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75 Publications visible to you, out of a total of 75
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.

Abstract (Expand)

Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies … and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.

Authors: Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés

Date Published: 5th Sep 2019

Publication Type: Journal

A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data

Abstract

Not specified

Authors: Yuwei Zhang, Kelin Xia, Zexing Cao, Frauke Gräter, Fei Xia

Date Published: 15th May 2019

Publication Type: Journal

Molecular Dynamics Simulations of Molecules in Uniform Flow

Abstract (Expand)

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of … flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated flow is well-behaved. A maximal velocity of 1.3 m/s can be generated if a pull slice of 8 nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected, the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform flow, in which protein extensions depend on the flow conditions. Our implementation provides an efficient computational tool to investigate the effect of the flow at the molecular level.

Authors: Ana M. Herrera-Rodríguez, Vedran Miletić, Camilo Aponte-Santamaría, Frauke Gräter

Date Published: 1st May 2019

Publication Type: Journal

How Fast Is Too Fast in Force-Probe Molecular Dynamics Simulations?

Abstract

Not specified

Authors: Steven Sheridan, Frauke Gräter, Csaba Daday

Date Published: 19th Apr 2019

Publication Type: Journal

Structural and mechanistic insights into mechanoactivation of focal adhesion kinase

Abstract

Not specified

Authors: Magnus Sebastian Bauer, Fabian Baumann, Csaba Daday, Pilar Redondo, Ellis Durner, Markus Andreas Jobst, Lukas Frederik Milles, Davide Mercadante, Diana Angela Pippig, Hermann Eduard Gaub, Frauke Gräter, Daniel Lietha

Date Published: 2nd Apr 2019

Publication Type: Journal

Inositol hexakisphosphate increases the size of platelet aggregates

Abstract (Expand)

The inositol phosphates, InsP5 and InsP6, have recently been identified as binding partners of fibrinogen, which is critically involved in hemostasis by crosslinking activated platelets at sites of … vascular injury. Here, we investigated the putative physiological role of this interaction and found that platelets increase their InsP6 concentration upon stimulation with the PLC-activating agonists thrombin, collagen I and ADP and present a fraction of it at the outer plasma membrane. Cone and plate analysis in whole blood revealed that InsP6 specifically increases platelet aggregate size. This effect is fibrinogen-dependent, since it is inhibited by an antibody that blocks fibrinogen binding to platelets. Furthermore, InsP6 has only an effect on aggregate size of washed platelets when fibrinogen is present, while it has no influence in presence of von Willebrand factor or collagen. By employing blind docking studies we predicted the binding site for InsP6 at the bundle between the γand βhelical subunit of fibrinogen. Since InsP6 is unable to directly activate platelets and it did not exhibit an effect on thrombin formation or fibrin structure, our data indicate that InsP6 might be a hemostatic agent that is produced by platelets upon stimulation with PLC-activating agonists to promote platelet aggregation by supporting crosslinking of fibrinogen and activated platelets.

Authors: Maria A. Brehm, Ulrike Klemm, Christoph Rehbach, Nina Erdmann, Katra Kolšek, Hongying Lin, Camilo Aponte-Santamaría, Frauke Gräter, Bernhard H. Rauch, Andrew M. Riley, Georg W. Mayr, Barry V.L. Potter, Sabine Windhorst

Date Published: 1st Mar 2019

Publication Type: Journal

How ARVC-Related Mutations Destabilize Desmoplakin: An MD Study

Abstract (Expand)

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial heart disease linked to mutations in several desmosomal proteins, but the specific effects of these mutations on the molecular level … are poorly understood. Among the many documented ARVC-related genetic variants, a striking hotspot of nine mutations has been identified in the plakin domain of desmoplakin. This hotspot can be found at the meeting point of three different subdomains of desmoplakin: two spectrin repeats and a Src homology 3 domain. We set out to understand the effect of these mutations. We determine, using molecular dynamics simulations, how these mutations affect the mechanics of this interface, performing two different classes of simulations. First, we sample the dynamics of the plakin domain, in particular the tendency of the interdomain hinge to buckle, and then we apply an external force onto the constructs and determine the force necessary to break them. We find that surface-exposed mutations are not affecting the dynamics to a very large degree but that most buried mutations make the junction more flexible and decrease the rupture forces observed. Our data suggest that buried ARVC mutations destabilize desmoplakin and thereby impair desmosome integrity under tension.

Authors: Csaba Daday, Laura Marlene Mateyka, Frauke Gräter

Date Published: 1st Mar 2019

Publication Type: Journal

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