PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.09.331900v1?rss=1

Authors: Strom, A. R., Biggs, R. J., Banigan, E. J., Wang, X., Chiu, K., Herman, C., Collado, J., Yue, F., Ritland Politz, J. C., Tait, L. J., Scalzo, D., Telling, A., Groudine, M., Brangwynne, C. P., Marko, J., Stephens, A. D.

Abstract:

Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation contributes to nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1 (CBX5) is unknown. Here we used a novel HP1 auxin-inducible degron human cell line to rapidly degrade HP1. Degradation did not alter transcription, chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1 is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1I165E indicate that chromatin crosslinking via HP1 dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1 similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1 is therefore a critical chromatin-crosslinking protein that supports cellular functions by providing mechanical strength to chromosomes and the nucleus throughout the cell cycle.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.08.330829v1?rss=1

Authors: Song, J.

Abstract:

Very recently, liquid-liquid phase separation (LLPS) of cytoplasmic TDP-43 independent of forming stress granule (SG) has been decoded to initiate the neuron death for ALS. Mysteriously neurons maintain ATP concentrations of ~3 mM, but whether ATP modulates TDP-43 LLPS remains completely unknown. Here we characterized the effects of ATP on LLPS of TDP-43 PLD and its six mutants by DIC and NMR. For the first time, the results revealed: 1) ATP does induce and subsequently dissolve LLPS of TDP-43 PLD. 2) ATP achieves the modulation all by specifically binding Arg mostly saturated at 1:100. 3) LLPS of TDP-43 PLD and its exaggeration into aggregation are controlled by a delicate network composed of both attractive and inhibitory interactions, thus rationalizing the susceptibility of TDP-43 PLD to various ALS-causing mutations. Our studies together establish that ATP specifically binds Arg in intrinsically-disordered domains even not RGG-/R-rich, implying that ATP might be a universal regulator for most, if not all, R-containing intrinsically-disordered domains by altering their physicochemical features, conformations, dynamics, LLPS and assembly. Under physiological conditions, TDP-43 even in neuronal cytoplasm is highly bound with ATP and thus inhibited for its toxic LLPS, highlighting a central role of ATP in TDP-43 pathogenesis and aging.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.08.331629v1?rss=1

Authors: Rojas Molina, R. V., Liese, S., Carlson, A.

Abstract:

Diffusion is a fundamental mechanism for protein distribution in cell membranes. These membranes often exhibit complex shapes, which range from shallow domes to elongated tubular or pearl-like structures. Shape complexity of the membrane influences the diffusive spreading of proteins and molecules. Despite the importance membrane geometry plays in these diffusive processes, it is challenging to establish the dependence between diffusion and membrane morphology. We solve the diffusion equation numerically on various curved shapes representative for experimentally observed membrane shapes. Our results show that membrane necks become diffusion barriers. We determine the diffusive half time, i.e., the time that is required to reduce the amount of proteins in the budded region by one half and find a quadratic relation between the diffusive half time and the averaged mean curvature of the membrane shape. Our findings thus help to estimate the characteristic diffusive time scale based on the simple measure for membrane morphology.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.08.331116v1?rss=1

Authors: Zablotskii, V., Polyakova, T., Dejneka, A.

Abstract:

The diffusion of biologically active molecules is a ubiquitous process, controlling many mechanisms and the characteristic time scales for pivotal processes in living cells. Here, we show how a high static magnetic field (MF) affects the diffusion of paramagnetic and diamagnetic species, including oxygen, hemoglobin, ROS and drugs. We derive and solve the equation describing diffusion of such biologically active molecules in the presence of a MF as well as reveal the underlying mechanism of the MF effect on diffusion. We find that a high MF accelerates diffusion of diamagnetic species while slowing the diffusion of paramagnetic molecules in cell cytoplasm. When applied to oxygen and hemoglobin diffusion in red blood cells, our results suggest that a MF may significantly alter the gas exchange in an erythrocyte and cause swelling. Our prediction that the diffusion rate and characteristic time can be controlled by a MF opens new avenues for experimental studies foreseeing numerous biomedical applications.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.08.331470v1?rss=1

Authors: Liu, P., Zabala-Ferrera, O., Beltramo, P. J.

Abstract:

All biological cell membranes maintain an electric transmembrane potential of around 100 mV, due in part to an asymmetric distribution of charged phospholipids across the membrane. This asymmetry is crucial to cell health and physiological processes such as intracell signaling, receptor-mediated endocytosis, and membrane protein function. Experimental artificial membrane systems incorporate essential cell membrane structures, such as the phospholipid bilayer, in a controllable manner where specific properties and processes can be isolated and examined. Here, we describe a new approach to fabricate and characterize planar, free-standing, asymmetric membranes and use it to examine the effect of headgroup charge on membrane stiffness. The approach relies on a thin film balance used to form a freestanding membrane by adsorbing aqueous phase lipids to an oil-water interface and subsequently thinning the oil to form a bilayer. We validate this lipid-in-aqueous approach by analyzing the thickness and compressibility of symmetric membranes with varying zwitterionic DOPC and anionic DOPG content as compared to previous lipid-in-oil methods. We find that as the concentration of DOPG increases, membranes become thicker and stiffer. By controlling the lipid composition in the aqueous compartments on either side of the oil within the thin film balance, asymmetric membranes are then examined. Membrane compositional asymmetry is qualitatively demonstrated using a fluorescence quenching assay and quantitatively characterized through voltage-dependent capacitance measurements. Stable asymmetric membranes with DOPC on one side and DOPC/DOPG mixtures on the other were created with transmembrane potentials ranging from 10 to 25 mV. Introducing membrane charge asymmetry also increases the stiffness of the membrane. These initial successes demonstrate a viable pathway to quantitatively characterize asymmetric bilayers that can be extended to accommodate more complex membrane processes in the future.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.08.331546v1?rss=1

Authors: Franklin, M. W., Krise, J., Stevens, J. J., Slusky, J. S. G.

Abstract:

Protein loops can be difficult to design and predict. There have been multiple different algorithms developed to predict the structure of loops. Outer membrane proteins are all beta barrels and these barrels have a variety of well-documented loop conformations. Here we test three different algorithms to predict the structure of outer membrane protein loops. We find the PETALS algorithm is superior for this purpose. We then experimentally test the effect of replacing the long loops of outer membrane protein OmpA with twelve shorter designed loops. Though we succeeded in creating the smallest known outer membrane barrel, we find that the designed loops do not have a strong effect on OmpA folding.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.06.327676v1?rss=1

Authors: Nousi, A., Sogaard, M. T., Jauffred, L.

Abstract:

Cell migration is a fundamental characteristic of vital processes such as tissue morphogenesis, wound healing and immune cell homing to lymph nodes and inflamed or infected sites. Therefore, various brain defect diseases, chronic inflammatory diseases as well as tumor formation and metastasis are associated with aberrant or absent cell migration. With embedment of multicellular brain cancer spheroids in Matrigel and single-particle tracking, we extracted the paths of cells migrating away from the spheroids. We found that - in contrast to local invasion - single cell migration is independent of the mechanical load exerted by the environment and is characterized by high directionality and persistence. Furthermore, we identified a subpopulation of super-spreading cells with >200-fold longer persistence times than the majority of cells. These results highlight yet another aspect of between-cell heterogeneity in tumors.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.06.328245v1?rss=1

Authors: Kang, B. E., Leong, L. M., Kim, Y., Miyazaki, K., Ross, W., Baker, B. J.

Abstract:

The genetically encoded voltage indicators, ArcLight and its derivatives, mediate voltage dependent optical signals by intermolecular, electrostatic interactions between neighboring fluorescent proteins (FPs) via proton wires. A random mutagenesis event placed a negative charge on the exterior of the FP resulting in a greater than 10-fold improvement of the voltage-dependent optical signal. Repositioning this negative charge on the exterior of the FP reversed the polarity of voltage-dependent optical signals suggesting the presence of 'hot spots' capable of interacting with the negative charge on a neighboring FP thereby changing the fluorescent output. To explore the potential effect on the chromophore state, voltage-clamp fluorometry was performed with alternating excitation at 390 nm followed by excitation at 470 nm resulting in several mutants exhibiting voltage-dependent, ratiometric optical signals of opposing polarities. However, the kinetics, voltage ranges, and optimal FP fusion sites were different depending on the wavelength of excitation. These results suggest that the FP has external, electrostatic pathways capable of quenching fluorescence that are wavelength specific. ArcLight-derived GEVIs may therefore offer a novel way to map how conditions external to the {beta}-can structure can affect the fluorescence of the chromophore and transiently manipulate those pathways via conformational changes mediated by whole cell voltage clamp.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.07.329623v1?rss=1

Authors: Duelfer, J., Yan, H., Brodmerkel, M. N., Creutznacher, R., Mallagaray, A., Peters, T., Caleman, C., Marklund, E. G., Uetrecht, C.

Abstract:

Noroviruses are the major cause of gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. We also further examine structural effects of N373 deamidation upon glycan binding in partially deamidated GII.4 P dimers, which are likely present during infection. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric population. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a role of deamidation in modulating cell attachment and entry in GII.4 strains.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.05.327239v1?rss=1

Authors: Chadda, R., Bernhardt, N., Kelley, E. G., Teixeira, S. C. M., Griffith, K., Gil-Ley, A., Ozturk, T. N., Hughes, L. E., Forsythe, A., Krishnamani, V., Faraldo-Gomez, J., Robertson, J. L.

Abstract:

Over two-thirds of membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins in the membrane remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid an energetic penalty for solvating a thinned-membrane defect caused by their exposed dimerization interfaces. Supporting this theory, we demonstrate that this penalty is drastically reduced with minimal amounts of short-chain lipids, which stabilize the monomeric state by preferentially solvating the defect rather than altering the physical state of the membrane. We thus posit that the energy differentials for local lipid-solvation define membrane-protein association equilibria, and describe a molecular-level physical mechanism for lipid regulation of such processes in biological conditions.

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