PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.372730v1?rss=1

Authors: Novev, J. K., Heltberg, M. L., Jensen, M. H., Doostmohammadi, A.

Abstract:

How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotem-poral model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio's time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.371344v1?rss=1

Authors: Shave, S., Chen, Y.-K., Pham, N. T., Auer, M.

Abstract:

Understanding multicomponent binding interactions in protein-ligand, protein-protein and competition systems is essential for fundamental biology and drug discovery. Hand deriving equations quickly becomes unfeasible when the number of components is increased, and direct analytical solutions only exist to a certain complexity. To address this problem and allow easy access to simulation, plotting and parameter fitting to complex systems at equilibrium, we present the Python package PyBindingCurve. We apply this software to explore homodimer and heterodimer formation culminating in the discovery that under certain conditions, homodimers are easier to break with an inhibitor than heterodimers and may also be more readily depleted. This is a potentially valuable and overlooked phenomenon of great importance to drug discovery. PyBindingCurve may be expanded to operate on any equilibrium binding system and allows definition of custom systems using a simple syntax. PyBindingCurve is available under the MIT license at: https://github.com/stevenshave/pybindingcurve as Python source code accompanied by examples and as an easily installable package within the Python Package Index.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.371484v1?rss=1

Authors: Basu, I., Gorai, B., Chandran, T., Maiti, P. K., Hussain, T.

Abstract:

During translational initiation in eukaryotes, the small ribosomal subunit forms a 48S preinitiation complex (PIC) with initiation factors. The 48S PIC binds to the 5' end of mRNA and inspects long untranslated region (UTR) for the presence of the start codon (AUG). Accurate and high speed of scanning 5' UTR and subsequent selection of the correct start codon are crucial for protein synthesis. However, the conformational state of 48S PIC required for inspecting every codon is not clearly understood. Whether the scanning or open conformation of 48S PIC can accurately select the cognate start codon over near/non-cognate codons, or this discrimination is carried out only in the scanning-arrested or closed conformation of 48S PIC. Here, using atomistic molecular dynamics (MD) simulations and free energy calculations, we show that the scanning conformation of 48S PIC can reject all but 4 of the 63 non-AUG codons. Among nine near-cognate codons with a single mismatch, only codons with a first position mismatch (GUG, CUG and UUG) or a pyrimidine mismatch at the second position (ACG) are not discriminated by scanning state of 48S PIC. In contrast, any mismatch in the third position is rejected. Simulations runs in absence of one or more eukaryotic initiation factors (eIF1, eIF1+eIF1A, eIF2[a] or eIF2{beta}) from the system show critical role of eIF1 and eIF2[a] in start codon selection. The structural analysis indicates that tRNAi dynamics at the widened P site of 48S open state drives codon selection. Further, a stable codon: anticodon interaction prepares the PIC to transit to the closed state. Overall, we provide insights into the selection of start codon during scanning and how the open conformation of 48S PIC can scan long 5' UTRs with accuracy and high speed without the requirement of sampling the closed state for every codon.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.371278v1?rss=1

Authors: Hickey, R. J., Leblanc Latour, M., Harden, J. L., Pelling, A.

Abstract:

In regenerative medicine, the healing of the interfacial zone between tissues is a major challenge, yet approaches for engineering and studying the complex microenvironment of this interface remain lacking. Here, we create and study these complex living interfaces by manufacturing modular "blocks" of decellularized plant-derived scaffolds with varying shapes and sizes with a computer numerical controlled mill. Each block can then be seeded with different cell types and easily assembled in a manner akin to LEGO bricks to create an engineered tissue interface (ETI). As a proof-of-concept study we utilize ETIs to investigate the interaction between lab grown bone and connective tissues. We also demonstrate how ETIs are biocompatible in vivo, stimulating the formation of blood vessels, cell infiltration, and tissue integration after implantation. This work creates possibilities for new tissue design avenues for understanding fundamental biological processes or the development of synthetic artificial tissues.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.372094v1?rss=1

Authors: Taye, M.

Abstract:

Developing antiviral drugs is an exigent task since viruses mutate to overcome the effect of antiviral drugs. As a result, the efficacy of most antiviral drugs is short-lived. To include this effect, we modify the Neumann and Dahari model. Considering the fact that the efficacy of the antiviral drug varies in time, the differential equations introduced in the previous model systems are rewritten to study the correlation between the viral load and antiviral drug. The effect of antiviral drug that either prevents infection or stops the production of a virus is explored. First, the efficacy of the drug is considered to decreases monotonously as time progresses. In this case, our result depicts that when the efficacy of the drug is low, the viral load decreases and increases back in time revealing the effect of the antiviral drugs is short-lived. On the other hand, for the antiviral drug with high efficacy, the viral load as well as the number of infected cells monotonously decreases while the number of uninfected cells increases. The dependence of the critical drug efficacy on time is also explored. Moreover, the correlation between viral load, the antiviral drug, and CTL response is also explored. In this case, not only the dependence for the basic reproduction ratio on the model parameters is explored but also we analyze the critical drug efficacy as a function of time. We show that the term related to the basic reproduction ratio increases when the CTL response step up. A simple analytically solvable mathematical model is also presented to analyze the correlation between viral load and antiviral drugs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.08.372763v1?rss=1

Authors: Sun, M., Azumaya, C. M., Tse, E., Frost, A., Southworth, D., Verba, K. A., Cheng, Y., Agard, D. A.

Abstract:

Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera (Gatan K2), the latest K3 camera is faster, larger, and now offers a correlated-double sampling mode (CDS). Importantly this results in a higher DQE and improved throughput compared to its predecessor. In this study, we focused on optimizing camera data collection parameters for daily use within a cryo-EM facility and explored the balance between throughput and resolution. In total, eight data sets of murine heavy-chain apoferritin were collected at different dose rates and magnifications, using 9-hole image shift data collection strategies. The performance of the camera was characterized by the quality of the resultant 3D reconstructions. Our results demonstrated that the Gatan K3 operating in CDS mode outperformed nonCDS mode in terms of reconstruction resolution in all tested conditions with 8 electrons per pixel per second being the optimal dose rate. At low magnification (64kx) we were able to achieve reconstruction resolutions of 149% of the physical Nyquist limit (1.8 [A] with a 1.346 [A] physical pixel). Low magnification allows more particles to be collected per image, aiding analysis of heterogeneous samples requiring large data sets. At moderate magnification (105kx, 0.834 [A] physical pixel size) we achieved a resolution of 1.65 [A] within 9 hours of data collection, a condition optimal for achieving high-resolution on well behaved samples. Our results also show that for an optimal sample like apoferritin, one can achieve better than 2.5 [A] resolution with 5 minutes of data collection. Together, our studies validate the most efficient ways of imaging protein complexes using the K3 direct detector and will greatly benefit the cryo-EM community.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.371393v1?rss=1

Authors: Ghosh, A., Largy, E., Gabelica, V.

Abstract:

G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually 100 mM) K+, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM TMAA. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.06.369579v1?rss=1

Authors: Bartsch, A., Ives, C. M., Kattner, C., Pein, F., Tanabe, M., Munk, A., Zachariae, U., Steinem, C., Llabres, S.

Abstract:

Gram-negative bacteria cause the majority of highly drug-resistant bacterial infections. To cross the outer membrane of the complex Gram-negative cell envelope, antibiotics permeate through porins, trimeric channel proteins that enable the exchange of small polar molecules. Mutations in porins contribute to the development of drug-resistant phenotypes. In this work, we show that a single point mutation in the porin PorB from Neisseria meningitidis, the causative agent of bacterial meningitis, can strongly affect the binding and permeation of beta-lactam antibiotics. Using X-ray crystallography, high-resolution electrophysiology, atomistic biomolecular simulation, and liposome swelling experiments, we demonstrate differences in drug binding affinity, ion selectivity and drug permeability of PorB. Our work further reveals distinct interactions between the transversal electric field in the porin eyelet and the zwitterionic drugs, which manifest themselves under applied electric fields in electrophysiology and are altered by the mutation. These observations may apply more broadly to drug-porin interactions in other channels. Our results improve the molecular understanding of porin-based drug-resistance in Gram-negative bacteria.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369645v1?rss=1

Authors: Aldehaiman, A., Momin, A. A., Restouin, A., Wang, L., Shi, X., Aljedani, S., Opi, S., Lugari, A., Hameed, U. F. S., Ponchon, L., Morelli, X., Huang, M., Dumas, C., Collette, Y., Arold, S. T.

Abstract:

The Nef protein of human and simian immunodeficiency viruses (HIV and SIV, respectively) boosts viral pathogenicity through its interactions with host cell proteins. Nef has a folded core domain and large flexible regions, each carrying several protein interaction sites. By combining the polyvalency intrinsic to unstructured regions with the binding selectivity and strength of a 3D folded domain, Nef can bind to many different host cell proteins, perturbing their cellular functions. For example, the combination of a linear proline-rich motif and a hydrophobic core domain surface allows Nef to increase affinity and selectivity for particular Src family SH3 domains. Here we investigated whether the interplay between Nefs flexible regions and its core domain can allosterically influence ligand selection. We found that the flexible regions can bind back to the core domain in different ways, producing distinct conformational states that alter the SH3 domain selectivity and availability of Nefs functional motifs. The resulting cross-talk might help synergising certain subsets of ligands while excluding others, promoting functionally coherent Nef-bound protein ensembles. Further, we combined proteomic and bioinformatic analyses to identify human proteins that select SH3 domains in the same way as does Nef. We found that only 2-3% of clones from a whole human fetal library displayed a Nef-like SH3 selectivity. However, in most cases this selectivity appears to be achieved by a canonical linear interaction rather than a Nef-like tertiary interaction. This analysis suggests that Nefs SH3 recognition surface has no (or marginally few) cellular counterparts, validating the Nef tertiary binding surface as a promising unique drug target.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369801v1?rss=1

Authors: Stehnach, M. R., Waisbord, N., Walkama, D. M., Guasto, J. S.

Abstract:

Gradients in fluid viscosity characterize microbiomes ranging from mucus layers on marine organisms and human viscera to biofilms. While such environments are widely recognized for their protective effects against pathogens and their ability to influence cell motility, the physical mechanisms controlling cell transport in viscosity gradients remain elusive, primarily due to a lack of quantitative observations. Through microfluidic experiments with a model biflagellated microalga (Chlamydomonas reinhardtii), we show that cells accumulate in high viscosity regions of weak gradients as expected, stemming from their locally reduced swimming speed. However, this expectation is subverted in strong viscosity gradients, where a novel viscophobic turning motility - consistent with a flagellar thrust imbalance - reorients the swimmers down the gradient and causes striking accumulation in low viscosity zones. Corroborated by Langevin simulations and a three-point force model of cell propulsion, our results illustrate how the competition between viscophobic turning and viscous slowdown ultimately dictates the fate of population scale microbial transport in viscosity gradients.

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