An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Protein complexes represent major functional units for the execution of biological processes. Systematic affinity purification coupled with mass spectrometry (AP-MS) yielded a wealth of information on the compendium of protein complexes expressed in Saccharomyces cerevisiae. However, global AP-MS analysis of human protein complexes is hampered by the low throughput, sensitivity and data robustness of existing procedures, which limit its application for systems biology research. Here, we address these limitations by a novel integrated method, which we applied and benchmarked for the human protein phosphatase 2A system. We identified a total of 197 protein interactions with high reproducibility, showing the coexistence of distinct classes of phosphatase complexes that are linked to proteins implicated in mitosis, cell signalling, DNA damage control and more. These results show that the presented analytical process will substantially advance throughput and reproducibility in future systematic AP-MS studies on human protein complexes

Deriving strong rain hazard risk maps from geo-morphology

In the last summer a long time stationary rain event struck parts of western Germany leading to massive floodings especially in the Ahr valley. Such long-term stationary weather conditions get actually more and more frequent and can lead to long extreme heat or massive continuous rainfall as shown in a study of the Potsdam-Institut für Klimafolgenforschung (PIK) last year (Rousi, E., Selten, F., Rahmstorf, S., Coumou, D. (2021): Changes in North Atlantic atmospheric circulation in a warmer climate favor winter flooding and summer drought over Europe. Journal of Climate, 34, 6, 2277-2295. https://doi.org/10.1175/JCLI-D-20-0311.1 ). The flood of the Ahr revealed that the existing modelling for flood probabilities is not sufficient. Possible causes may be the comparatively short observation period of the underlying measurements, missing historical data or the dynamics of climate change are not taken into account. For this reason, our approach is based on simulations of individually adapted worst case scenarios to derive possible effects of heavy rainfall more generally and over a wide area just based on satellite data and digital elevation models. So its a simplified model which can be adapted and applied fast to regions all over the world - especially regions with only sparse available data

A new Approach to Hazard Analysis of Heavy Rainfall Events based on the Catchment Area of the Ahr River

In this summer a long time stationary rain event struck parts of western Germany leading to massive floodings - especially in the valley of the Ahr approximately 20 km south of Bonn. Such long-term stationary weather conditions get actually more and more frequent and can lead to long extreme heat or massive continous rainfall as shown in a study of the Potsdam-Institut für Klimafolgenforschung (PIK) this year. The flood of the Ahr revealed that the existing modelling for flood probabilities is not sufficient. Possible causes may be the comparatively short observation period of the underlying measurements, missing historical data or the dynamics of climate change are not taken into account. For this reason, our approach is based on simulations of individually adapted worst case scenarios to derive possible effects of heavy rainfall more generally and over a wide area. In the last years we developed a methodology for classification of strong rain dangers depending only on the terrain. We calculated strong rain danger maps covering hole Germany and Austria estimating a worst case scenario by not taking into account local drains since those are mostly blocked by leaves and branches at such sudden events. But these maps are only based on the influence of the direct surrounding in strong rain events and do not consider water coming from other areas. So we developed an additional component for including water-run-off from up-stream areas. In the presented study we calculate the maximum run-off for a whole water catchment area assuming a massive strong rain event and the following flash flood. For each position in the run-off-map a local height profile perpendicular to the flow direction is calculated and filled up with the maximum estimated water volume at this position. So cross sections along a river in a valley giving a maximum water level for the maximum possible run-off for a given strong rain event are derived. Since some part of the rain will drain away and not contribute to the run-off this is also a worst case estimation. The results are compared to aerial imagery acquired on 2021-07-16 - two days after the flooding struck the Ahr valley -, flood-masks derived from Sentinel-1 imagery and Copernicus damage assessment maps. Based on this imagery and measurements and estimations of water gauge levels we calculate the effective rain-height of the catchment and the simulation is calibrated and adapted to the observed water levels. Based on these results we can derive also an estimation of the flooding situation in the whole catchment area including tributary valleys

Phosphorylation-based signaling networks mediate the effect of ligand affinity of the activation of naive primary T-cells

Comunicaciones a congreso

Interaction proteome of human Hippo signaling : modular control of the co-activator YAP1

Peer reviewe

Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen

Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays

Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases

Protein kinases are essential for signal transduction and control of most cellular processes, including metabolism, membrane transport, motility, and cell cycle. Despite the critical role of kinases in cells and their strong association with diseases, good coverage of their interactions is available for only a fraction of the 535 human kinases. Here, we present a comprehensive mass-spectrometry-based analysis of a human kinase interaction network covering more than 300 kinases. The interaction dataset is a high-quality resource with more than 5,000 previously unreported interactions. We extensively characterized the obtained network and were able to identify previously described, as well as predict new, kinase functional associations, including those of the less well-studied kinases PIM3 and protein O-mannose kinase (POMK). Importantly, the presented interaction map is a valuable resource for assisting biomedical studies. We uncover dozens of kinase-disease associations spanning from genetic disorders to complex diseases, including cancer.Peer reviewe

‘Sciencenet’—towards a global search and share engine for all scientific knowledge

Summary: Modern biological experiments create vast amounts of data which are geographically distributed. These datasets consist of petabytes of raw data and billions of documents. Yet to the best of our knowledge, a search engine technology that searches and cross-links all different data types in life sciences does not exist

The Protein Interaction Landscape of the Human CMGC Kinase Group

Peer reviewe