.; Litzau, L. A.; Nelson, A. T.; Peterson, T. M.; Reid, T. A.; Evans, R. L.; Gordon, W. R.

2020-08-31 biophysics 10.1101/2020.08.30.274373 medRxiv
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Advanced biological molecule force probing methods such as atomic force microscopy and optical tweezers used to quantify forces at the single-molecule level are expensive and require extensive training and technical knowledge. However, the technologies underlying a centrifuge force microscope (CFM) are relatively straight forward, allowing for construction by labs with relatively low budgets and minimal training. Design ideas from previously constructed CFMs served as a guide in the development of this CFM. There were two primary goals: first, to develop an inexpensive, functional CFM using off-the-shelf and 3D printed parts; and second, to do so in the context of providing an educational experience for a broad range of students. The team included high school students and undergraduates from local high schools, the University of Minnesota, and other local higher education institutions. This project created an environment for student-focused development of the CFM that fostered active learning, individual ownership, as well as excellence in research. The instrument discussed herein represents a fully functional CFM designed and built by a postdoctoral researcher and a graduate student who together mentored several high school and undergraduate students. STATEMENT OF SIGNIFICANCEThe presented centrifuge force microscope (CFM) builds on features of existing designs specifically engineered for probing macromolecular force interactions at the single-molecule level. In the coming years, more versatile and modular CFM designs will be utilized in the force spectroscopy field, and the presented design is a step in that direction. In addition to constructing a functional instrument, true student ownership of the project design was equally an end goal. Students from high school through graduate school were included, and the project was structured so that everyone was seen as peers. This active learning project allowed students to acquire scientific concepts and techniques and apply them to real-life situations.

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The time of strong actomyosin binding depends on electrostatic interactions within the force generating region in human cardiac myosin

Iragavarapu, A. G.; Iragavarapu, S. B.; Grdzelishvili, A. V.; Nesmelov, Y. E.

2020-04-22 biophysics 10.1101/2020.04.21.054403 medRxiv
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Two single mutations, R694N and E45Q, were introduced in the beta isoform of human cardiac myosin to remove permanent salt bridges E45:R694 and E98:R694 in the force-generating region of myosin head. Beta isoform-specific bridges E45:R694 and E98:R694 were discovered in the molecular dynamics simulations of the alpha and beta myosin isoforms. Alpha and beta isoforms exhibit different kinetics, ADP dissociates slower from actomyosin containing beta myosin isoform, therefore, beta myosin stays strongly bound to actin longer. We hypothesize that the electrostatic interactions in the force-generating region modulate affinity of ADP to actomyosin, and therefore, the time of the strong actomyosin binding. Wild type and the mutants of the myosin head construct (1-843 amino acid residues) were expressed in differentiated C2C12 cells, and duration of the strongly bound state of actomyosin was characterized using transient kinetics spectrophotometry. All myosin constructs exhibited a fast rate of ATP binding to actomyosin and a slow rate of ADP dissociation, showing that ADP release limits the time of the strongly bound state of actomyosin. Mutant R694N showed faster rate of ADP release from actomyosin, compared to the wild type and the E45Q mutant, thus confirming that electrostatic interactions within the force-generating region of human cardiac myosin regulate ADP release and the duration of the strongly bound state of actomyosin.

12
Decoupling diffusion, turnover, and advection in long-term FRAP

Nakashima, O.; Saito, T.; Deguchi, S.

2025-02-04 biophysics 10.1101/2025.02.04.636435 medRxiv
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Intracellular molecular turnover is a dynamic process governed by diffusion, biochemical reactions, and intracellular transport dynamics. While fluorescence recovery after photobleaching (FRAP) has been widely used to quantify fluorescence recovery mechanisms, conventional models primarily focus on diffusion and reaction kinetics, often overlooking the influence of intracellular advection. However, in cytoskeletal structures such as stress fibers, myosin-driven actin retrograde flow generates a significant advective component, which complicates the interpretation of FRAP data, particularly in long-term observations where advective effects become sufficiently pronounced. Here, we develop an analytical framework that extends FRAP modeling to incorporate the coupled effects of diffusion, turnover, and intracellular advection within the photobleached region of interest. By deriving exact solutions to a reaction-diffusion-advection system, we identify three key dimensionless parameters that govern fluorescence recovery dynamics: the turnover-to-diffusion ratio, the monomer-to-filament ratio, and the advection magnitude. Our results demonstrate that, even in the absence of biochemical reactions, fluorescence recovery in a fixed region can occur due to advection, leading to potential misinterpretations of molecular exchange rates. The model provides a theoretical foundation for distinguishing these effects and offers a practical tool for long-term FRAP analysis, where the interplay of diffusion, turnover, and advection becomes increasingly relevant over extended timescales. By systematically characterizing the interplay between molecular diffusion, reaction kinetics, and intracellular transport, our framework provides deeper insight into protein turnover in complex biological environments.

13
Impact of modification of envelope proteins on the mechanical properties of HIV virus-like particles

Kruse, E.; van Diepen, M.; Chapman, R.; Horn, E.; Abdalrahman, T.; Williamson, A.-L.; Rybicki, E. P.; Roos, W. H.; Franz, T.

2025-10-15 biophysics 10.1101/2025.10.15.682533 medRxiv
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The mechanical interactions between virus-like particles and host cells may offer targets for new viral treatments and vaccines with modes of action that are independent of the immune system. The physical properties of structures involved govern the particle-cell interactions. While the mechanical properties of virions and mammalian cells have been widely studied, data on virus-like particles are limited. This study aimed to determine the mechanical and morphological properties of HIV-1 virus-like particles with different envelopes. Three HIV-like particles, i.e. GagM + gp150, GagM + gp140HA2tr, and GagM + gp120HA2, were produced by combining the same Gag protein shell with different trimeric glycoprotein envelopes. The particles spring constant, breaking force, and dimensions were determined using atomic force microscopy, and the elastic modulus was quantified using finite element analysis. Spring constant, elastic modulus, and breaking force were higher for GagM + gp140HA2tr and GagM + gp120HA2 than for GagM + gp150. The particle height was smaller for GagM + gp120HA2 than for GagM + gp150 and GagM + gp140HA2tr. Possible mechanisms underlying the increase of the particles stiffness and mechanical strength are the inclusion of the influenza virus HA transmembrane domain in the HIV Env protein, and the lower expression and packing density of Env in GagM + gp140HA2tr and GagM + gp120HA2 compared to GagM + gp150 found previously. Upon confirmation, the proposed mechanisms offer potential to tailor the mechanics of HIV virus-like particles and guide mechanical interactions between VLPs and host cells towards improving vaccines.

14
Solvent Isotope Effect on the Stability of a Heterodimeric Protein

Bhattacharjee, R.; Udgaonkar, J. B.

2026-02-14 biophysics 10.64898/2026.02.12.705670 medRxiv
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Protein stability arises from a fine balance between stabilizing forces such as hydrophobic interactions, hydrogen bonding, and ionic interactions, and destabilizing contributions from solvent exposure and electrostatics. Although hydrophobic burial is the dominant driving force for folding, intra-chain hydrogen bonds and ionic interactions modulate stability in context-dependent ways, with effects that vary depending on their location and environment within the protein. Most studies of protein stability have focused on perturbations induced by pH, solvent composition, or mutations in protonated water, leaving the influence of solvent isotopes relatively underexplored. Notably, despite stronger hydrogen bonding in D2O, proteins exhibit diverse stability responses upon transfer from H2O to D2O, suggesting that differential hydration of nonpolar groups plays a key role. Here, the solvent isotope effect on protein stability is investigated using double-chain monellin (dcMN), a {beta}-sheet-rich, two-chain protein with well-characterized folding behavior. By combining conventional equilibrium unfolding measurements with hydrogen-deuterium exchange mass spectrometry (HDX-MS), the stability of wild-type and a less hydrophobic mutant (C42A) dcMN was compared in H2O and D2O, revealing greater stabilization of the wild-type protein in D2O and highlighting the importance of hydrophobic interactions in governing isotope-dependent stability.

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Structural basis of the interaction between ESV1 and LESV from Arabidopsis thaliana with starch glucans.

Osman, R.; Bossu, M.; Dauvillee, D.; Spriet, C.; Liu, C.; Zeeman, S. C.; D'Hulst, C.; Bompard, C.

2023-06-10 biophysics 10.1101/2023.06.09.544376 medRxiv
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Starch is the major energy storage compound in plants. Whether it is transient or stored, it is accumulated in the form of insoluble, semi-crystalline granules. The structure of these granules is related to the structure of the main component: amylopectin. Amylopectin consists of linear polymers of glucose units linked by -1,4 bonds, forming double helices that combine to form the semi-crystalline lamellae of the granules, and -1,6 branching points that form the amorphous lamellae. This particular structure of amylopectin is linked to the action of isoamylases, which cut the excess of branching points and allow the granules to be structured. For a long time, it was thought that the action of these enzymes was responsible for the structuring of starch granules. Recently, two new proteins, LESV and ESV1, have been characterized and are involved in the phase transition of amylopectin (LESV) or in the maintenance of the granule structure (ESV1). These proteins share a tryptophan-rich domain folded into an antiparallel {beta}-sheet that is particularly well suited to bind amylopectin double helices. In this paper we present the structural study of these interactions using integrative structural biology approaches and show that LESV, in contrast to ESV1 can intervenes during amylopectin biosynthesis.

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The Physical Basis of Osmosis in a Donnan Ionic System

Manning, G. S.

2024-07-23 biophysics 10.1101/2024.07.22.604593 medRxiv
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Impermeant molecules inside a cell would lead to an inward osmotic flow of water, causing swelling, were it not for the pumping of permeant sodium ions out of the cell as soon as they leak in. The energy barrier model for a semipermeable membrane, first introduced by Debye to provide a molecular-level explanation of the vant Hoff equation for osmotic pressure, can be used to advantage in this situation, since the pump can be conceptualized as increasing the energy barrier for the sodium ion. The Debye model has previously been extended to include osmosis induced by electrostatically neutral solutes. Discussion of the effect of ion pumping on water transport requires an understanding of osmosis in systems containing permeant ions, that is, Donnan systems. We have obtained an equation for Donnan osmosis across a Debye energy barrier that separates an aqueous solution of permeant sodium, potassium, and chloride ions from a solution containing these permeant ions and additionally an impermeant anion, the latter representing intra-cellular impermeant charged species. Donnan osmosis occurs even if osmolarities on the two sides of the membrane are equal. Numerical representation shows that the Donnan-Debye model provides a quantitative theoretical framework for the action of the sodium/potassium/ATPase ion pump as effectively rendering the extracellular sodium ions impermeant, thus balancing the impermeant molecules inside the cell. Another application of Donnan osmosis shows that ion charge effects, missing from lists of Starling forces, are nonetheless expected to be a major contributor to transport across capillary walls. SummaryOsmosis as driven by Starling forces is applicable only if the solute is electrostatically neutral. For ions, Donnan charge effects dominate. An equation for Donnan osmosis is presented and applied to ion pumps and to transport across capillary walls.

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Investigation of ice nucleation properties of Pseudomonas syringae bacterium and insoluble low molecular weight substances

Vorobeva, D. E.; Majorina, M. A.; Marchenko, N. Y.; Melnik, B. S.

2023-12-10 biophysics 10.1101/2023.12.09.570762 medRxiv
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Control of the water freezing process is considerable in different fields of science and technology: from the artificial snow production to the cryopreservation of biological materials. To date, there is no conventional theory that predicts the influence of various biological and non-biological ice nucleators on the formation of ice and, accordingly, on the freezing point of supercooled water. In this work, we investigated the influence of bacterium Pseudomonas syringae, a biological ice nucleator, and heterodisperse insoluble powders of low molecular weight substances on the process of water freezing. AgCl, ZnO and SnO2 were found to be ice nucleators. This property has not been described previously in the literature. It has also been established that insoluble low molecular weight substances affect both the freezing point of water and the temperature of coexistence of water and ice.

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Bacterial Normalized Binary Fission Growth Model

Keady, J. P.

2021-10-05 biophysics 10.1101/2021.10.05.463248 medRxiv
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Mathematical models have traditionally been used to facilitate the interpretation of bacterial growth curves in order to more accurately understand and identify variations in bacterial proliferation. Here, a binary fission growth model was developed to normalize starting bacterial levels, allowing for the identification of changes in bacterial growth and the separation of a bacterial population as it correlates to size. This normalized binary fission model (NBF) relies on a multi-bin growth mode, where each bin is associated with a size range during a growth cycle. The proposed NBF model allows for a determination of the percentage of treated bacteria eradicated compared to a control sample, either generally across all bacterial binary fission sizes or specific to a size range or bin. Comparisons between the NBF model and experimental observations demonstrates that bacterial growth curves, and the ratio of sample growth to a control, can be used to both determine and normalize initial variations in bacterial size, and quantity, among test samples, as well as identify final nutrient levels and the percentage of bacteria affected by treatment. Significance StatementIt is difficult to determine the effectiveness of selective bacterial eradication based upon a bacterias characteristics size, related to acoustic resonance. Here we develop a binary fission model to analyze effect on growth curves of size depend eradications. Understanding the effect on growth curves provides a method to extract the eradication percentage and initial bacterial level differences between treated sample and control sample, by using the ratio of treated growth curve to control growth curve.

19
Probing the toxic interactions between the reactive dye Drimaren Red and Human Serum Albumin

Menezes, T. M.; de Assis, C. R. D.; da Silva Neto, A. M.; Gubert, P.; Ghislandi, M. G.; Neves, J. L.

2021-07-18 biophysics 10.1101/2021.07.17.452798 medRxiv
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Azo dyes like Drimaren Red CL-5B (DR, CI Reactive Red 241) represent a class of compounds extensively used in the textile industry and are extremely dangerous to the environment and human health. Therefore, understanding the binding characteristics between such substances and biological macromolecules is essential from a toxic-kinetic perspective. The molecular interaction between DR and Human Serum Albumin (HSA) was investigated through spectroscopic techniques and molecular docking approaches. The results indicate that DR quenches HSA fluorescence following a static mechanism (corroborated by UV-Vis studies) with a moderate interaction (Ka~105 M-1), guided by electrostatic interactions ({Delta}S{degrees}> 0 and {Delta}H{degrees}< 0). DR is 5.52 nm distant from fluorophore residue Trp-214 (according to FRET investigations), and the interaction is mainly related to Tyr residues (as revealed by synchronous fluorescence). The Ellman assay identified a decrease in the content of HSA free thiol. The results of the RLS demonstrate that there are HSA alterations, suggesting damage to the confirmation of the protein. Molecular docking suggests the binding site of DR was located in subdomain IIB HSA, corroborating the experimental properties. Finally, the results suggest a high potential for DR toxicity triggered by contact with key proteins, which affects the biomolecule functionalities.

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The Curli Accessory Protein CsgF Influences the Aggregation of Human Islet Amyloid Polypeptide

Meza-Barajas, O.; Aranda, I.; Binmahfooz, A.; Newell, A.; Jayasinghe, S.

2019-09-21 biophysics 10.1101/772392 medRxiv
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Gram-negative bacteria, such as E. coli and Salmonella, contain proteinaceous, hair-like, cell surface filaments known as curli. Curli serve to facilitate cell-cell interactions and are essential for host cell colonization. Curli assembly involves six proteins, CsgA, CsgB, CsgC, CsgE, CsgF, and CsgG. CsgE and CsgF are thought to act as chaperones to help prevent the premature aggregation of CsgA and/or CsgB, and to help transport these proteins, through the outer-membrane protein CsgG, to the cell surface where they assemble to form Curli. It has been observed that CsgF is able to inhibit the aggregation of CsgA, the major protein component of Curli. This article describes CsgFs ability to influence the aggregation of human islet amyloid polypeptide (hIAPP), an amyloidogenic polypeptide that is unrelated to Curli. In the presence of CsgF no increase in Thioflavin T fluorescence was observed for freshly solubilized hIAPP monitored as a function of time, suggesting that CsgF prevents the aggregation of hIAPP during the time period of observation. An analog of CsgF lacking the N-terminal unstructured region retained the ability to inhibit the aggregation of hIAPP. The nature of the CsgF-hIAPP interaction was probed via fluorescence quenching using a series of single cysteine mutants of CsgF labeled via the individual cysteine side chains with the fluorophore IAEDANS. In the presence of hIAPP, but not in the presence of the non-amyloidogenic rat islet amyloid polypeptide, the fluorophore attached to position of 23 of CsgF was found to be less exposed the quencher acrylamide suggesting that the interaction of hIAPP changes the solvent exposure of the N-terminus of CsgF. Taken together these data suggest that the structured region of CsgF, between residues 66 and 128, is involved in the proteins interaction with hIAPP and that upon interaction structural changes make the N-terminus less solvent exposed.