520 Folgen

Audio versions of bioRxiv paper abstracts

PaperPlayer biorxiv biophysics Multimodal LLC

    • Biowissenschaften

Audio versions of bioRxiv paper abstracts

    Machine learning models for predicting protein condensate formation from sequence determinants and embeddings

    Machine learning models for predicting protein condensate formation from sequence determinants and embeddings

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.26.354753v1?rss=1

    Authors: Saar, K. L., Morgunov, A. S., Qi, R., Arter, W. E., Krainer, G., Lee, A. A., Knowles, T.

    Abstract:
    Intracellular phase separation of proteins into biomolecular condensates is increasingly recognised as an important phenomenon for cellular compartmentalisation and regulation of biological function. Different hypotheses about the parameters that determine the tendency of proteins to form condensates have been proposed with some of them probed experimentally through the use of constructs generated by sequence alterations. To broaden the scope of these observations, here, we established an in silico strategy for understanding on a global level the associations between protein sequence and condensate formation, and used this information to construct machine learning classifiers for predicting liquid-liquid phase separation (LLPS) from protein sequence. Our analysis highlighted that LLPS-prone sequences are more disordered, hydrophobic and of lower Shannon entropy than sequences in the Protein Data Bank or the Swiss-Prot database, and have their disordered regions enriched in polar, aromatic and charged residues. Using these determining features together with neural network based word2vec sequence embeddings, we developed machine learning classifiers for predicting protein condensate formation. Our model, trained to distinguish LLPS-prone sequences from structured proteins, achieved high accuracy (93%; 25-fold cross-validation) and identified condensate forming sequences from external independent test data at 97% sensitivity. Moreover, in combination with a classifier that had developed a nuanced insight into the features governing protein phase behaviour by learning to distinguish between sequences of varying LLPS propensity, the sensitivity was supplemented with high specificity (approximated ROC-AUC of 0.85). These results provide a platform rooted in molecular principles for understanding protein phase behaviour. The predictor is accessible from https://deephase.ch.cam.ac.uk/ .

    Copy rights belong to original authors. Visit the link for more info

    Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device

    Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.25.354381v1?rss=1

    Authors: Honda, S., Minagawa, Y., Noji, H., Tabata, K. V.

    Abstract:
    Single-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multi-conditional or multi-parametric assays, hindering understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a new digital bioassay platform with easy solution exchanges, called multi-dimensional (MD) digital bioassay, and tested its quantitativity and utility. We immobilized single analytes in arrayed femtoliter (10-15 L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. To show the utility of our system, we investigated neuraminidase inhibitor (NAI) sensitivity on single influenza A virus (IAV) particles in a multi-conditional assay. We proved that IAV particles show a heterogeneous response to the NAI. Further, to demonstrate multi-parametric assays, we examined the sensitivity of individual IAV particles or model enzyme molecules to two different inhibitors. Our results support that MD digital bioassay is a versatile platform to unveil heterogeneities of biological entities in unprecedented resolution.

    Copy rights belong to original authors. Visit the link for more info

    Structural basis of rotavirus RNA chaperone displacement and RNA annealing

    Structural basis of rotavirus RNA chaperone displacement and RNA annealing

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.26.354233v1?rss=1

    Authors: Bravo, J. P. K., Bartnik, K., Venditti, L., Gail, E. H., Davidovich, C., Lamb, D. C., Tuma, R., Calabrese, A. N., Borodavka, A.

    Abstract:
    Rotavirus genomes are distributed between 11 distinct RNA segments, all of which are essential for virus replication. Stoichiometric genome segment selection and assembly is achieved through a series of sequence-specific, intersegment RNA-RNA interactions that are facilitated by the rotavirus RNA chaperone protein NSP2. The C-terminal region (CTR) of NSP2 has been proposed to play a role in rotavirus replication, although its mechanistic contribution to the RNA chaperone activity of NSP2 remained unknown. Here, we use single-molecule fluorescence assays to directly demonstrate that the CTR is required for promoting RNA-RNA interactions and that it limits the RNA unwinding activity of NSP2. Unexpectedly, hydrogen-deuterium exchange-mass spectrometry and UV-crosslinking data indicate that the CTR does not interact with RNA. However, removal of the CTR reduced the RNA release activity of NSP2, suggesting that the CTR is important for chaperone recycling. To further interrogate the role of the CTR, we determined cryo-EM structures of NSP2 and its ribonucleoprotein complexes. These reveal that although the CTR is ampholytic in nature, it harbours a highly conserved acidic patch that is poised towards bound RNA. Using a reverse genetics approach, we demonstrate that rotavirus mutants harbouring triple alanine mutations within the acidic patch failed to replicate, while mutations that preserve the charge of the CTR successfully restored viral replication. Together, our data suggest that the CTR reduces the accumulation of kinetically trapped NSP2-RNA complexes by accelerating RNA dissociation via charge repulsion, thus promoting efficient intermolecular RNA-RNA interactions during segment assembly.

    Copy rights belong to original authors. Visit the link for more info

    Reversible coating of cells with synthetic polymers for mechanochemical regulation of cell adhesion

    Reversible coating of cells with synthetic polymers for mechanochemical regulation of cell adhesion

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.25.354480v1?rss=1

    Authors: KAIZUKA, Y., Machida, R.

    Abstract:
    The chemical control of cell-cell interactions using synthetic materials is useful for a wide range of biomedical applications. Herein, we report a method to regulate cell adhesion and dispersion by introducing repulsive forces to live cell membranes. To induce repulsion, we tethered amphiphilic polymers, such as cholesterol-modified polyethylene glycol (PEG-CLS) to cell membranes. These amphiphilic polymers both bind to and dissociate rapidly from membranes and thus, enable the reversible coating of cells by mixing and washout without requiring genetic manipulation or chemical synthesis in the cells. We found that the repulsive forces introduced by these tethered polymers can induce cell detachment from a substrate and allow cell dispersion in a suspension, modulate the speed of cell migration, and improve the separation of cells from tissues. Our analyses showed that coating the cells with tethered polymers most likely generated two distinct repulsive forces, lateral tension and steric repulsion, on the surface, which can be tuned by altering the polymer size and density. We also modeled how these two forces can be generated in kinetically distinctive manners to explain the various responses of cells to the coating. Collectively, our observations and analyses show how we can mechanochemically regulate cell adhesion and dispersion and may contribute to the optimization of chemical coating strategies for regulating various types of cell-cell interacting systems.

    Copy rights belong to original authors. Visit the link for more info

    Not so optimal: The evolution of mutual information in potassium voltage-gated channels

    Not so optimal: The evolution of mutual information in potassium voltage-gated channels

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.26.354928v1?rss=1

    Authors: Marzen, S., Duran, A.

    Abstract:
    Potassium voltage-gated (Kv) channels need to detect and respond to rapidly changing ionic concentrations in their environment. With an essential role in regulating electric signaling, they would be expected to be optimal sensors that evolved to predict the ionic concentrations. To explore these assumptions, we use statistical mechanics in conjunction with information theory to model how animal Kv channels respond to changes in potassium concentrations in their environment. By estimating mutual information in representative Kv channel types across a variety of environments, we find two things. First, under a wide variety of environments, there is an optimal gating current that maximizes mutual information between the sensor and the environment. Second, as Kv channels evolved, they have moved towards decreasing mutual information with the environment. This either suggests that Kv channels do not need to act as sensors of their environment or that Kv channels have other functionalities that interfere with their role as sensors of their environment.

    Copy rights belong to original authors. Visit the link for more info

    Roughness and dynamics of proliferating cell fronts as a probe of cell-cell interactions

    Roughness and dynamics of proliferating cell fronts as a probe of cell-cell interactions

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.26.354878v1?rss=1

    Authors: Rapin, G., Caballero, N., Gaponenko, I., Ziegler, B., Rawleight, A., Moriggi, E., Giamarchi, T., Brown, S. A., Paruch, P.

    Abstract:
    Juxtacellular interactions play an essential but still not fully understood role in both normal tissue development and tumour invasion. Using proliferating cell fronts as a model system, we explore the effects of cell-cell interactions on the geometry and dynamics of these one-dimensional biological interfaces. We observe two distinct scaling regimes of the steady state roughness of in-vitro propagating Rat1 fibroblast cell fronts, suggesting different hierarchies of interactions at sub-cell lengthscales and at a lengthscale of 2--10 cells. Pharmacological modulation significantly affects the proliferation speed of the cell fronts, and those modulators that promote cell mobility or division also lead to the most rapid evolution of cell front roughness. By comparing our experimental observations to numerical simulations of elastic cell fronts with purely short-range interactions, we demonstrate that the interactions at few-cell lengthscales play a key role. Our methodology provides a simple framework to measure and characterise the biological effects of such interactions, and could be useful in tumour phenotyping.

    Copy rights belong to original authors. Visit the link for more info

Top‑Podcasts in Biowissenschaften