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1579 Publications visible to you, out of a total of 1579
Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site

Abstract (Expand)

Focal adhesions (FAs) mediate the interaction of the cytoskeleton with the extracellular matrix in a highly dynamic fashion. Talin is a central regulator, adaptor protein, and mechano-sensor of FA … complexes. For recruitment and firm attachment at FAs, talin’s N-terminal FERM domain binds to phosphatidylinositol 4,5-bisphosphate (PIP2)-enriched membranes. A newly published autoinhibitory structure of talin-1, where the known PIP2 interaction sites are covered up, lead us to hypothesize that a hitherto less examined loop insertion of the FERM domain acts as an additional and initial site of contact. We evaluated direct interactions of talin-1 with a PIP2 membrane by means of atomistic molecular dynamics simulations. We show that this unstructured, 33-residue-long loop strongly interacts with PIP2 and can facilitate further membrane contacts, including the canonical PIP2 interactions, by serving as a flexible membrane anchor. Under force as present at FAs, the extensible FERM loop ensures talin maintains membrane contacts when pulled away from the membrane by up to 7 nm. We identify key basic residues of the anchor mediating the highly dynamic talin-membrane interaction. Our results put forward an intrinsically disordered loop as a key and highly adaptable PIP2 recognition site of talin and potentially other PIP2-binding mechano-proteins.

Authors: Jannik Buhr, Florian Franz, Frauke Gräter

Date Published: 21st Feb 2023

Publication Type: Journal

EnzymeML: seamless data flow and modeling of enzymatic data.

Abstract (Expand)

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, … reproducibility of enzymatic experiments and reusability of enzymatic data are challenging. We developed the XML-based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, the time course of the substrate and the product, kinetic parameters and the kinetic model, thus making enzymatic data findable, accessible, interoperable and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, for which data and metadata of different enzymatic reactions are collected and analyzed. EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modeling of enzyme kinetics, publication platforms and enzymatic reaction databases. EnzymeML is open and transparent, and invites the community to contribute. All documents and codes are freely available at https://enzymeml.org .

Authors: S. Lauterbach, H. Dienhart, J. Range, S. Malzacher, J. D. Sporing, D. Rother, M. F. Pinto, P. Martins, C. E. Lagerman, A. S. Bommarius, A. V. Host, J. M. Woodley, S. Ngubane, T. Kudanga, F. T. Bergmann, J. M. Rohwer, D. Iglezakis, A. Weidemann, U. Wittig, C. Kettner, N. Swainston, S. Schnell, J. Pleiss

Date Published: 9th Feb 2023

Publication Type: Journal

Modeling photometric reverberation mapping data for the next generation of big data surveys. Quasar accretion disks sizes with the LSST

Abstract (Expand)

Abstract Photometric reverberation mapping can detect the radial extent of the accretion disc (AD) in Active Galactic Nuclei by measuring the time delays between light curves observed in different …rves observed in different continuum bands. Quantifying the constraints on the efficiency and accuracy of the delay measurements is important for recovering the AD size-luminosity relation, and potentially using quasars as standard candles. We have explored the possibility of determining the AD size of quasars using next-generation Big Data surveys. We focus on the Legacy Survey of Space and Time (LSST) at the Vera C. Rubin Observatory, which will observe several thousand quasars with the Deep Drilling Fields and up to 10 million quasars for the main survey in six broadband filter during its 10-year operational lifetime. We have developed extensive simulations that take into account the characteristics of the LSST survey and the intrinsic properties of the quasars. The simulations are used to characterise the light curves from which AD sizes are determined using various algorithms. We find that the time delays can be recovered with an accuracy of 5 and 15% for light curves with a time sampling of 2 and 5 days, respectively. The results depend strongly on the redshift of the source and the relative contribution of the emission lines to the bandpasses. Assuming an optically thick and geometrically thin AD, the recovered time-delay spectrum is consistent with black hole masses derived with 30% uncertainty.

Authors: F Pozo Nuñez, C Bruckmann, S Desamutara, B Czerny, S Panda, A P Lobban, G Pietrzyński, K L Polsterer

Date Published: 6th Feb 2023

Publication Type: Journal

Stellar gravitational collapse, singularity formation and theory breakdown

Abstract (Expand)

We review three definitions (missing point(s) unsteadiness, infinite quadratic curvature invariant, and geodesic incompleteness) of what a gravitational singularity is, and argue that prediction of a …a gravitational singularity is problematic for General Relativity (GR), indicating breakdown of Lorentzian geometry, only insofar as it concerns the infinite curvature singularity characterization. In contrast, the geodesic incompleteness characterization is GR’s innovating hallmark, which is not meaningfully available in Newtonian gravity formulations (locally infinite density field, and locally infinite gravitational force) of what a gravitational singularity is. It is the continuous, non-quantized, nature of Lorentzian geometry which admits gravitational contraction be continued indefinitely. The Oppenheimer-Snyder 1939 analytical solution derives formation of a locally infinite curvature singularity and of incomplete geodesics, while Penrose’s 1965 theorem concerns formation of incomplete (null) geodesics only. We critically examine the main physical arguments against gravitational singularity formation in stellar collapse, with scope restriction to decades spanning in between Schwarzschild’s 1916 solution and Penrose’s 1965 singularity theorem. As the most robust curvature singularity formation counter-argument, we assess Markov’s derivation of an upper bound on the quadratic curvature invariant RμνλδRμνλδ≤1ℓP4 from a ratio of natural constants ħ, c and G, in connection with Wheeler’s grounding of the premise that the Planck scale ℓP is ultimate.

Author: Kiril Maltsev

Date Published: 1st Feb 2023

Publication Type: Journal

Modeling Type Ia supernovae with explosions in white dwarfs near and below the Chandrasekhar mass

Abstract (Expand)

The progenitor evolution and the explosion mechanism of Type Ia supernovae remain unexplained. Nonetheless, substantial progress has been made over the past years with three-dimensional hydrodynamic …c simulations of different scenarios. Here, we review some recent work pertaining to the leading paradigms of modeling: thermonuclear explosions of white dwarf stars near and below the Chandrasekhar mass limit. We discuss implications of the different explosion channels and their predictions of observables.

Authors: Friedrich K. Röpke, Florian Lach, Sabrina Gronow, Stuart A. Sim, Fionntan P. Callan, Christine E. Collins

Date Published: 1st Feb 2023

Publication Type: Journal

Family dispute: do Type IIP supernova siblings agree on their distance?

Abstract

Not specified

Authors: Géza Csörnyei, Christian Vogl, Stefan Taubenberger, Andreas Flörs, Stéphane Blondin, Maria Gabriela Cudmani, Alexander Holas, Sabrina Kressierer, Bruno Leibundgut, Wolfgang Hillebrandt

Date Published: 1st Feb 2023

Publication Type: Journal

Probabilistic Modelling of Time Series for explorative Big Data Analysis in Astronomy

Abstract

Not specified

Author: Fenja Schweder

Date Published: 1st Feb 2023

Publication Type: Master's Thesis

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