Mechanistic insights into dopaminergic and serotonergic neurotransmission – concerted interactions with helices 5 and 6 drive the functional outcome

Brain functions rely on neurotransmitters that mediate communication between billions of neurons. Disruption of this communication can result in a plethora of psychiatric and neurological disorders. In this work, we combine molecular dynamics simulations, live-cell biosensor and electrophysiological assays to investigate the action of the neurotransmitter dopamine at the dopaminergic D₂ receptor (D₂R). The study of dopamine and closely related chemical probes reveals how neurotransmitter binding translates into the activation of distinct subsets of D₂R effectors (i.e.: G_i2, G_oB, G_z and β-arrestin 2). Ligand interactions with key residues in TM5 (S5.42) and TM6 (H6.55) in the D₂R binding pocket yield a dopamine-like coupling signature, whereas exclusive TM5 interaction is typically linked to preferential G protein coupling (in particular G_oB) over β-arrestin. Further experiments for serotonin receptors indicate that the reported molecular mechanism is shared by other monoaminergic neurotransmitter receptors. Ultimately, our study highlights how sequence variation in position 6.55 is used by nature to fine-tune β-arrestin recruitment and in turn receptor signaling and internalization of neurotransmitter receptors.

Neurotransmitter contacts within the receptor binding site differentially contribute to the overall functional response: transmembrane helix (TM) 5 contacts promote G protein coupling whereas concerted TM5–TM6 contacts enhance β-arrestin recruitment.     

Effectiveness of the Oxygenation over Classical Protonolysis Reactions: A Case of Alkylzinc Complexes Incorporating an Aminoalcoholate Ligand

Alkylzinc aminoalcoholates have emerged as powerful catalysts in organic synthesis and polymerization processes. Despite extensive research, difficulties in the rational design of these catalytic systems and in-depth understanding of their modes of action have hitherto been encountered. Most of the major obstacles stem largely from the relatively limited knowledge of the structure-activity relationship of zinc catalysts. In fact, the key active species are often generated in situ via the protonolysis of the alkylzinc precursors, which precludes their isolation and detailed characterization. Herein, the effectiveness of the oxygenation over the classical protonolysis in the synthesis of zinc alkylperoxides stabilized by an aminoalcoholate ligand is demonstrated. The controlled oxygenation of a tert-butylzinc complex incorporating a pridinolum (prinol) ligand leads to well-defined a dinuclear adduct of a (prinol)ZnOOtBu moiety with the parent tBuZn(prinol) complex and a novel dimer [tBuOOZn(prinol)]₂ with terminal alkylperoxide groups. The observed reaction outcomes strongly depend on the reaction conditions. Although sparse examples of heteroleptic adducts of the [RZn(L)]_x[ROOZn(L)]_y-type are known, the herein reported homoleptic [ROOZn(L)]_x aggregate is unprecedented. Strikingly, comparative studies involving reactions between tBuZn(prinol) and tert-butylhydroperoxide or ethanol revealed that the respective seemingly simple zinc alkylperoxides, or zinc alkoxides, respectively, are not accessible via the classical alcoholysis. We believe that these game-changing results concerning multifaceted chemistry of organozinc aminoalcoholates should pave the way for more rational development of various Zn-based catalytic systems.     

Blockade of NF-κB Translocation and of RANKL/RANK Interaction Decreases the Frequency of Th2 and Th17 Cells Capable of IL-4 and IL-17 Production,Respectively, in a Mouse Model of Allergic Asthma

The main purpose of this study was to investigate whether the blockade of the interaction between the receptor activator of nuclear factor-κB (NF-ĸB) ligand (RANKL) and its receptor RANK as well as the blockade of NF-κB inhibitor kinase (IKK) and of NF-κB translocation have the potential to suppress the pathogenesis of allergic asthma by inhibition and/or enhancement of the production by CD4⁺ and CD8⁺ T cells of important cytokines promoting (i.e., IL-4 and IL-17) and/or inhibiting (i.e., IL-10 and TGF-β), respectively, the development of allergic asthma. Studies using ovalbumin(OVA)-immunized mice have demonstrated that all the tested therapeutic strategies prevented the OVA-induced increase in the absolute number of IL-4- and IL-17-producing CD4⁺ T cells (i.e., Th2 and Th17 cells, respectively) indirectly, i.e., through the inhibition of the clonal expansion of these cells in the mediastinal lymph nodes. Additionally, the blockade of NF-κB translocation and RANKL/RANK interaction, but not IKK, prevented the OVA-induced increase in the percentage of IL-4-, IL-10- and IL-17-producing CD4⁺ T cells. These latter results strongly suggest that both therapeutic strategies can directly decrease IL-4 and IL-17 production by Th2 and Th17 cells, respectively. This action may constitute an important mechanism underlying the anti-asthmatic effect induced by the blockade of NF-κB translocation and of RANKL/RANK interaction. Thus, in this context, both these therapeutic strategies seem to have an advantage over the blockade of IKK. None of the tested therapeutic strategies increased both the absolute number and frequency of IL-10- and TGF-β-producing Treg cells, and hence they lacked the potential to inhibit the development of the disease via this mechanism.     

Design,synthesis and application of new bile acid ligands with 1,2,3-triazole ring

New dimers have been obtained from propargyl ester of bile acids and α,α′-diazide-m-xylene by intermolecular 1,3-dipolar cycloaddition. These compounds have been used as ligands to form intermolecular hydrogen bonds with various aromatic acids. The structures of all products were confirmed by spectroscopic (¹H NMR, ¹³C NMR and FT-IR) analysis, mass spectrometry (ESI, MALDI) and PM5 semiempirical methods.     

Vibrational Properties of LaNb0.8M0.2O4-δ (M=As,Sb, V,and Ta)

LaNb_0.8M_0.2O_4-δ (where M=As, Sb, V, and Ta) oxides with pentavalent elements of different ionic sizes were synthesized by a solid-state reaction method. The vibrational properties of these oxides have been investigated. These studies revealed that the substituent element influences both Debye temperature value as well as the Raman active vibrational modes. Additionally, the low-temperature vibrational properties of LaNb_0.8Sb_0.2O_4-δ have been determined to show the phase transition occurrence at 260 K which is lower than previously reported.     

S‐inequality for certain product measures

In this paper we prove the S‐inequality for certain product probability measures and ideals in . As a result, for the Weibull and Gamma product distributions we derive concentration of measure type estimates as well as optimal comparison of moments.     

Triangle-Free Geometric Intersection Graphs with Large Chromatic Number

Several classical constructions illustrate the fact that the chromatic number of a graph may be arbitrarily large compared to its clique number. However, until very recently no such construction was known for intersection graphs of geometric objects in the plane. We provide a general construction that for any arc-connected compact set $X$ X in $\mathbb{R }^2$ R 2 that is not an axis-aligned rectangle and for any positive integer $k$ k produces a family $\mathcal{F }$ F of sets, each obtained by an independent horizontal and vertical scaling and translation of $X$ X , such that no three sets in $\mathcal{F }$ F pairwise intersect and $\chi (\mathcal{F })>k$ χ ( F ) > k . This provides a negative answer to a question of Gyárfás and Lehel for L-shapes. With extra conditions we also show how to construct a triangle-free family of homothetic (uniformly scaled) copies of a set with arbitrarily large chromatic number. This applies to many common shapes, like circles, square boundaries or equilateral L-shapes. Additionally, we reveal a surprising connection between coloring geometric objects in the plane and on-line coloring of intervals on the line.     

The Cubical Cohomology Ring: An Algorithmic Approach

A cohomology ring algorithm in a dimension-independent framework of combinatorial cubical complexes is developed with the aim of applying it to the topological analysis of high-dimensional data. This approach is convenient in the cup-product computation and motivated, among others, by interpreting pixels or voxels in digital images as cubes. The S-complex theory and so called co-reductions are adopted to build a cohomology ring algorithm speeding up the algebraic computations.     

MCQ4Structures to compute similarity of molecule structures

Comparison of molecular structures in order to identify their similarity is an important step in solving various problems derived from computational biology, like structure alignment and modelling, motif search or clustering. Thus, there is a constant need for the development of good measures to determine distances between the structures and tools to display these distances in an easily interpretable form. In the paper we present MCQ4Structures, a new method and tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss its unique features as compared with the other measures, including RMSD and LGA, and we show its experimental use in comparison of a number of 3D structures as well as evaluation of models predicted within RNA-Puzzles contest. MCQ4Structures software is available as a free Java WebStart application at: http://www.cs.put.poznan.pl/tzok/mcq/. The source code licensed under BSD can be downloaded from the same website.     

Unified encoding for hyper-heuristics with application to bioinformatics

This paper introduces a new approach to applying hyper-heuristic algorithms to solve combinatorial problems with less effort, taking into account the modelling and algorithm construction process. We propose a unified encoding of a solution and a set of low level heuristics which are domain-independent and which change the solution itself. This approach enables us to address NP-hard problems and generate good approximate solutions in a reasonable time without a large amount of additional work required to tailor search methodologies for the problem in hand. In particular, we focused on solving DNA sequencing by hybrydization with errors, which is known to be strongly NP-hard. The approach was extensively tested by solving multiple instances of well-known combinatorial problems and compared with results generated by meta heuristics that have been tailored for specific problem domains.