Biophysical Characterization of Pro-apoptotic BimBH3 Peptides Reveals an Unexpected Capacity for Self-Association

Bcl-2 proteins orchestrate the mitochondrial pathway of apoptosis, pivotal for cell death. Yet, the structural details of the conformational changes of pro- and antiapoptotic proteins and their interactions remain unclear. Pulse dipolar spectroscopy (double electron-electron resonance [DEER], also known as PELDOR) in combination with spin-labeled apoptotic Bcl-2 proteins unveils conformational changes and interactions of each protein player via detection of intra- and inter-protein distances. Here, we present the synthesis and characterization of pro-apoptotic BimBH3 peptides of different lengths carrying cysteines for labeling with nitroxide or gadolinium spin probes. We show by DEER that the length of the peptides modulates their homo-interactions in the absence of other Bcl-2 proteins and solve by X-ray crystallography the structure of a BimBH3 tetramer, revealing the molecular details of the inter-peptide interactions. Finally, we prove that using orthogonal labels and three-channel DEER we can disentangle the Bim-Bim, Bcl-xL-Bcl-xL, and Bim-Bcl-xL interactions in a simplified interactome.This work was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2033—Projektnummer 390677874, the DFG Priority Program SPP1601 “New Frontiers in Sensitivity in EPR Spectroscopy” (to E.B.), DFG BO 3000/5-1 (to E.B.), SFB958 – Z04 (to E.B.), DFG grant INST 130/972-1 FUGG (to E.B.). P.E.C. is supported by an Australian NHMRC fellowship (1079700

Protection heterogeneity in a harmonized European patent system

This study proposes a divergent expectation model for patent infringement disputes, where both litigation and settlement are driven by patent quality. Under the model, patent quality depends on both broadness and definiteness of the patent. The model predicts that technologies where the definiteness attribute can be estimated with high accuracy will have higher settlement rates. At trial, it is rather the assessment of the patent quality by the judge which decides the outcome. In its empirical section, the paper evaluates over a thousand hand-collected and hand-coded patent infringement and counterclaim decisions rendered by courts in the three largest patent granting European countries—Germany, France and the United Kingdom. The paper utilizes empirical methods to investigate whether the characteristics of the patents or the country of litigation predict the outcome of litigation. Examination of the patent characteristics is guided by the factors of our model, in that the patent quality, and underlying technology and industry are tested. The findings provide evidence of the continuing heterogeneity of the patent systems in Europe, despite the harmonization efforts. Demonstrated was the lack of importance of the characteristics of the litigated patent; rather, it was the forum to which the case was brought that was decisive. At the dawn of the Unified Patent Court, our study provides for a window into the extent of heterogeneity still prevailing and a starting point for monitoring the further development of European patent harmonization

Rare event analysis using the Limited Relative Error algorithm for OMNeT++ simulations

The Limited Relative Error algorithm is an alternative statistical method for data evaluation. Through online result analysis it continuously requests more samples until it deems the evaluation confident enough. With this it allows researchers to hand over the control of simulation time to the algorithm, and through a-priori configuration the target result resolution is set so that arbitrarily rare events can be investigated. We provide a new description of the method as well as a stand-alone implementation and an integration of the algorithm into the OMNeT++ simulator