PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.19.345710v1?rss=1

Authors: Berkeley, R. F., Kashefi, M., Debelouchina, G. T.

Abstract:

Many of the proteins found in pathological protein fibrils also exhibit tendencies for liquid-liquid phase separation (LLPS) both in vitro and in cells. The mechanisms underlying the connection between these phase transitions have been challenging to study due to the heterogeneous and dynamic nature of the states formed during the maturation of LLPS protein droplets into gels and solid aggregates. Here, we interrogate the liquid-to-solid transition of the low complexity domain of the RNA binding protein FUS (FUS LC), which has been shown to adopt LLPS, gel-like, and amyloid states. We employ magic-angle spinning (MAS) NMR spectroscopy which has allowed us to follow these transitions in real time and with residue specific resolution. We observe the development of ?-sheet structure through the maturation process and show that the final state of FUS LC fibrils produced through LLPS is distinct from that grown from fibrillar seeds. We also apply our methodology to FUS LC G156E, a clinically relevant FUS mutant that exhibits accelerated fibrillization rates. We observe significant changes in dynamics during the transformation of the FUS LC G156E construct and begin to unravel the sequence specific contributions to this phenomenon with computational studies of the phase separated state of FUS LC and FUS LC G156E.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.19.344861v1?rss=1

Authors: Gouridis, G., Muthahari, Y., de Boer, M., Tassis, K., Tsirigotaki, A., Zijlstra, N., Eleftheriadis, N., Xu, R., Zacharias, M., Griffith, D. A., Sugijo, Y., Doemling, A., Karamanou, S., Economou, A., Cordes, T.

Abstract:

Novel biophysical tools allow the structural dynamics of proteins, and the regulation of such dynamics by binding partners, to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remains poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the type-II periplasmic binding protein domain family, have undergone divergent evolution leading to modification of their structural dynamics and function. We performed a structural analysis of ~600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Foerster resonance energy transfer and Hydrogen-Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enables distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extra-cytoplasmic transport-related proteins. Structural embellishments of the core created new interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately, altered substrate specificity. Our findings reveal an as yet unrecognized mechanism for the emergence of functional promiscuity during long periods of protein evolution and are applicable to a large number of domain architectures.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.18.344606v1?rss=1

Authors: Diosa, J. G., Moreno, R., Chica, E. L., Villarraga, J. A., Buganza Tepole, A.

Abstract:

Human skin enables interaction with diverse materials every day and at all times. The ability to grasp objects, feel textures, and perceive the environment depends on the mechanical behavior, complex structure, and microscale topography of human skin. At the same time, abrasive interactions, such as sometimes occur with prostheses or textiles, can damage the skin and impair its function. Previous theoretical and computational efforts have shown that skin's surface topography or microrelief, is crucial for its tribological behavior. However, current understanding is limited to adult surface profiles and simplified two-dimensional simulations. Yet, the skin has a rich set of features in three dimensions, and the geometry of skin is known to change with aging. Here we create a numerical model of a dynamic indentation test to elucidate the effect of changes in microscale topography with aging on the skin's response under indentation and sliding contact with a spherical indenter. We create three different microrelief geometries representative of different ages based on experimental reports from the literature. We perform the indentation and sliding steps, and calculate the normal and tangential forces on the indenter as it moves in three distinct directions based on the characteristic skin lines. The model also evaluates the effect of varying the material parameters. Our results show that the microscale topography of the skin in three dimensions, together with the mechanical behavior of the skin layers, lead to distinctive trends on the stress and strain distribution. The major finding is the increasing role of anisotropy which emerges from the geometric changes seen with aging.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.16.343459v1?rss=1

Authors: Marti, D., Torras, J., Bertran, O., Turon, P., Aleman, C.

Abstract:

Recent studies have shown that SARS-CoV-2 virus can be inactivated by effect of heat, even though, little is known about the molecular changes induced by the temperature. Here, we unravel the basics of such inactivation mechanism over the SARS-CoV-2 spike glycoprotein by executing atomistic molecular dynamics simulations. Both the closed down and open up states, which determine the accessibility to the receptor binding domain, were considered. Results suggest that the spike undergoes drastic changes in the topology of the hydrogen bond network while salt bridges are mainly preserved. Reorganization in the hydrogen bonds structure produces conformational variations in the receptor binding subunit and explain the thermal inactivation of the virus. Conversely, the macrostructure of the spike is preserved at high temperature because of the retained salt bridges. The proposed mechanism has important implications for engineering new approaches to inactivate the SARS-CoV-2 virus.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.18.336891v1?rss=1

Authors: Ueno, H., Kato, M., Minagawa, Y., Hirose, Y., Noji, H.

Abstract:

Alkaline phosphatase (ALP), a homo-dimeric enzyme has been widely used in various bioassays as disease markers and enzyme probes. Recent advancements of digital bioassay revolutionized ALP-based diagnostic assays as seen in rapid growth of digital ELISA and the emerging multiplex profiling of single-molecule ALP isomers. However, the intrinsic heterogeneity found among ALP molecules hampers the ALP-based quantitative digital bioassays. This study aims quantitative analysis of single-molecule activities of ALP from Escherichia coli and reveals the static heterogeneity in catalytic activity of ALP with two distinct populations: half-active and fully active portions. Digital assays with serial buffer exchange uncovered single-molecule Michaelis-Menten kinetics of ALP; half-active molecules have halved values of the catalytic turnover rate, kcat, and the rate constant of productive binding, kon, of the fully active molecules. These findings suggest that half-active ALP molecules are heterogenic dimers composed of inactive and active monomer units, while fully active ALP molecules comprise two active units. Static heterogeneity was also observed for ALP with other origins: calf intestine or shrimp, showing how the findings can be generalized across species. Cell-free expression of ALP with disulfide bond enhancer and spiked zinc ion resulted in homogenous population of ALP of full activity, revealing that inactive monomer units of ALP are deficient in disulfide bond formation and zinc ion coordination, and also offering the way to prepare homogenous and active populations of ALP for quantitative digital bioassays of ALP.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.18.343715v1?rss=1

Authors: Choi, Y. K., Cao, Y., Frank, M., Woo, H., Park, S.-J., Yeom, M. S., Croll, T. I., Seok, C., Im, W.

Abstract:

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2), and is considered the major target for drug and vaccine development. We previously built fully-glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of receptor binding domain (RBD) and different templates for the stalk region. In this work, multiple s-long all-atom molecular dynamics simulations were performed to provide deeper insight into the structure and dynamics of S protein, and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of RBD, and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody-glycan clash analysis instead of a commonly-used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibody. Overall, our observations offer structural and dynamic insight into SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.16.341644v1?rss=1

Authors: Lantoine, J., Proces, A., Villers, A., Halliez, S., Buee, L., Ris, L., Gabriele, S.

Abstract:

Traumatic brain injury (TBI) remains one of the leading causes of mortality and morbidity worldwide. Despite its high prevalence and extensive efforts to develop neuroprotective therapies, effective treatments for TBI are still limited. Among important neuronal damages, TBI induces structural and functional alterations of astrocytes, the most abundant cell type in the brain. Injured astrocytes respond in diverse mechanisms that result in reactive astrogliosis and are involved in the physiopathological mechanisms of TBI in an extensive and sophisticated manner. The establishment of effective neuroprotective treatments for TBI requires to better understand the complex biochemical interactions between activated astrocytes and neurons that contribute to the secondary injury. To address this challenge, we studied in vitro the role of mechanically injured astrocytes on the growth and synaptic connections of cortical neuronal networks of controlled architectures grown on well-defined protein micropatterns. Astrocytes were cultivated on elastic membranes and mechanically activated by stretching cycles. The culture media of healthy or activated astrocytes was then introduced on neuronal networks. We analyzed the neuronal viability, the neurite growth and the synaptic density of neuronal networks to understand the role of the inflammatory molecules secreted by mechanically activated astrocytes. Furthermore, we cultivated neuronal networks during 13 days with different doses of TNF- in order to decipher its individual contribution among the other cytokines. Here we show that the ratio of tubulin to synapsin area was significantly higher in neuronal networks treated with either 4 or 2 doses of TNF-, suggesting that TNF- can promote the tubulin polymerization process. Assuming that TNF- can bind to either TNFR1 or TNFR2 receptors, which lead respectively to the cell survival or the cell apoptosis, we studied the modulation of the both TNF- receptors in response to the medium of mechanically activated astrocytes and different doses of TNF-. Our findings indicate that the amount of both receptors increases with the maturation of the network. In addition, we observed a significant modulation of the amount of TNFR1 and TNFR2 in response to the media of injured astrocytes that leads to a large imbalance between both receptors, suggesting an important role for TNF-signaling in the physiopathological mechanisms of TBI.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.15.342006v1?rss=1

Authors: Ebata, H., Kidoaki, S.

Abstract:

Intracellular stresses affect various cell functions, including proliferation, differentiation and movement, which are dynamically modulated in migrating cells through continuous cell-shaping and remodeling of the cytoskeletal architecture induced by spatiotemporal interactions with extracellular matrix stiffness. When cells migrate on a matrix with cell-scale stiffness-heterogeneity, which is a common situation in living tissues, what intracellular stress dynamics (ISD) emerge? In this study, to explore this issue, finite element method-based traction force microscopy was applied to cells migrating on microelastically patterned gels. Two model systems of microelastically patterned gels (stiff/soft stripe and stiff triangular patterns) were designed to characterize the effects of a spatial constraint on cell-shaping and of the presence of different types of cues to induce competing cellular taxis (usual and reverse durotaxis) on the ISD, respectively. As the main result, the prolonged fluctuation of traction stress on a whole-cell scale was markedly enhanced on single cell-size triangular stiff patterns compared with homogeneous gels. Such ISD enhancement was found to be derived from the interplay between the nomadic migration of cells to regions with different degrees of stiffness and domain shape-dependent traction force dynamics, which should be an essential factor for keeping cells far from tensional equilibrium.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.15.341305v1?rss=1

Authors: Gerguri, T., Fu, X., Kakui, Y., Khatri, B. S., Barrington, C., Bates, P. A., Uhlmann, F.

Abstract:

Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long S. pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin density enrichment. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.16.343145v1?rss=1

Authors: Tsygvintsev, A.

Abstract:

We consider the mathematical model introduced by Batholdy et al. describing the interaction between viral pathogens and immune system. We prove the global asymptotic stability of the infection steady-state if the basic reproductive ratio is greater than unity. That solves the early announced conjecture.

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