PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.09.332734v1?rss=1

Authors: Zhao, D., Xu, W., Zhang, X., Wang, X., Yuan, E., Xiong, Y., Wu, S., Li, S., Wu, N., Tian, T., Feng, X., Shu, H., Lang, P., Shen, X., Li, H., Li, P., Zeng, J.

Abstract:

The ongoing coronavirus disease 2019 (COVID-19) pandemic has raised an urgent need to develop effective therapeutics against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a potential antiviral drug target, the nucleocapsid (N) protein of SARS-CoV-2 functions as a viral RNA chaperone and plays vital and multifunctional roles during the life cycle of coronavirus1-3. In this study, we discovered that the N protein of SARS-CoV-2 undergoes liquid-liquid phase separation (LLPS) both in vitro and in vivo, which is further modulated by viral RNA. In addition, we found that, the core component of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2, nsp12, preferentially partitions into the N protein condensates. Moreover, we revealed that, two small molecules, i.e., CVL218 and PJ34, can be used to intervene the N protein driven phase separation and loosen the compact structures of the condensates of the N-RNA-nsp12 complex of SARS-CoV-2. The discovery of the LLPS-mediated interplay between N protein and nsp12 and the corresponding modulating compounds illuminates a feasible way to improve the accessibility of antiviral drugs (e.g., remdesivir) to their targets (e.g., nsp12/RdRp), and thus may provide useful hints for further development of effective therapeutic strategies against SARS-CoV-2.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.09.333948v1?rss=1

Authors: Peter, E., Schug, A.

Abstract:

In this article, we investigate the effect of electrolytes on the stability of the complex between the coronavirus type 2 spike protein receptor domain (CoV-2 RBD) and ACE2, which plays an important role in the activation cascade at the viral entry of CoV-2 into human cells. At the cellular surface, electrolytes play an important role, especially in the interaction of proteins near the membrane surface. Additionally, the binding interface of the CoV-2 RBD - ACE2 complex is highly hydrophilic. We simulated the CoV-2 RBD - ACE2 complex at varying salt concentrations over the concentration range from 0.03 M to 0.3 M of calcium and sodium chloride over an individual simulation length of 750 ns in 9 independent simulations (6.75 micro s total). We observe that the CoV-2 RBD - ACE2 complex is stabilized independent of the salt concentration. We identify a strong negative electrostatic potential at the N-terminal part of CoV-2 RBD and we find that CoV-2 RBD binds even stronger at higher salt concentrations. We observe that the dynamics of the N-terminal part of CoV-2 RBD stabilize the protein complex leading to strong collective motions and a stable interface between CoV-2 RBD and ACE2. We state that the sequence of CoV-2 RBD might be optimized for a strong binding to ACE2 at varying salt concentrations at the cellular surface, which acts as a key component in the activation of CoV-2 for its viral entry.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.09.333989v1?rss=1

Authors: Appshaw, P., Hanna, S., Seddon, A.

Abstract:

Due to the high computational cost of full-cell coarse-grained molecular dynamics modelling, being able to simulate "miniature" cells that effectively represent their full-sized counterparts would be highly advantageous. To accurately represent the morphological and elastic properties of a human red blood cell in silico, such a model is employed utilising the molecular dynamics package LAMMPS. The scale invariance of the model is first tested qualitatively by following the shape evolution of red blood cells of various diameters, then quantitatively by evaluating the membrane shear modulus from simulations of optical tweezer-style stretching. Cells of physical diameter of at least 0.5m were able to form the characteristic biconcave shape of human red blood cells, though smaller cells instead equilibrated to bowl-shaped stomatocytes. A positive correlation was found between the cell size and both magnitude of deformation from optical tweezer stretching and scaled shear modulus, indicating a lack of scale invariance in the models elastic response. However, the stable morphology and measured shear modulus of the 0.5 - 1.0m diameter cells are deemed close enough to past in vitro studies on human red blood cells for them to still offer valuable use in making simplified predictions of whole-cell mechanics.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336164v1?rss=1

Authors: Hoffecker, I. T., Shaw, A., Sorokina, V., Smyrlaki, I., Högberg, B.

Abstract:

Viruses and bacteria commonly exhibit spatial repetition of surface molecules that directly interface with the host immune system. However the complex interaction of patterned surfaces with multivalent immune molecules such as immunoglobulins and B-cell receptors is poorly understood, and standard characterization typically emphasizes the monovalent affinity. We developed a mechanistic model of multivalent antibody-antigen interactions as well as a pipeline for constructing such models from a minimal dataset of patterned surface plasmon resonance experiments in which antigen pattern geometries are precisely defined using DNA origami nanostructures. We modeled the change in binding enhancement due to multivalence and spatial tolerance,i.e. the strain-dependent interconversion of bound antibodies from monovalently bound to bivalently bound states at varying antigen separation distances. The parameterized model enables mechanistic post hoc characterization of binding behavior in patterned surface plasmon resonance experiments as well as de novo simulation of transient dynamics and equilibrium properties of arbitrary pattern geometries. Simulation on lattices shows that antigen spacing is a spatial control parameter that can be tuned to determine antibody residence time and migration speed. We found that gradients in antigen spacing are predicted to drive persistent, directed antibody migration toward favorable spacing. These results indicate that antigen pattern geometry can influence antibody interactions, a phenomenon that could be significant during the coevolution of pathogens and immunity in processes like pathogen neutralization or affinity maturation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336511v1?rss=1

Authors: Waudby, C. A., Burridge, C., Christodoulou, J.

Abstract:

NMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the measurement of cross-correlated relaxation in methyl spin systems by analysis of the differential relaxation of transitions within the 13C multiplet. We describe the application of optimal design theory to implement a real-time 'on-the-fly' adaptive sampling scheme that maximizes the accuracy of the measured rate constants. The increase in sensitivity obtained using this approach enables, for the first time, quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome-nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336503v1?rss=1

Authors: Grabner, C. P., Moser, T.

Abstract:

Rod photoreceptors (PRs) use ribbon synapses to transmit visual information. To signal 'no light detected' they release glutamate continually to activate post-synaptic receptors, and when light is detected glutamate release pauses. How a rod's individual ribbon enables this process was studied here by recording evoked changes in whole-cell membrane capacitance from wild type and ribbonless (RIBEYE-ko) rods. Wild type rods created a readily releasable pool (RRP) of 92 synaptic vesicles (SVs) that emptied as a single kinetic phase with a {tau} < 0.4 msec. Lowering intracellular Ca2+-buffering accelerated Cav channel opening and facilitated release kinetics, but RRP size was unaltered. In contrast, ribbonless rods created an RRP of 24 SVs, and lacked Cav channel facilitation; however, Ca2+ channel-release coupling remained tight. The release deficits caused a sharp attenuation of rod-driven light responses measured from RIBEYE-ko mice. We conclude that the synaptic ribbon facilitates Ca2+-influx and establishes a large RRP of SVs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336214v1?rss=1

Authors: Glaeser, R. M., Hagen, W. J. H., Han, B.-G., Henderson, R., McMullan, G., Russo, C. J.

Abstract:

The brightness of modern Schottky field-emission guns can produce electron beams that have very high spatial coherence, especially for the weak-illumination conditions that are used for single-particle electron cryo-microscopy in structural biology. Even so, many users have observed defocus-dependent Thon-ring fading that has led them to restrict their data collection strategy to imaging with relatively small defocus values. In this paper, we reproduce the observation of defocus-dependent Thon-ring fading and produce a quantitative analysis and clear explanation of its causes. We demonstrate that a major cause is the delocalization of high-resolution Fourier components outside the field of view of the camera. We also show that it is important to make a correction for linear magnification anisotropy, even if it is quite small, before circular averaging of the Thon rings, as is also true before merging data from particles in many orientations. Under the conditions used in this paper, which are typical of those used in single-particle electron cryomicroscopy, fading of the Thon rings due to source coherence is negligible. The principal conclusion is that much higher values of defocus can be used than is currently thought to be possible. This increased understanding should give electron microscopists the confidence to use higher amounts of defocus to allow, for example, better visibility of their particles and Ewald sphere correction.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336412v1?rss=1

Authors: Zhen, Y., Ewert, K. K., Fisher, W. S., Steffes, V. M., Li, Y., Safinya, C. R.

Abstract:

Lipid-based carriers of the hydrophobic drug paclitaxel (PTX) are used in clinical trials as next-generation agents for cancer chemotherapy. Improving the loading capacity of these carriers requires enhanced PTX solubilization. We compared the solubility of PTX in cationic liposomes (CLs) with lipid tails containing one (oleoyl; C18:1 {Delta}9 DOTAP/DOPC) or two (linoleoyl; C18:2 {Delta}9 DLinTAP/DLinPC) cis double bonds with newly synthesized cationic DLinTAP (2,3-dilinoleoyloxy-propyl-trimethyl-ammonium methylsufate). We used differential-interference-contrast microscopy to directly observe PTX crystal formation and generate kinetic phase diagrams representing the time-dependence of PTX solubility as a function of PTX content in the membrane. Replacing tails bearing one cis double bond (DO lipids) with those bearing two (DLin lipids) significantly increased PTX membrane solubility in CLs. Remarkably, 8 mol% PTX in DLinTAP/DLinPC CLs remained soluble for approximately as long as 3 mol% PTX (the membrane solubility limit which has been the focus of most previous fundamental studies and clinical trials) in DOTAP/DOPC CLs. The large increase in solubility is likely caused by enhanced molecular affinity between lipid tails and PTX upon replacement of oleoyl by linoleoyl tails, rather than by the transition in membrane structure from lipid bilayers to inverse cylindrical micelles observed in small-angle X-ray scattering. Importantly, the efficacy of PTX-loaded CLs against human prostate cancer (PC3) cells from measurements of the IC50 of PTX cytotoxicity was unaffected by changing the lipid tails, and toxicity of the CL carrier alone was negligible. Moreover, efficacy was approximately doubled against human melanoma (M21) cells for PTX-loaded DLinTAP/DLinPC over DOTAP/DOPC CLs. The findings demonstrate the potential of chemical modifications of the lipid tails to increase the PTX membrane loading well over the typically used 3 mol% while maintaining (and in some cases even increasing) the efficacy of CLs. The increased PTX solubility will aid the development of liposomal PTX carriers that require significantly less lipid to deliver a given amount of PTX, reducing side effects and costs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.11.335232v1?rss=1

Authors: Yan, S., Yuan, Y., Fang, Q.

Abstract:

The mesh-based Monte Carlo (MMC) technique has grown tremendously since its initial publication nearly a decade ago. It is now recognized as one of the most accurate Monte Carlo (MC) methods, providing accurate reference solutions for the development of novel biophotonics techniques. In this work, we aim to further advance MMC to address a major challenge in biophotonics modeling, i.e. light transport within highly complex tissues, such as dense microvascular networks, porous media and multi-scale tissue structures. Although the current MMC framework is capable of simulating light propagation in such media given its generality, the run-time and memory usage grow rapidly with increasing media complexity and size. This greatly limits our capability to explore complex and multi-scale tissue structures. Here, we propose a highly efficient implicit mesh-based Monte Carlo (iMMC) method that incorporates both mesh- and shape-based tissue representations to create highly complex yet memory efficient light transport simulations. We demonstrate that iMMC is capable of providing accurate solutions for dense vessel networks and porous tissues while reducing memory usage by greater than a hundred- or even thousand-fold. In a sample network of microvasculature, the reduced shape complexity results in nearly 3x speed acceleration. The proposed algorithm is now available in our open-source MMC software at http://mcx.space/#mmc.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336495v1?rss=1

Authors: Ahmed, T., Nisler, C. R., Fluck, E. C., Sotomayor, M. M., Moiseenkova-Bell, V. Y.

Abstract:

Transient Receptor Potential (TRP) channels have evolved in eukaryotes to control various cellular functions in response to a wide variety of chemical and physical stimuli. This large and diverse family of channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the molecular details of channel modulation remain elusive so far. Here, we describe the full-length cryo-electron microscopy structure of TRPY1 at 3.1 A resolution. The structure reveals a distinctive architecture for TRPY1 among all eukaryotic TRP channels with an evolutionarily conserved and archetypical transmembrane domain, but distinct structural folds for the cytosolic N- and C-termini. We identified the inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid binding site, which sheds light into the lipid modulation of TRPY1 in the vacuolar membrane. The structure also exhibited two Ca2+-binding sites: one in the cytosolic side, implicated in channel activation, and the other in the vacuolar lumen side, involved in channel inhibition. These findings, together with data from molecular dynamics simulations, provide structural insights into the basis of TRPY1 channel modulation by lipids and calcium.

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