The Eighth Central European Conference "Chemistry towards Biology": snapshot

The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on 28 August – 1 September 2016The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on 28 August-1 September 2016 to bring together experts in biology, chemistry and design of bioactive compounds; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topics of the conference covered "Chemistry towards Biology", meaning that the event welcomed chemists working on biology-related problems, biologists using chemical methods, and students and other researchers of the respective areas that fall within the common scope of chemistry and biology. The authors of this manuscript are plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting

PDBe: improved findability of macromolecularstructure data in the PDB

© 2019 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkz990The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.The Protein Data Bank in Europe is supported by European Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome Trust [104948]; Biotechnology and Biological Sciences Research Council [BB/N019172/1, BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1, BB/P024351/1]; European Union [284209]; ELIXIR and Open Targets. Funding for open access charge: EMB

PDBe-KB: a community-driven resource for structural and functional annotations.

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession

The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae)

<div><p>Yellow-related proteins (YRPs) present in sand fly saliva act as affinity binders of bioamines, and help the fly to complete a bloodmeal by scavenging the physiological signals of damaged cells. They are also the main antigens in sand fly saliva and their recombinant form is used as a marker of host exposure to sand flies. Moreover, several salivary proteins and plasmids coding these proteins induce strong immune response in hosts bitten by sand flies and are being used to design protecting vaccines against <i>Leishmania</i> parasites. In this study, thirty two 3D models of different yellow-related proteins from thirteen sand fly species of two genera were constructed based on the known protein structure from <i>Lutzomyia longipalpis</i>. We also studied evolutionary relationships among species based on protein sequences as well as sequence and structural variability of their ligand-binding site. All of these 33 sand fly YRPs shared a similar structure, including a unique tunnel that connects the ligand-binding site with the solvent by two independent paths. However, intraspecific modifications found among these proteins affects the charges of the entrances to the tunnel, the length of the tunnel and its hydrophobicity. We suggest that these structural and sequential differences influence the ligand-binding abilities of these proteins and provide sand flies with a greater number of YRP paralogs with more nuanced answers to bioamines. All these characteristics allow us to better evaluate these proteins with respect to their potential use as part of anti-<i>Leishmania</i> vaccines or as an antigen to measure host exposure to sand flies.</p></div

A comparison of tunnels in sand fly salivary YRPs.

<p>A comparison of tunnels in sand fly salivary YRPs.</p

Amino acid alignment within the YRP ligand-binding sites.

<p>The alignment was created in ClustalX, and shows high conservancy in binding sites (letters in brackets below the sequences, slashes indicate amino acid substitutions in appropriate positions). Ligand binding sites are highlighted in black, three bold stars below the sequences represent the main binding sites where hydrogen bonds between amino acids and the ligand are predicted. Protein codes refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166191#pone.0166191.t001" target="_blank">Table 1</a>.</p

Visualization of the tunnel in 3Q6K_Llon1.

<p>The structure was visualized in PyMOL using the MOLE script for calculating the tunnel. The 3Q6K_Llon1 protein is drawn in green, the tunnel through this protein structure is in black mesh and the red-stick molecule represents serotonin.</p

Sequence conservation of the amino acids lining the ligand-binding tunnel.

<p>The WebLogo server was used to visualize the sequence conservation of the amino acids lining the ligand-binding tunnel in 31 YRPs. The amino acids are colored according to their physical-chemical properties. LS and OS below the x-axis indicate the side closer to the ligand-binding site and the opposite side of the tunnel, respectively.</p

Identified sand fly salivary YRPs.

<p>Identified sand fly salivary YRPs.</p

Phylogenetic tree of 33 sand fly salivary YRPs with putative glycosylation sites marked.

<p>The maximum likelihood phylogenetic tree was created in TREEPUZZLE with WAG model using quartet puzzling with 10000 puzzling steps. For rooting, the related protein (ACCN: NP650247) from <i>Drosophila melanogaster</i> (Dmel) was used. Bootstraps with support for branching are shown. The letters N, O, and C indicate putative N-, O-, and C-glycosylation sites, respectively. Protein codes refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166191#pone.0166191.t001" target="_blank">Table 1</a>.</p