Claude Sinner

Filopodia-based Wnt transport during vertebrate tissue patterning

Paracrine Wnt/β-catenin signalling is important during developmental processes, tissue regeneration and stem cell regulation. Wnt proteins are morphogens, which form concentration gradients across responsive tissues. Little is known about the transport mechanism for these lipid-modified signalling proteins in vertebrates. Here we show that Wnt8a is transported on actin-based filopodia to contact responding cells and activate signalling during neural plate formation in zebrafish. Cdc42/N-Wasp regulates the formation of these Wnt-positive filopodia. Enhanced formation of filopodia increases the effective signalling range of Wnt by facilitating spreading. Consistently, reduction in filopodia leads to a restricted distribution of the ligand and a limited signalling range. Using a simulation, we provide evidence that such a short-range transport system for Wnt has a long-range signalling function. Indeed, we show that a filopodia-based transport system for Wnt8a controls anteroposterior patterning of the neural plate during vertebrate gastrulation.

eSBMTools 1.0: enhanced native structure-based modeling tools

MOTIVATION Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. RESULTS We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. AVAILABILITY http://sourceforge.net/projects/esbmtools/. CONTACT alexander.schug@kit.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Revealing the global map of protein folding space by large-scale simulations.

The full characterization of protein folding is a remarkable long-standing challenge both for experiment and simulation. Working towards a complete understanding of this process, one needs to cover the full diversity of existing folds and identify the general principles driving the process. Here, we want to understand and quantify the diversity in folding routes for a large and representative set of protein topologies covering the full range from all alpha helical topologies towards beta barrels guided by the key question: Does the majority of the observed routes contribute to the folding process or only a particular route? We identified a set of two-state folders among non-homologous proteins with a sequence length of 40-120 residues. For each of these proteins, we ran native-structure based simulations both with homogeneous and heterogeneous contact potentials. For each protein, we simulated dozens of folding transitions in continuous uninterrupted simulations and constructed a large database of kinetic parameters. We investigate folding routes by tracking the formation of tertiary structure interfaces and discuss whether a single specific route exists for a topology or if all routes are equiprobable. These results permit us to characterize the complete folding space for small proteins in terms of folding barrier ΔG(‡), number of routes, and the route specificity RT.

Integration of eSBMTools into the MoSGrid Portal Using the gUSE Technology

Native structure based models are a broadly used technique in bio molecular simulation allowing understanding of complex processes in the living cell involving bio macromolecules. Based on energy landscape theory and the principle of minimal frustration, these models find wide application in simulating complex biological processes as diverse as protein or RNA folding and assembly, conformational transitions associated with allostery, to structure prediction. To allow rapid adoption by scientists, especially experimentalists, having no background in programming or high performance computing, we here provide an effective user interface to existing applications running on distributed computing resources. Based on the gateway technologies WS-PGRADE and gUSE, we developed a web-based community application service for native structure based modeling by integrating a powerful user interface to an existing UNICORE grid application based on the eSBMTools package. The eSBM port let has been integrated into the MoSGrid portal and is immediately accessible for the bioinformatics, biophysics and structural biology communities.

Native structure-based modeling and simulation of biomolecular systems per mouse click

BackgroundMolecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization.ResultsHere, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins.ConclusionsWe present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research.

Pcdh18a-positive tip cells instruct notochord formation in zebrafish

The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result of major cell reorganization in the mesoderm, the convergence and the extension of the axial cells. However, it is currently not known how these processes act together in a coordinated way during notochord formation. Analysing the tissue flow, we determined the displacement of the axial mesoderm and identified, relative to the ectoderm, an actively-migrating notochord tip cell population and a group of trailing notochordal plate cells. Molecularly, these tip cells express Protocadherin18a, a member of the cadherin superfamily. We show that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms these tip cells into a cohesive and fast migrating cell group. In turn, these tip cells subsequently instruct the trailing mesoderm. We simulated cell migration during early mesoderm formation using a lattice-based mathematical framework, and predicted that the requirement for an anterior, local motile cell cluster could guide the intercalation of the posterior, axial cells. Indeed, grafting experiments validated the predictions and induced ectopic notochord-like rods. Our findings indicate that the tip cells influence the trailing mesodermal cell sheet by inducing the formation of the notochord.

3D Simulations of Morphogen Transport in an Early Fish Embryo

During the early stages of embryonic development, various means of cell communication orchestrate tissue development within the highly dynamic environment. Signalling gradients of morphogens determine cell fates, tissue generation, and in the long run organs of the final organism. In our research we focus on the distribution and effects of Wnt8a, a morphogen involved in the development and differentiation of the brain. In a previous work we were able to show experimentally that this protein is distributed by a novel short-range propagation mechanism by means of specialized filopodia[1]. Here we present our results on extending these simulations of a simple flat tissue towards a more accurate description of the embryo in a 3D environment.The simulation models the tissue expansion on a 3D spherical surface and morphogen distribution via filopodia formation. It integrates length and angle distributions as well as growth frequencies of the filopodia, cell migration, and a slight ligand decay consistently with experimental measurements. Additionally it extends our previous model by explicitly considering the movement of the Wnt8a source.[1] Filopodia-based Wnt transport during vertebrate tissue patterning. Stanganello, E., Hagemann, A. I. H., Mattes, B., Sinner, C., Meyen, D., Weber, S., Schug, A., Raz, E. and Scholpp, S., Nature Communications 6, 2015