PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.16.288415v1?rss=1

Authors: Jutzeler, E., Asp, M., Kerr, K., Patteson, A. E.

Abstract:

Rheology and the study of viscoelastic materials is an integral part of engineering and the study of biophysical systems however the cost of a rheometer is only feasible for colleges, universities and research laboratories. Even if a rheometer can be purchased it is bulky and delicately calibrated limiting its usefulness to the laboratory itself. The design presented here is less than a tenth of the cost of a professional rheometer and portable making it the ideal solution for high school students as a way to introduce viscoelasticity at a younger age as well as for use in the field for obtaining preliminary rheological data.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.15.278408v1?rss=1

Authors: Nielsen, A. W., Sari, L., Fraser, R., Lin, M. M.

Abstract:

Proteins can aggregate into disordered liquid droplets or ordered assemblies such as amyloid fibrils. These two distinct phases determine the spatial organization within cells and serve differing roles in a wide range of biological functions including gene regulation, organelle and synapse formation, and memory consolidation. The ordered phase can also give rise to diseases such as Alzheimer's. However, how the protein sequence determines aggregation fate is an open question. Here we establish a general statistical mechanical theory of the disordered-to-ordered transition for polymer aggregates, including proteins, thereby completing the phase diagram for this general class of matter. The theory produces a simple universal equation determining the favored phase as a function of the temperature, polymer length, and inter-residue interaction energy variance. We show that the sequence-dependent energy variance can be efficiently calculated from all-atom molecular dynamics simulations, so that the theory has no adjustable parameters. The equation accurately predicts the experimental length-dependent crystallization temperature of synthetic polymers. The theory shows that all protein aggregates, regardless of sequence, will thermodynamically order, even in the most extreme thermophiles. Therefore, energy must be expended to maintain the disordered protein aggregate at steady state. More broadly, the theory establishes a lower bound on the ordering transition temperature for polymers. This bound indicates that condensates of any organic polymer will spontaneously order on all habitable planets.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.16.299396v1?rss=1

Authors: Junglas, B., Orru, R., Axt, A., Siebenaller, C., Steinchen, W., Heidrich, J., Hellmich, U. A., Hellmann, N., Wolf, E., Weber, S. A. L., Schneider, D.

Abstract:

Members of the phage shock protein A (PspA) family, including the inner membrane-associated protein of 30 kDa (IM30), are suggested to stabilize stressed cellular membranes. Furthermore, IM30 is essential in thylakoid membrane-containing chloroplasts and cyanobacteria, where it is involved in membrane biogenesis and/or remodeling. While it is well known that PspA and IM30 bind to membranes, the mechanism of membrane stabilization is still enigmatic. Here we report that ring-shaped IM30 super-complexes disassemble on membranes, resulting in formation of a membrane-protecting protein carpet. Upon ring dissociation, the C-terminal domain of IM30 unfolds, and the protomers self-assemble on membranes. IM30 assemblies at membranes have been observed before in vivo and were associated to stress response in cyanobacteria and chloroplasts. These assemblies likely correspond to the here identified carpet structures. Our study defines the thus far enigmatic structural basis for the physiological function of IM30 and related proteins, including PspA, and highlights a hitherto unrecognized concept of membrane stabilization by intrinsically disordered proteins.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.16.299644v1?rss=1

Authors: Du, Y., An, W., Ye, K.

Abstract:

Previously, we determined a cryo-EM structure of Saccharomyces cerevisiae 90S preribosome obtained after depletion of the RNA helicase Mtr4 at 4.5 Angstrom resolution (Sun et al., 2017). The 90S preribosome is an early assembly intermediate of small ribosomal subunit. Here, the structure was improved to 3.4 Angstrom resolution and reveals many previously unresolved structures and interactions, in particular around the central domain of 18S rRNA. The central domain adopts a closed conformation in our structure, in contrast to an open conformation in another high-resolution structure of S. cerevisiae 90S. The new model of 90S would serve as a better reference for investigation of the assembly mechanism of small ribosomal subunit.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.15.296665v1?rss=1

Authors: Meredith, S. A., Yoneda, T., Hancock, A. M., Connell, S. D., Evans, S. D., Morigaki, K., Adams, P. G.

Abstract:

The light-harvesting (LH) biomembranes from photosynthetic organisms perform solar energy absorption and transfer with high efficiency. There is great interest in the nanoscale biophysics of photosynthesis, however, natural membranes are complex and highly curved so can be challenging to study. Here we present model photosynthetic "hybrid membranes" assembled from a combination of natural LH membranes and synthetic lipids deposited into a patterned polymerized lipid template on glass. This arrangement offers many advantages over previous model systems including: a sufficiently complex mixture of natural proteins to mimic the biological processes, a modular self-assembly mechanism, and a stabilizing template promoting the formation of supported lipid bilayers from complex natural membranes with high protein content (that would not otherwise form). These hybrid membranes can be used as a platform to delineate the complex relationship between LH energy pathways and membrane organization. Atomic force microscopy and fluorescence lifetime microscopy revealed that hybrid membranes have an elongated fluorescence lifetime (~4 ns) compared to native membranes (~0.5 ns), a direct consequence of reduced protein density and an uncoupling of protein-protein interactions. We observed the real time self-assembly and migration of LH proteins from natural membrane extracts into the hybrid membranes and monitored the photophysical state of the membranes at each stage. Finally, experiments utilizing our hybrid membranes suggest that assays currently used in the photosynthesis community to test the electron transfer activity of Photosystem II may have non-specific interactions with other proteins, implying that new methods are needed for reliable quantification of electron transfers in photosynthesis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.16.298463v1?rss=1

Authors: Carrillo, M., Pandey, S., Sanchez, J., Noda, M., Poudyal, I., Aldama, L., Malla, T. N., Claesson, E., Yuan Wahlgreen, W., Feliz, D., Srajer, V., Maj, M., Castillon, L., Iwata, S., Nango, E., Tanaka, R., Tanaka, T., Fangjia, L., Tono, K., Owada, S., Westenhoff, S., Stojkovic, E., Schmidt, M.

Abstract:

Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in which light signals are received and transduced as structural change through the entire protein to modulate the activity of the protein. It is unknown how the Pr-to-Pfr interconversion occurs as the structure of intermediates remain notoriously elusive. Here, we present short-lived crystal structures of the classical phytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray Free Electron Laser 5 ns and 33ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway. The snapshots show with atomic precision how the signal progresses from the chromophore towards the output domains, explaining how plants, bacteria and fungi sense red light.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.15.297887v1?rss=1

Authors: Bell, N. A. W., Haynes, P. J., Brunner, K., Maia de Oliveira, T., Flocco, M., Hoogenboom, B. W., Molloy, J. E.

Abstract:

Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme that plays important roles in DNA repair, chromatin organization and transcription regulation. Although binding and activation of PARP1 by DNA damage sites has been extensively studied, little is known about how PARP1 binds to long stretches of undamaged DNA and how it could shape chromatin architecture. Here, using a combination of single-molecule techniques including magnetic tweezers and atomic force microscopy, we show that PARP1 binds and condenses undamaged, kilobase-length DNA subject to sub-picoNewton mechanical forces. Decondensation by high force proceeds through a series of discrete increases in extension, indicating that PARP1 stabilizes loops of DNA. This model is supported by DNA braiding experiments which show that PARP1 can bind at the intersection of two separate DNA molecules. PARP inhibitors do not affect the level of condensation of undamaged DNA, but act to block condensation reversal for damaged DNA in the presence of NAD+. Our findings establish a mechanism for PARP1 in the organization of chromatin structure.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.15.295964v1?rss=1

Authors: Sadoun, A., Biarnes-Pelicot, M., Ghesquiere-Dierickx, L., Wu, A., Theodoly, O., Limozin, L., Hamon, Y., Puech, P.-H.

Abstract:

We designed a strategy, based on a careful examination of the activation capabilities of proteins and antibodies used as substrates for adhering T cells, coupled to protein microstamping. This allowed us to control at the same time the position, shape, mechanics and activation state of T cells. Once adhered on shaped patterns we examined the capacities of T cells to be activated with soluble aCD3, in comparison to T cells adhered to a continuously decorated substrate with the same density of ligands. We show that, in our hand, adhering onto an anti CD45 (aCD45) antibody decorated surface is not affecting T cell calcium fluxes, even adhered on variable size micro-patterns. We further demonstrate this by expressing MEGF10 as a non immune adhesion receptor in T cells to obtain the very same spreading area on PLL substrates and Young modulus than immobilized cells on aCD45, while retaining similar activation capabilities using soluble aCD3 or through model APC contacts. We propose that our system is a way to test activation or anergy of T cells with defined adhesion and mechanical characteristics, and may allow to dissect fine details of these mechanisms since it allows to observe homogenised populations in standardized T cell activation assays.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.14.296863v1?rss=1

Authors: Li, Z., Nolte, D., Turek, J., Matei, D., Swetzig, W., Nwani, N., An, R.

Abstract:

Development of an assay to predict response to chemotherapy has remained an elusive goal in cancer research. We report a phenotypic chemosensitivity assay for epithelial ovarian cancer based on Doppler spectroscopy of infrared light scattered from intracellular motions in living three-dimensional tumor biopsy tissue measured in vitro. The study analyzed biospecimens from 20 human patients with epithelial ovarian cancer. Matched primary and metastatic tumor tissues were collected for 3 patients, and an additional 3 patients provided only metastatic tissues. Doppler fluctuation spectra were obtained using full-field optical coherence tomography through off-axis digital holography. Frequencies in the range from 10 mHz to 10 Hz are sensitive to changes in intracellular dynamics caused by platinum-based chemotherapy. Metastatic tumor tissues were found to display a biodynamic phenotype that was similar to primary tissue from patients who had poor clinical outcomes. The biodynamic phenotypic profile correctly classified 90% [88% to 91% c.i.] of the patients when the metastatic samples were characterized as having a chemoresistant phenotype. This work suggests that Doppler profiling of tissue response to chemotherapy has the potential to predict patient clinical outcomes based on primary, but not metastatic, tumor tissue.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.14.296442v1?rss=1

Authors: Schneider, M. M., Scheidt, T., Priddey, A. J., Xu, C. K., Hu, M., Devenish, S. R. A., Meisl, G., Dobson, C. M., Kosmoliaptsis, V., Knowles, T. P. J.

Abstract:

The detection and characterisation of antibodies in human blood is a key for clinical diagnostics and risk assessment for autoimmunity, infectious diseases and transplantation. Antibody titre derived from immunoassays is a commonly used measure for antibody response, but this metric does not resolve readily the two fundamental properties of antibodies in solution, namely their affinity and concentration. This difficulty originates from the fact that the fundamental parameters describing the binding interaction, affinity and ligand concentration, are convoluted into the titre measurement; moreover, the difficulty of controlling the surface concentration and activity of the immobilised ligand can make it challenging to distinguish between avidity and affinity. To address these challenges, we developed microfluidic antibody affinity profiling, an assay which allows the simultaneous determination of both affinity and antibody concentration, directly in solution, without surface immobilisation or antibody purification. We demonstrate these measurements in the context of alloantibody characterisation in organ transplantation, using complex patient sera, and quantify the concentration and affinity of alloantibodies against donor Human Leukocyte Antigens (HLA), an extensively used clinical biomarker to access the risk of allograft rejection. These results outline a path towards detection and in depth profiling of antibody response in patient sera.

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