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A large harvested corpus of location metonymy

Abstract

Not specified

Authors: Kevin Mathews, Michael Strube

Date Published: 11th May 2020

Publication Type: InProceedings

Mechanoradicals in tensed tendon collagen as a source of oxidative stress

Abstract (Expand)

As established nearly a century ago, mechanoradicals originate from homolytic bond scission in polymers. The existence, nature and biological relevance of mechanoradicals in proteins, instead, are … unknown. We here show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species, essential biological signaling molecules. Electron-paramagnetic resonance (EPR) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calculations show that the radicals form by bond scission in the direct vicinity of crosslinks in collagen. Radicals migrate to adjacent clusters of aromatic residues and stabilize on oxidized tyrosyl radicals, giving rise to a distinct EPR spectrum consistent with a stable dihydroxyphenylalanine (DOPA) radical. The protein mechanoradicals, as a yet undiscovered source of oxidative stress, finally convert into hydrogen peroxide. Our study suggests collagen I to have evolved as a radical sponge against mechano-oxidative damage and proposes a mechanism for exercise-induced oxidative stress and redox-mediated pathophysiological processes.

Authors: Christopher Zapp, Agnieszka Obarska-Kosinska, Benedikt Rennekamp, Markus Kurth, David M Hudson, Davide Mercadante, Uladzimir Barayeu, Tobias P Dick, Vasyl Denysenkov, Thomas Prisner, Marina Bennati, Csaba Daday, Reinhard Kappl, Frauke Gräter

Date Published: 8th May 2020

Publication Type: Journal

Chromatosome Structure and Dynamics from Molecular Simulations

Abstract

Not specified

Authors: Mehmet Ali Öztürk, Madhura De, Vlad Cojocaru, Rebecca C. Wade

Date Published: 20th Apr 2020

Publication Type: Journal

Advances in molecular simulations of protein mechanical properties and function

Abstract (Expand)

Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and … MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.

Authors: Florian Franz, Csaba Daday, Frauke Gräter

Date Published: 1st Apr 2020

Publication Type: Journal

A fast and memory-efficient implementation of the transfer bootstrap

Abstract (Expand)

Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. …. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

Authors: Sarah Lutteropp, Alexey M Kozlov, Alexandros Stamatakis

Date Published: 1st Apr 2020

Publication Type: Journal

Flows on the $$\mathbf{PGL(V)}$$-Hitchin Component

Abstract (Expand)

In this article we define new flows on the Hitchin components for PSL(n,R). Special examples of these flows are associated to simple closed curves on the surface and give generalized twist flows. Other … examples, so called eruption flows, are associated to pair of pants in S and capture new phenomena which are not present in the case when n = 2. We determine a global coordinate system on the Hitchin component. Using the computation of the Goldman symplectic form on the Hitchin component, that is developed by two of the authors in a companion paper to this article (Sun and Zhang in The Goldman symplectic form on the PGL(V)-Hitchin component, 2017. arXiv:1709.03589), this gives a global Darboux coordinate system on the Hitchin component.

Authors: Zhe Sun, Anna Wienhard, Tengren Zhang

Date Published: 1st Apr 2020

Publication Type: Journal

Druggability Assessment in TRAPP Using Machine Learning Approaches

Abstract

Not specified

Authors: Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade, Daria B. Kokh

Date Published: 23rd Mar 2020

Publication Type: Journal

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