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Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics

Abstract

Not specified

Authors: Manuel Glaser, Neil J. Bruce, Sungho Bosco Han, Rebecca C. Wade

Date Published: 13th May 2021

Publication Type: Journal

Spatial Effect on Separatrix of Two-Cell System and Parameter Sensitivity Analysis

Abstract

Not specified

Authors: Chen Song, Jonas Roller, Ana Victoria Ponce-Bobadilla, Nicolas Palacio-Escat, Julio Saez-Rodriguez, Vincent Heuveline

Date Published: 11th May 2021

Publication Type: Unpublished

How multisite phosphorylation impacts the conformations of intrinsically disordered proteins.

Abstract (Expand)

Phosphorylation of intrinsically disordered proteins (IDPs) can produce changes in structural and dynamical properties and thereby mediate critical biological functions. How phosphorylation effects … intrinsically disordered proteins has been studied for an increasing number of IDPs, but a systematic understanding is still lacking. Here, we compare the collapse propensity of four disordered proteins, Ash1, the C-terminal domain of RNA polymerase (CTD2'), the cytosolic domain of E-Cadherin, and a fragment of the p130Cas, in unphosphorylated and phosphorylated forms using extensive all-atom molecular dynamics (MD) simulations. We find all proteins to show V-shape changes in their collapse propensity upon multi-site phosphorylation according to their initial net charge: phosphorylation expands neutral or overall negatively charged IDPs and shrinks positively charged IDPs. However, force fields including those tailored towards and commonly used for IDPs overestimate these changes. We find quantitative agreement of MD results with SAXS and NMR data for Ash1 and CTD2' only when attenuating protein electrostatic interactions by using a higher salt concentration (e.g. 350 mM), highlighting the overstabilization of salt bridges in current force fields. We show that phosphorylation of IDPs also has a strong impact on the solvation of the protein, a factor that in addition to the actual collapse or expansion of the IDP should be considered when analyzing SAXS data. Compared to the overall mild change in global IDP dimension, the exposure of active sites can change significantly upon phosphorylation, underlining the large susceptibility of IDP ensembles to regulation through post-translational modifications.

Authors: Fan Jin, Frauke Gräter

Date Published: 4th May 2021

Publication Type: Journal

Comparison of Machine Learning Methods for Predicting Employee Absences

Abstract

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Authors: Alejandra Jayme, Philipp Lösel, Vincent Heuveline

Date Published: 4th May 2021

Publication Type: Unpublished

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2

Abstract

Not specified

Authors: Benedict-Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinrich, Martin Schröder, Rebecca Neil, Jing Wang, Iva Navratilova, Joerg Bomke, Jonathan M. Elkins, Susanne Müller, Matthias Frech, Rebecca C. Wade, Stefan Knapp

Date Published: 1st May 2021

Publication Type: Journal

A Bittersweet Computational Journey among Glycosaminoglycans

Abstract

Not specified

Authors: Giulia Paiardi, Maria Milanesi, Rebecca C. Wade, Pasqualina D’Ursi, Marco Rusnati

Date Published: 1st May 2021

Publication Type: Journal

Simulating the formation of \ensuremathη Carinae’s surrounding nebula through unstable triple evolution and stellar merger-induced eruption

Abstract

Not specified

Authors: Ryosuke Hirai, Philipp Podsiadlowski, Stanley P. Owocki, Fabian R. N. Schneider, Nathan Smith

Date Published: 1st May 2021

Publication Type: Journal

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