PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.22.351163v1?rss=1

Authors: Dhankhar, D., Nagpal, A., Li, R., Chen, J., Cesario, T. C., Rentzepis, P.

Abstract:

The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet (UV) radiation dose have been used to differentiate between live and dead bacteria. The enhanced resonance Raman spectra of color-pigmented bacteria were recorded after excitation with visible light diode lasers. In addition, the resonance enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations ( 10^8 cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in-situ was designed, constructed and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses and plants, in-situ, and detect infections within a very short period of time.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.22.351205v1?rss=1

Authors: Voldsgaard Clausen, M., Ulstrup, J., Poulsen, H., Nissen, P.

Abstract:

The two-pore domain potassium selective (K2P) ion-channels TREK-1, TREK-2, and TRAAK essential mechanical stimulation sensors, and TREK-1/2 also targets for the antidepressant Nor-fluoxetine (Prozac). They respond directly to membrane tension by moving from the down to up conformation, a transition that is associated with a rise in open-probability. However, the mechanosensitive K2P (mK2P) channels can also open while occupying the down conformation, and although these channels are mostly closed, all structural models represent seemingly open conformations. To understand the dynamics between open/closed and up/down states and determine how membrane tension influences transitions between specific conformations, we use a novel method to analyze tension-driven activation of single purified and reconstituted TREK-2 channels. We screen a panel of prospective schemes to find the mechanism that best accounts for specific TREK-2 characteristics as tension-driven activation, suppression by Nor-fluoxetine, and single-channel kinetics. To adequately describe TREK-2 behavior, mechanistic schemes require two separate tension-sensitive transitions, one that occurs between distinct down conformations and one that moves the channel between down and up states. As membrane tension activates TREK-2, it is a transition within the structural down conformations that account for the major increase in open-probability (> 100 fold); the move from down to up further promotes channel opening, but with much lower potency (~3 fold activation).

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.22.351015v1?rss=1

Authors: Immadisetty, k., Moradi, M.

Abstract:

Proton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemo-mechanical couplings involved in substrate/proton transport and protein structural changes is missing. We therefore performed microsecond-level molecular dynamics (MD) simulations of bacterial POT transporter PepTSt, which shares ~80 % sequence identity with the human POT, PepT1, in the substrate binding region. Three different conformational states of PepTSt were simulated including, (i) occluded, apo, (ii) inward-facing, apo, and (iii) inward-acingoccluded, Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward- to outward-facing state) in the substrate transport. Additionally, E299 and E400 should disengage from interacting with the substrate either through protonation or through co-ordination with a cation for the substrate to get transported.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.22.351148v1?rss=1

Authors: Leckband, D., Rehman, J., Schwarz, G., Gajwani, P.

Abstract:

One of the central functions of the endothelium is to maintain a vascular barrier that prevents fluid leakiness and immune cell influx from the circulating blood into the tissue. The barrier integrity of the endothelium is largely controlled by adherens junctions (AJs) and the key AJ molecule VE-cadherin, which maintains cell cohesion via homotypic trans-interaction with VE-cadherin molecules on neighboring endothelial cells. Tension is required to maintain junction homeostasis, but little is known about the role of endothelial metabolism and bioenergetics in regulating junctional forces. Because glycolysis is the main source of ATP generation in endothelial cells, we examined the bioenergetic control of the mechanics of VE-cadherin junctions, by focusing on the glycolysis regulatory enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Results from traction force imbalance measurements and a VE-cadherin tension sensor revealed that inhibiting PFKFB3 significantly reduced the average junctional tension and the force on VE-cadherin complexes. The decrease in tension was largely due to mechanical changes distal from the cell-cell contacts. Specifically, inhibiting glycolysis perturbs focal adhesions and disrupts actin organization, directly impacting the net force on intercellular contacts. These findings identify a critical role of cellular metabolism for the mechanics and integrity of vascular endothelial junctions, by maintaining global cell mechanics.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.21.349696v1?rss=1

Authors: Odermatt, P. D., Bostan, E., Huang, K. C., Chang, F.

Abstract:

Intracellular density is a critical parameter that impacts the physical nature of the cytoplasm and has the potential to globally affect cellular processes. How density is regulated during cell growth is poorly understood. Here, using a new quantitative phase imaging method, we show that dry-mass density varies during the cell cycle in the fission yeast Schizosaccharomyces pombe. Density decreased during G2 phase, increased in mitosis and cytokinesis, and rapidly dropped at cell birth. These density variations can be explained mostly by a constant rate of biomass synthesis throughout the cell cycle, coupled to slowdown of volume growth during mitosis and cytokinesis and rapid expansion post-cytokinesis. Arrest at specific cell-cycle stages led to continued increases or decreases in density. Spatially heterogeneous patterns of density suggested a link between tip growth and density regulation. Density differences between daughter cells in cells delayed in cytokinesis resulted in bending of the septum away from the high-density daughter, suggesting that intracellular density correlates with turgor pressure. Our results demonstrate that the systematic variations in density during the cell cycle are determined predominantly by modulation of volume expansion, and reveal functional consequences of intracellular density gradients.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.21.349712v1?rss=1

Authors: Tsai, Y.-H., Liu, C.-W., Lin, W.-K., Wang, C.-S., Chiang, C.-H., Singh, V. R., So, P. T. C., Chou, C.-F., Chu, S.-W.

Abstract:

We demonstrate a multi-focal multi-photon volumetric microscopy via combination of 32-beam parallel lateral-scanning, a 70-kHz axial-scanning acoustic lens, and a 32-channel photodetector, enabling unprecedented data rate (2-10 GHz) and >500-volumes/second imaging speed over ~200x200x200-m3.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.21.348664v1?rss=1

Authors: Reddy, G., Thirumalai, D.

Abstract:

Nucleosomes, the building blocks of chromosomes, are also transcription regulators. Single molecule pulling experiments have shown that nucleosomes unwrap in two major stages, releasing nearly equal length of DNA in each stage. The first stage, attributed to the rupture of the outer turn is reversible, occurs at low forces ({approx} (3 - 5) pNs) whereas in the second stage the inner turn ruptures irreversibly at high forces (between {approx} (9 - 15) or higher) pNs. We show that Brownian dynamics simulations using the Self-Organized Polymer model of the nucleosome capture the experimental findings, thus permitting us to discern the molecular details of the structural changes not only in DNA but also in the Histone Protein Core (HPC). Upon unwrapping of the outer turn, which is independent of the pulling direction, there is a transition from 1.6 turns to 1.0 turn DNA wound around the HPC. In contrast, the rupture of the inner turn, leading to less than 0.5 turn DNA around the HPC, depends on the pulling direction, and is controlled by energetic and kinetic barriers. The latter arises because the mechanical force has to produce sufficient torque to rotate (in an almost directed manner) the HPC by 180{degrees}. In contrast, during the rewrapping process, HPC rotation is stochastic, with the quenched force fQ playing no role. Interestingly, if fQ = 0 the HPC rotation is not required for rewrapping because the DNA ends are unconstrained. The assembly of the outer wrap upon force quench, as assessed by the decrease in the end-to-end distance (Ree) of the DNA, nearly coincides with the increase in Ree as force is increased, confirming the reversible nature of the 1.6 turns to 1.0 turn transition. The asymmetry in HPC rotation during unwrapping and rewrapping accounts for the observed hysteresis in the stretch-release cycles in single molecule pulling experiments. Experiments that could validate the prediction that HPC rotation, which gives rise to the kinetic barrier in the unwrapping process, are proposed.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.20.344978v1?rss=1

Authors: Niemela, A., Koivuniemi, A. S.

Abstract:

Lecithin:cholesterol acyltransferase protein (LCAT) promotes the esterification reaction between cholesterol and phospholipid derived acyl chains. Positive allosteric modulators have been developed to treat LCAT deficiencies and, plausibly, also cardiovascular diseases in the future. The mechanism of action of these compounds is poorly understood. Here computational docking and atomistic molecular dynamics simulations were utilized to study the interactions between LCAT and the activating compounds. Results indicate that all drugs bind to the allosteric binding pocket in the membrane-binding domain in a similar fashion. The presence of the compounds in the allosteric site results in a distinct spatial orientation and sampling of the membrane-binding domain (MBD). The MBD's different spatial arrangement plausibly affects the lid's movement from closed to open state and vice versa, as suggested by steered molecular dynamics simulations.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.20.347922v1?rss=1

Authors: Zareiesfandabadi, P., Elting, M. W.

Abstract:

A microtubule-based machine called the mitotic spindle segregates chromosomes when eukaryotic cells divide. In the fission yeast S. pombe, which undergoes closed mitosis, the spindle forms a single bundle of microtubules inside the nucleus. During elongation, the spindle extends via antiparallel microtubule sliding by molecular motors. These extensile forces from the spindle are thought to resist compressive forces from the nucleus. We probe the mechanism and maintenance of this force balance via laser ablation of spindles at various stages of mitosis. We find that spindle pole bodies collapse toward each other following ablation, but spindle geometry is often rescued, allowing spindles to resume elongation and segregate chromosomes. While this basic behavior has been previously observed, many questions remain about this phenomenon's dynamics, mechanics, and molecular requirements. In this work, we find that previously hypothesized viscoelastic relaxation of the nucleus cannot fully explain spindle shortening in response to laser ablation. Instead, spindle collapse requires microtubule dynamics and is powered at least partly by the minus-end directed motor protein dynein. These results suggest a role for dynein in redundantly supporting force balance and bipolarity in the S. pombe spindle.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.20.348060v1?rss=1

Authors: KHODR, V., MACHILLOT, P., MIGLIORINI, E., REISER, J.-b., PICART, C.

Abstract:

Bone morphogenetic proteins (BMP) are an important family of growth factors playing a role in a large number of physiological and pathological processes, including bone homeostasis, tissue regeneration and cancers. In vivo, BMPs bind successively to both BMP receptors (BMPR) of type I and type II, and a promiscuity has been reported. In this study, we used bio-layer interferometry to perform parallel real-time biosensing and to deduce the kinetic parameters (ka, kd) and the equilibrium constant (KD) for a large range of BMPs/BMPR combinations in similar experimental conditions. We selected four members of the BMP family (BMP-2, 4, 7, 9) known for their physiological relevance and studied their interactions with five type-I BMP receptors (ALK1, 2, 3, 5, 6) and three type-II BMP receptors (BMPR-II, ACTR-IIA, ACTR-IIB). We reveal that BMP-2 and BMP-4 behave differently, especially regarding their kinetic interactions and affinities with the type-II BMPR. We found that BMP-7 has a higher affinity for ACTR-IIA and a tenfold lower affinity with the type-I receptors. While BMP-9 has a high and similar affinity for all type-II receptors, it can interact with ALK5 and ALK2, in addition to ALK1. Interestingly, we also found that all BMPs can interact with ALK5. The interaction between BMPs and both type-I and type II receptors immobilized on the same surface did not reveal further cooperativity. Our work provides a synthetic view of the interactions of these BMPs with their receptors and paves the way for future studies on their cell-type and receptor specific signaling pathways.

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