PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.23.310086v1?rss=1

Authors: Woodward, X., Kelly, C. V.

Abstract:

The cellular homeostasis requires precise control of membrane shape and lipid phases. The membrane curvature likely sorts lipids and proteins to regulate the membrane composition of <100-nm radius endocytic pits and viral buds. However, the interplay between membrane curvature and local membrane composition is poorly understood at the nanoscale. Here, we employed single-molecule localization microscopy to observe single-lipid diffusion in model bilayers with varying lipid compositions, phase, temperature, and nanoscale membrane curvature. Engineered membrane buds were observed for the creation of lateral compositional heterogeneity in otherwise homogeneous membranes. Membrane curvature recruited liquid-disordered lipid phases in phase-separated membranes and altered the diffusion of the lipids. Supported lipid bilayers were created over 50-nm radius nanoparticles to engineer nanoscale membrane curvature that mimics the size of naturally occurring endocytic pits and viral buds. The disorder-preferring lipids sorted to the nanoscale curvature at all temperatures, but only when embedded in a membrane capable of sustaining liquid-liquid phase separation at low temperatures. This result suggests that lipid sorting by the membrane curvature was only possible when coupled with lipid phase separation. The curvature affected the local membrane composition most strongly when the curvature was locally surrounded by a liquid-ordered phase typically associated with a stiffer bending modulus. The curvature-induced sorting of lipid phases was quantified by the sorting of disorder-preferring fluorescent lipids, single-lipid diffusion measurements, and simulations that couple the lipid phase separation to the membrane shape. Unlike single-component membranes, lipids in phase-separated membranes demonstrated faster diffusion on curved membranes than the surrounding, flat membrane. These results demonstrate that curvature-induced membrane compositional heterogeneity can be achieved by collective behavior with lipid phase separation when single-molecule properties (i.e., packing parameter) are insufficient. These results support the hypothesis that the coupling of lipid phases and membrane shape may yield lateral membrane composition heterogeneities with functional consequences.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.24.295337v1?rss=1

Authors: Nolte, D.

Abstract:

Significance: Tumor heterogeneity poses a challenge for the chemotherapeutic treatment of cancer. Tissue dynamics spectroscopy (TDS) captures dynamic contrast and can capture the response of living tissue to applied therapeutics, but the current analysis averages over the complicated spatial response of living biopsy samples. Aim: To develop tissue dynamics spectroscopic imaging (TDSI) to map the heterogeneous spatial response of tumor tissue to anticancer drugs. Approach: TDSI is applied to tumor spheroids grown from cell lines and to ex vivo living esophageal biopsy samples. Doppler fluctuation spectroscopy is performed on a voxel basis to extract spatial maps of biodynamic biomarkers. Functional images and bivariate spatial maps are produced using a bivariate color merge to represent the spatial distribution of pairs of signed drug-response biodynamic biomarkers. Results: We have mapped the spatial variability of drug responses within biopsies and have tracked sample-to-sample variability. Sample heterogeneity observed in the biodynamic maps is associated with histological heterogeneity observed using inverted Selective-Plane Illumination Microscopy (iSPIM). Conclusion: We have demonstrated the utility of TDSI as a functional imaging method to measure tumor heterogeneity and its potential for use in drug-response profiling.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.23.310169v1?rss=1

Authors: Le Roux, A.-L., Tozzi, C., Walani, N., Quiroga, X., Zalvidea, D., Trepat, X., Staykova, M., Arroyo, M., Roca-Cusachs, P.

Abstract:

In many physiological situations, BAR proteins interact with, and reshape, pre-existing curved membranes, contributing to essential cellular processes. However, the non-equilibrium and time-dependent process of reshaping, and its dependence on initial membrane shape, remains largely unknown. Here we explain, both experimentally and through modelling, how a BAR protein dynamically interacts with mechanically bent lipid membranes. We capture protein binding to curved membranes, and characterize a variety of dynamical reshaping events depending on membrane shape and protein arrangement. The events can be generally understood by an isotropic-to-nematic phase transition, in which low curvature templates with isotropic protein orientation progress towards highly curved lipid tubes with nematic protein arrangement. Our findings also apply in cells, where mechanical stretch triggers BAR-protein-membrane interactions that enable potential mechanotransduction mechanisms. Our results characterize and broaden the reshaping processes of BAR proteins on mechanically constrained membranes, demonstrating the interplay between membrane mechanical stimuli and BAR protein response.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.25.313528v1?rss=1

Authors: De Zitter, E., Hugelier, S., Duwe, S., Vandenberg, W., Tebo, A. G., Van Meervelt, L., Dedecker, P.

Abstract:

Photochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.25.310755v1?rss=1

Authors: Lastra, L., Nguyen, M., Farajpour, N., Freedman, K. J.

Abstract:

Despite the highly negatively charged backbone of DNA, electroosmotic flow (EOF) within a nanopore can lead to DNA travelling opposite to electrophoretic force at low ionic strengths. However, EOF-pumping and its role in producing current-enhancing events is ambiguous and debated due to the complicated interactions between nanopore walls, DNA grooves, ion mobility, and counterion clouds. Here, we discuss how current-enhancing DNA events could be the result of a flux imbalance between anions and cations. The contributing factors for driving a flux imbalance within a nanopore include pore size, voltage bias, and type of alkali chloride electrolyte. Once the mechanism behind conductive events is established, the physics of transducing a DNA translocation into an electrical signal can be further exploited for improving DNA sequencing and, more broadly, bio-sensing.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.25.312868v1?rss=1

Authors: Gorin, G., Pachter, L.

Abstract:

Intrinsic and extrinsic noise sources in gene expression, originating respectively from transcriptional stochasticity and from differences between cells, complicate the determination of transcriptional models. In particularly degenerate cases, the two noise sources are altogether impossible to distinguish. However, the incorporation of downstream processing, such as the mRNA splicing and export implicated in gene expression buffering, recovers the ability to identify the relevant source of noise. We report analytical copy-number distributions, discuss the noise sources' qualitative effects on lower moments, and provide simulation routines for both models.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.24.312330v1?rss=1

Authors: Weiner, B. G., Meir, Y., Wingreen, N. S.

Abstract:

Cells are home to a host of biomolecular condensates - phase-separated droplets that lack a membrane. In addition to nonspecific interactions, phase separation depends on specific binding motifs between constituent molecules. Nevertheless, few rules have been established on how these specific, heterotypic interactions drive phase separation. Using lattice-polymer simulations and mean-field theory, we find that the sequence of binding motifs strongly affects a polymer's ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity). Notably, sequence primarily acts by determining the conformational entropy of self-bonding by single polymers.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.24.311712v1?rss=1

Authors: Morin, J. A., Wittmann, S., Choubey, S., Klosin, A., Golfier, S., Hyman, A. A., Julicher, F., Grill, S. W.

Abstract:

In the last decade, extensive studies on the properties of non-membrane-bound compartments in the cellular cytoplasm have shown that concepts in phase separation drawn from physical chemistry can describe their formation and behaviour. Current evidence also suggests that phase separation plays a role in the organization inside the cell nucleus. However, the influence and role of DNA on the physical chemistry of phase separation is not well understood. Here, we are interested in the role of interactions between phase separating proteins and the DNA surface. The interaction of liquid phases with surfaces has been extensively studied in soft matter physics, in the context of macroscopic surfaces and non-biological liquids. The conditions in the nucleus are different from those studied in conventional soft matter physics because DNA with a diameter of about 2 nm provides a microscopic surface, and liquid-like phases are complex mixtures of proteins subject to a myriad of biochemical modifications. Transcriptional condensates, which are thought to serve as regulatory hubs in gene expression, provide an accessible system to investigate the physics of condensates that emerge from DNA-protein and protein-protein interactions. These condensates are typically small, and the mechanisms that determine their size are unknown. Whether they can be understood as phase separated compartments has been subject to debate. Here, we use optical tweezers to directly observe the condensation of the pioneer transcription factor Klf4 on DNA in vitro. We demonstrate that Klf4 forms microphases that are enabled by interaction with the DNA surface. This sets their typical size and allows them to form below the saturation concentration for liquid-liquid phase separation. We combine experiment with theory to show that these microphases can be understood as forming by surface condensation on DNA via a switch-like transition similar to prewetting. Polymer surface mediated condensation reconciles several observations that were previously thought to be at odds with the idea of phase separation as an organizing principle in the nucleus.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.24.311795v1?rss=1

Authors: Phung, L. A., Foster, A., Miller, M., Lowe, D., Thomas, D. D.

Abstract:

The myosin super-relaxed state (SRX) in skeletal muscle is hypothesized to play an important role in regulating muscle contractility and thermogenesis in humans, but has only been examined in model organisms. Here we report the first human skeletal muscle SRX measurements, using quantitative epifluorescence microscopy of fluorescent 2'/3'-O-(N-methylanthraniloyl) ATP (mantATP) single-nucleotide turnover. Myosin heavy chain (MHC) isoform expression was determined using gel electrophoresis for each permeabilized vastus lateralis fiber, to allow for novel comparisons of SRX between fiber-types. We find that the fraction of myosin in SRX is less in MHC IIA fibers than in MHC I and IIAX fibers (p = 0.008). ATP turnover of SRX is faster in MHC IIAX fibers compared to MHC I and IIA fibers (p = 0.001). We conclude that SRX biochemistry is measurable in human skeletal muscle, and our data indicate that SRX depends on fiber type as classified by MHC isoform. Extension from this preliminary work would provide further understanding regarding the role of SRX in human muscle physiology.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.21.306092v1?rss=1

Authors: Smrek, J., Michieletto, D.

Abstract:

DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained -- or supercoiled -- DNA plasmids are largely neglected; this is partly due to the limited understanding of how supercoiling affects the rheology of entangled DNA. To address this open question we perform large scale Molecular Dynamics (MD) simulations of entangled solutions of DNA plasmids modelled as twistable chains. We discover that, contrarily to what generally assumed in the literature, larger supercoiling increases the average size of plasmids in the entangled regime. At the same time, we discover that this is accompanied by an unexpected increase of diffusivity. We explain our findings as due to a decrease in inter-plasmids threadings and entanglements.

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