Identifying and Visualizing Macromolecular Flexibility in Structural Biology

Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features

Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors

Discovery of new diketopiperazines inhibiting Burkholderia cenocepacia quorum sensing in vitro and in vivo

Burkholderia cenocepacia, an opportunistic respiratory pathogen particularly relevant for cystic fibrosis patients, is difficult to eradicate due to its high level of resistance to most clinically relevant antimicrobials. Consequently, the discovery of new antimicrobials as well as molecules capable of inhibiting its virulence is mandatory. In this regard quorum sensing (QS) represents a good target for anti-virulence therapies, as it has been linked to biofilm formation and is important for the production of several virulence factors, including proteases and siderophores. Here, we report the discovery of new diketopiperazine inhibitors of the B. cenocepacia acyl homoserine lactone synthase CepI, and report their anti-virulence properties. Out of ten different compounds assayed against recombinant CepI, four were effective inhibitors, with IC50 values in the micromolar range. The best compounds interfered with protease and siderophore production, as well as with biofilm formation, and showed good in vivo activity in a Caenorhabditis elegans infection model. These molecules were also tested in human cells and showed very low toxicity. Therefore, they could be considered for in vivo combined treatments with established or novel antimicrobials, to improve the current therapeutic strategies against B. cenocepacia

Creation and characterization of He-related color centers in diamond

Diamond is a promising material for the development of emerging applications in quantum optics, quantum information and quantum sensing. The fabrication and characterization of novel luminescent defects with suitable opto-physical properties is therefore of primary importance for further advances in these research fields. In this work we report on the investigation in the formation of photoluminescent (PL) defects upon MeV He implantation in diamond. Such color centers, previously reported only in electroluminescence and cathodoluminescence regime, exhibited two sharp emission lines at 536.5 nm and 560.5 nm, without significant phonon sidebands. A strong correlation between the PL intensities of the above-mentioned emission lines and the He implantation fluence was found in the 10^15-10^17 cm^{-2} fluence range. The PL emission features were not detected in control samples, i.e. samples that were either unirradiated or irradiated with different ion species (H, C). Moreover, the PL emission lines disappeared in samples that were He-implanted above the graphitization threshold. Therefore, the PL features are attributed to optically active defects in the diamond matrix associated with He impurities. The intensity of the 536.5 nm and 560.5 nm emission lines was investigated as a function of the annealing temperature of the diamond substrate. The emission was observed upon annealing at temperatures higher than 500{\deg}C, at the expenses of the concurrently decreasing neutral-vacancy-related GR1 emission intensity. Therefore, our findings indicate that the luminescence originates from the formation of a stable lattice defect. Finally, the emission was investigated under different laser excitations wavelengths (i.e. 532 nm and 405 nm) with the purpose of gaining a preliminary insight about the position of the related levels in the energy gap of diamond

Формування політичних інститутів в країнах Центральної Азії в умовах незалежності

Останні досягнення і соціально-економічні успіхи країн Центральної Азії, що отримали незалежність з розпадом СРСР ґрунтуються на багатьох чинниках, серед яких, у першу чергу, проведення ефективних економічних реформ, становлення середнього класу і формування зрілого суспільства