Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction.

In this study, we characterize the interactions between the extracellular matrix protein, procollagen C-proteinase enhancer-1 (PCPE-1), and glycosaminoglycans (GAGs), which are linear anionic periodic polysaccharides. We applied molecular modeling approaches to build a structural model of full-length PCPE-1, which is not experimentally available, to predict GAG binding poses for various GAG lengths, types and sulfation patterns, and to determine the effect of calcium ions on the binding. The computational data are analyzed and discussed in the context of the experimental results previously obtained using surface plasmon resonance binding assays. We also provide experimental data on PCPE-1/GAG interactions obtained using inhibition assays with GAG oligosaccharides ranging from disaccharides to octadecasaccharides. Our results predict the localization of GAG-binding sites at the amino acid residue level onto PCPE-1 and is the first attempt to describe the effects of ions on protein-GAG binding using modeling approaches. In addition, this study allows us to get deeper insights into the in silico methodology challenges and limitations when applied to GAG-protein interactions.

Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors.

Many drugs that are applied in anticancer therapy such as the anthracycline doxorubicin contain DNA-intercalating 9,10-anthraquinone (AQ) moieties. When Cu(II) cyclen complexes were functionalized with up to three (2-anthraquinonyl)methyl substituents, they efficiently inhibited DNA and RNA synthesis resulting in high cytotoxicity (selective for cancer cells) accompanied by DNA condensation/aggregation phenomena. Molecular modeling suggests an unusual bisintercalation mode with only one base pair between the two AQ moieties and the metal complex as a linker. A regioisomer, in which the AQ moieties point in directions unfavorable for such an interaction, had a much weaker biological activity. The ligands alone and corresponding Zn(II) complexes (used as redox inert control compounds) also exhibited lower activity.

Procedures for systematic capture and management of analytical data in academia.

Data management in universities is a challenging endeavor in particular due to the diverse infrastructure of devices and software in combination with limited budget. Nevertheless, in particular the analytical measurements and data sets need to be stored if possible digitally and in a well-organized manner. This manuscript describes how scientists can achieve a data management workflow focusing on data capture and storage by small adaptions to commonly used systems. The presented method includes data transfer options from ubiquitous devices like NMR instruments, GC (MS) or LC (MS), IR and Raman, or mass spectrometers to a central server and the visualization of the available data files in an electronic lab notebook (ELN). The given instruments were chosen according to the needs of synthetic chemists, in particular devices needed in organic, inorganic and polymer chemistry where single data files in the range of several megabytes per data set are produced. Altogether, three different data transfer systems were elaborated to allow a flexible handling of different devices running with different proprietary software: The first procedure allows data capture via the use of a mail server as data exchange point. With the second procedure, data are automatically mirrored from a local file folder to a central storage server where new files are monitored and processed. The third procedure was designed to transfer data with manual support to a central server which is supervised to register new information. All components that are necessary to install and use the herein elaborated functions are available as Open Source and the designed workflows are described step by step to facilitate the adaption of procedures in other universities accordingly if desired.