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Studying Functional Disulphide Bonds by Computer Simulations

Abstract (Expand)

Biochemical and structural data reveal important aspects of the properties and function of a protein disulphide bond. Molecular dynamics simulations can complement this experimental data and can yield … valuable insights into the dynamical behavior of the disulphide bond within the protein environment. Due to the increasing accuracy of the underlying energetic description and the increasing computational power at hand, such simulations have now reached a level, at which they can also make quantitative and experimentally testable predictions. We here give an overview of the computational methods used to predict functional aspects of protein disulphides, including the prestress, protein allosteric effects upon thiol/disulphide exchange, and disulphide redox potentials. We then outline in detail the use of free-energy perturbation methods to calculate the redox potential of a protein disulphide bond of interest. In a step-by-step protocol, we describe the workflow within the MD suite Gromacs, including practical advice on the simulation setup and choice of parameters. For other disulphide-related simulation methods, we refer to resources available online.

Authors: Frauke Gräter, Wenjin Li

Date Published: 2019

Publication Type: InBook

The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

Abstract

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Authors: Alexej Ballhausen, Moritz Jakob Przybilla, Michael Jendrusch, Saskia Haupt, Elisabeth Pfaffendorf, Markus Draxlbauer, Florian Seidler, Sonja Krausert, Aysel Ahadova, Martin Simon Kalteis, Daniel Heid, Johannes Gebert, Maria Bonsack, Sarah Schott, Hendrik Bläker, Toni Seppälä, Jukka-Pekka Mecklin, Sanne Ten Broeke, Maartje Nielsen, Vincent Heuveline, Julia Krzykalla, Axel Benner, Angelika Beate Riemer, Magnus von Knebel Doeberitz, Matthias Kloor

Date Published: 2019

Publication Type: Journal

A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging

Abstract

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Authors: Jiaguo Huang, Cinzia Brenna, Arif ul Maula Khan, Cristina Daniele, Rüdiger Rudolf, Vincent Heuveline, Norbert Gretz

Date Published: 2019

Publication Type: Journal

GOODE: A Gaussian Off-The-Shelf Ordinary Differential Equation Solver

Abstract

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Authors: David John, Vincent Heuveline, Michael Schober

Date Published: 2019

Publication Type: InProceedings

Uncertainty Assessment of the Blood Damage in a FDA Blood Pump

Abstract

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Authors: Chen Song, Vincent Heuveline

Date Published: 2019

Publication Type: Journal

Bio-entity recognition for SABIO-RK database

Abstract

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Authors: Sucheta Ghosh, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 2019

Publication Type: Journal

Second Order Finite Volume Scheme for Euler Equations with Gravity which is Well-Balanced for General Equations of State and Grid Systems

Abstract

Not specified

Authors: Berberich, Jonas P, Chandrashekar, Praveen, Klinengerg, Christian, Friedrich K. Röpke

Date Published: 2019

Publication Type: Journal

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