PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.29.360214v1?rss=1

Authors: Gielen, V., Mönkemöller, V., Shen, Y., Hofkens, J., Vanden Berghe, P., Campbell, R. E., Moeyaert, B., Dedecker, P.

Abstract:

Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled analyte quantification (PEAQ) biosensing, a method that leverages photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop photochromic variants of the popular GCaMP family of calcium ion biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also show how our method can be expanded to fast imaging with reduced illumination intensities or to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.28.359513v1?rss=1

Authors: Yang, E. C., Bu, W., Suma, A., Carnevale, V., Grasty, K., Loll, P., Woll, K., Bhanu, N., Garcia, B. A., Eckenhoff, R. G., Covarrubias, M.

Abstract:

Propofol, one of the most commonly used intravenous general anesthetics, modulates neuronal function by interacting with ion channels. The mechanisms that link propofol binding to the modulation of distinct ion channel states, however, are not understood. To tackle this problem, we investigated prokaryotic ancestors of eukaryotic voltage-gated Na+ channels (Navs) using unbiased photoaffinity labeling with a photoacitivatable propofol analog (AziPm), electrophysiological methods and mutagenesis. The results directly demonstrate conserved propofol binding sites involving the S4 voltage sensors and the S4-S5 linkers in NaChBac and NavMs, and also suggest state-dependent changes at these sites. Then, using molecular dynamics simulations to elucidate the structural basis of propofol modulation, we show that the S4 voltage sensors and the S4-S5 linkers shape two distinct propofol binding sites in a conformation-dependent manner. These interactions help explain how propofol binding promotes activation-coupled inactivation to inhibit Nav channel function.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.29.361261v1?rss=1

Authors: Kucherova, A., Strango, S., Sukenik, S., Theillard, M.

Abstract:

The recent COVID-19 pandemic has brought about a surge of crowd-sourced initiatives aimed at simulating the proteins of the SARS-CoV-2 virus. A bottleneck currently exists in translating these simulations into tangible predictions that can be leveraged for pharmacological studies. Here we report on extensive electrostatic calculations done on an exascale simulation of the opening of the SARS-CoV-2 spike protein, performed by the Folding@home initiative. We compute the electric potential as the solution of the non-linear Poisson-Boltzmann equation using a parallel sharp numerical solver. The inherent multiple length scales present in the geometry and solution are reproduced using highly adaptive Octree grids. We analyze our results focusing on the electro-geometric properties of the receptor-binding domain and its vicinity. This work paves the way for a new class of hybrid computational and data-enabled approaches, where molecular dynamics simulations are combined with continuum modeling to produce high-fidelity computational measurements serving as a basis for protein bio-mechanism investigations.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.29.355917v1?rss=1

Authors: Chang, B.-J., Sapoznik, E., Pohlkamp, T., Terrones, T., Welf, E. S., Manton, J. D., Roudot, P., Hake, K., Whitehead, L., York, A. G., Dean, K. M., Fiolka, R. P.

Abstract:

We introduce a cost-effective and easily implemented scan unit which enables any camera-based microscope to perform projection imaging from diverse viewing angles. We demonstrate this capability on Lattice Light-Sheet and Oblique Plane Microscopy by rapidly delivering projection images with an uncompromised lateral resolution and high optical contrast. By imaging the sample from one or multiple perspectives, our method enables visualization of rapid biological processes, real time stereoscopic imaging as well as three-dimensional particle localization throughout a cellular volume from just two images. Furthermore, because our projection imaging technique provides intuitive three-dimensional renderings in real-time, it improves microscope usability, allows users to more-readily optimize instrument performance and identify biological phenomena of interest on-the-fly, while also reducing data overhead by a factor of >100. We leverage our rapid projection method to image cancer cell morpho-dynamics and calcium signaling in cultured neurons, to perform three-dimensional localization of genetically encoded nanoparticles, as well as to image orthogonal views of an embryonic Zebrafish heart simultaneously.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.29.361212v1?rss=1

Authors: Abederemane-Ali, F., Rossen, N. D., Kobiela, M. E., Craig, R. A., Garrison, C. E., O'Connell, L. A., Du Bois, J., Dumbacher, J. P., Minor, D. L.

Abstract:

Poisonous organisms carry small molecule toxins that alter voltage-gated sodium channel (NaV) function. Among these, batrachotoxin (BTX) from Pitohui toxic birds and Phyllobates poison frogs, stands out because of its lethality and unusual effects on NaV function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore forming helix N->T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost that compromises channel function, and fails to produce BTX resistant channels when tested in the context of poison frog NaVs. We further show that captive-raised poison frogs are BTX resistant, even though they bear BTX sensitive NaVs. Hence, our data refute the hypothesis that BTX autoresistance is rooted in NaV mutations and instead suggest that more generalizable mechanisms such as toxin sequestration act to protect BTX bearing species from autointoxication.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.29.360966v1?rss=1

Authors: Proks, P., Schewe, M., Conrad, L. J., Rao, S., Rathje, K., Rodstrom, K. E., Carpenter, E. P., Baukrowitz, T., Tucker, S. J.

Abstract:

The TREK subfamily of Two-Pore Domain (K2P) K+ channels are inhibited by low micromolar concentrations of fluoxetine and its metabolite, norfluoxetine (NFx). Although not the principal target of this antidepressant, TREK channel inhibition by NFx has provided important insights into the conformational changes associated with channel gating and highlighted the role of the selectivity filter in this process. Yet despite the availability of TREK-2 crystal structures with NFx bound, the precise mechanisms which underlie NFx inhibition remain elusive. Such investigations ideally require examining the effects of the drug on single channel behavior. However, wild-type TREK channels normally exhibit a very low open probability which makes analysis of their inhibition at the single channel level extremely challenging. In this study, we show how the unique behavior of single TREK-2 channels reconstituted in lipid bilayers can be used to study NFx inhibition in detail. Our results reveal the primary mechanism of NFx inhibition is a complex allosteric process that results in both a reduced open probability and single channel conductance. Furthermore, we show the transduction mechanism involved in NFx inhibition can be disrupted by the action of ML335, and can also be subject to desensitization. We also uncover several voltage-dependent effects of NFx inhibition. In addition, we propose a gating scheme that accounts these effects and which provide important insights into the action of agonists and antagonists on K2P channel function.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.28.358663v1?rss=1

Authors: Balasubramaniam, L., Doostmohammadi, A., Saw, T. B., Sankara, G., Mueller, R., Dang, T., Thomas, M., Gupta, S., Sonam, S., Yap, A. S., Toyama, Y., Mege, R.-M., Yeomans, J., Ladoux, B.

Abstract:

Actomyosin machinery endows cells with contractility at a single cell level. However, at a tissue scale, cells can show either contractile or extensile behaviour based on the direction of pushing or pulling forces due to neighbour interactions or substrate interactions. Previous studies have shown that a monolayer of fibroblasts behaves as a contractile system while a monolayer of epithelial cells or neural crest cells behaves as an extensile system. How these two contradictory sources of force generation can coexist has remained unexplained. Through a combination of experiments using MDCK (Madin Darby Canine Kidney) cells, and in-silico modeling, we uncover the mechanism behind this switch in behaviour of epithelial cell monolayers from extensile to contractile as the weakening of intercellular contacts. We find that this switch in active behaviour also promotes the buildup of tension at the cell substrate interface through an increase in actin stress fibers and higher traction forces. This in turn triggers a mechanotransductive response in vinculin translocation to focal adhesion sites and YAP (Yes-associated protein) transcription factor activation. Our studies also show that differences in extensility and contractility act to sort cells, thus determining a general mechanism for mechanobiological pattern formation during cell competition, morphogenesis and cancer progression.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.28.358457v1?rss=1

Authors: Dwulet, J. M., Briggs, J. K., Benninger, R. K.

Abstract:

The islets of Langerhans exist as a multicellular network that is important for the regulation of blood glucose levels. The majority of cells in the islet are insulin-producing {beta}-cells, which are excitable cells that are electrically coupled via gap junction channels. {beta}-cells have long been known to display heterogeneous functionality. However, due to gap junction electrical coupling, {beta}-cells show coordinated [Ca2+] oscillations when stimulated with glucose, and global quiescence when unstimulated. Small subpopulations of highly functional {beta}-cells have been suggested to control the dynamics of [Ca2+] and insulin release across the islet. In this study, we investigated the theoretical basis of whether small subpopulations of {beta}-cells can disproportionality control islet [Ca2+] dynamics. Using a multicellular model of the islet, we generated continuous or bimodal distributions of {beta}-cell heterogeneity and examined how islet [Ca2+] dynamics depended on the presence of cells with increased excitability or increased oscillation frequency. We found that the islet was susceptible to marked suppression of [Ca2+] when a ~10% population of cells with high metabolic activity was hyperpolarized; where hyperpolarizing cells with normal metabolic activity had little effect. However, when these highly metabolic cells were removed from the islet model, near normal [Ca2+] remained. Similarly, when ~10% of cells with either the highest frequency or earliest elevations in [Ca2+] were removed from the islet, the [Ca2+] oscillation frequency remained largely unchanged. Overall these results indicate that small populations of {beta}-cells with either increased excitability or increased frequency, or signatures of [Ca2+] dynamics that suggest such properties, are unable to disproportionately control islet-wide [Ca2+] via gap junction coupling. As such, we need to reconsider the physiological basis for such small {beta}-cell populations or the mechanism by which they may be acting to control normal islet function.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.28.354738v1?rss=1

Authors: Bruot, N., Cicuta, P., Gadelha, H., Goldstein, R. E., Kotar, J. E., Lauga, E., Nadal, F.

Abstract:

A growing body of work on the dynamics of eukaryotic flagella has noted that their oscillation frequencies are sufficiently high that the viscous penetration depth of unsteady Stokes flow is comparable to the scales over which flagella synchronize. Incorporating these effects into theories of synchronization requires an understanding of the global unsteady flows around oscillating bodies. Yet, there has been no precise experimental test on the microscale of the most basic aspects of such unsteady Stokes flow: the orbits of passive tracers and the position-dependent phase lag between the oscillating response of the fluid at a distant point and that of the driving particle. Here, we report the first such direct Lagrangian measurement of this unsteady flow. The method uses an array of 30 submicron tracer particles positioned by a time-shared optical trap at a range of distances and angular positions with respect to a larger, central particle, which is then driven by an oscillating optical trap at frequencies up to 400 Hz. In this microscale regime, the tracer dynamics is considerably simplified by the smallness of both inertial effects on particle motion and finite-frequency corrections to the Stokes drag law. The tracers are found to display elliptical Lissajous figures whose orientation and geometry are in agreement with a low-frequency expansion of the underlying dynamics, and the experimental phase shift between motion parallel and orthogonal to the oscillation axis exhibits a predicted scaling form in distance and angle. Possible implications of these results for synchronization dynamics are discussed.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.28.359091v1?rss=1

Authors: Senicourt, L., le Maire, A., Allemand, F., Carvalho, J. E., Guee, L., Germain, P., Schubert, M., Bernado, P., Bourguet, W., Sibille, N.

Abstract:

Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved -helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRID by integrating several experimental (NMR, SAXS, CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a cooperative binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.

Copy rights belong to original authors. Visit the link for more info