Gold Standard Online Debates Summaries and First Experiments Towards Automatic Summarization of Online Debate Data

Usage of online textual media is steadily increasing. Daily, more and more news stories, blog posts and scientific articles are added to the online volumes. These are all freely accessible and have been employed extensively in multiple research areas, e.g. automatic text summarization, information retrieval, information extraction, etc. Meanwhile, online debate forums have recently become popular, but have remained largely unexplored. For this reason, there are no sufficient resources of annotated debate data available for conducting research in this genre. In this paper, we collected and annotated debate data for an automatic summarization task. Similar to extractive gold standard summary generation our data contains sentences worthy to include into a summary. Five human annotators performed this task. Inter-annotator agreement, based on semantic similarity, is 36% for Cohen's kappa and 48% for Krippendorff's alpha. Moreover, we also implement an extractive summarization system for online debates and discuss prominent features for the task of summarizing online debate data automatically.Comment: accepted and presented at the CICLING 2017 - 18th International Conference on Intelligent Text Processing and Computational Linguistic

The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells

Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells

Cryo-EM of ABC transporters: an ice-cold solution to everything?

High-resolution cryo-EM has revolutionized how we look at ABC transporters and membrane proteins in general. An ever-increasing number of software tools and faster processing now allow dissecting the molecular details of nanomachines at atomic precision. Considering the further benefits of significantly reduced sample demands and increased speed, cryo-EM will dominate the structure determination of membrane proteins in the near future without compromising on data quality or detail. Moreover, improved and new algorithms make it now possible to resolve the conformational spectrum of macromolecular machines under turnover conditions and to analyze heterogeneous samples at high-resolution. The future of cryo-EM is, therefore, bright, and the growing number of imaging facilities and groups active in this field will amplify this trend even further. Nevertheless, expectations have to be managed, as cryo-EM alone cannot provide an ultimate answer to all scientific questions. In this review, we discuss the capabilities and limitations of cryo-EM together with possible solutions for studies of ABC transporters

Single-Particle Cryo-EM of Membrane Proteins

In the recent years, the protein databank has been fueled by the exponential growth of high-resolution electron cryo-microscopy (cryo-EM) structures. This trend will be further accelerated through the continuous software and method developments and the increasing availability of imaging centers, which will open cryo-EM to a wide array of researchers with their diverse scientific goals and questions. Especially for structural biology of membrane proteins, cryo-EM offers significant advantages as it can overcome multiple limitations of classical methods. Most importantly, in cryo-EM, the sample is prepared as a vitrified suspension, which abolishes the need for crystallization, reduces the required sample amount and allows usage of a wide arsenal of hydrophobic environments. Despite recent improvements, high-resolution cryo-EM still poses some significant challenges, and standardized procedures, especially for the characterization of membrane proteins, are missing. While there can be no ultimate recipe toward a high-resolution cryo-EM structure for every membrane protein, certain factors seem to be universally relevant. Here, we share the protocols that have been successfully used in our laboratory. We hope that this may be a useful resource to other researchers in the field and may increase their chances of success

Structure of Merkel cell polyomavirus capsid and interaction with its glycosaminoglycan attachment receptor

Merkel cell polyomavirus (MCPyV) is a human double-stranded DNA tumor virus. MCPyV cell entry is unique among the polyomavirus family as it requires the engagement of two types of glycans, sialylated oligosaccharides and sulfated glycosaminoglycans (GAGs). Here, we present crystallographic and cryo-electron microscopic structures of the icosahedral MCPyV capsid and analysis of its glycan interactions via NMR spectroscopy. While sialic acid binding is specific for α2-3-linked sialic acid and mediated by the exposed apical loops of the major capsid protein VP1, a broad range of GAG oligosaccharides bind to recessed regions between VP1 capsomers. Individual VP1 capsomers are tethered to one another by an extensive disulfide network that differs in architecture from previously-described interactions for other PyVs. An unusual C-terminal extension in MCPyV VP1 projects from the recessed capsid regions. Mutagenesis experiments show that this extension is dispensable for receptor interaction