The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

Hibernation as a Stage of Ribosome Functioning

© 2020, Pleiades Publishing, Ltd. Abstract: In response to stress, eubacteria reduce the level of protein synthesis and either disassemble ribosomes into the 30S and 50S subunits or turn them into translationally inactive 70S and 100S complexes. This helps the cell to solve two principal tasks: (i) to reduce the cost of protein biosynthesis under unfavorable conditions, and (ii) to preserve functional ribosomes for rapid recovery of protein synthesis until favorable conditions are restored. All known genes for ribosome silencing factors and hibernation proteins are located in the operons associated with the response to starvation as one of the stress factors, which helps the cells to coordinate the slowdown of protein synthesis with the overall stress response. It is possible that hibernation systems work as regulators that coordinate the intensity of protein synthesis with the energy state of bacterial cell. Taking into account the limited amount of nutrients in natural conditions and constant pressure of other stress factors, bacterial ribosome should remain most of time in a complex with the silencing/hibernation proteins. Therefore, hibernation is an additional stage between the ribosome recycling and translation initiation, at which the ribosome is maintained in a “preserved” state in the form of separate subunits, non-translating 70S particles, or 100S dimers. The evolution of the ribosome hibernation has occurred within a very long period of time; ribosome hibernation is a conserved mechanism that is essential for maintaining the energy- and resource-consuming process of protein biosynthesis in organisms living in changing environment under stress conditions

Expression and Purification of HPF Protein from Staphylococcus aureus and Analysis of Its Structure by the Method of NMR Spectroscopy

Staphylococcus aureus hibernation-promoting factor (SaHPF) is a 22.2 kDa translation factor which under stress conditions (under amino acid starvation or antibiotic pressure) binds with the ribosome and inactivates it, thereby ensuring cell survival under stress. There are many problems with crystallization of this protein which still remain unsolved. Therefore, its analysis by NMR spectroscopy is of great interest. In this paper, we have described expression, purification, and NMR analysis of 13C/15N-labeled SaHPF protein and showed that it is present in a dimeric form in the solution. Notably, two types of signals in the NMR spectra have been observed: with weak intensity and high dispersion from N-terminal domain; with high intensity but low dispersion from a flexible loop between domains. No signals from C-terminal domain have been observed in the NMR spectra, which may indicate possible dimerization of this part of the protein. Protein dimerization has been also detected by the method of electrophoresis under native conditions

A SUPRAMOLECULAR STRUCTURE OF PHOSPHORYLATED N-PHENYL-1,2,4-TRIAZOLE- 3-THIONE AND ITS CRYSTAL SOLVATE

Abstract: A comparative analysis of the molecular and crystal structures is performed for 5-[(diphenylphosphoryl) methyl]-4-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (1) in individual crystal (1a) and a crystal solvate with dimethylformamide (DMF) in the 1:1 ratio (1b). The crystals of both modifications have the identical geometries of the molecule of the key compound, and the crystals (despite their different crystal systems and unit cells parameters) are characterized by the formation of an identical one-dimensional supramolecular motif in them due to classical N–H..O hydrogen bonds and weaker noncovalent – C-H.. S interactions in crystal 1a and CH.. N in crystal 1b. A tetragonal packing of one-dimensional motifs oriented along the smallest unit cell parameter are observed in both cases. Solvate molecules are localized in zero-dimensional cavities in crystal 1b. Despite a denser molecular packing in crystal 1b, the solid-state phase transformation is observed for its polycrystalline sample, and the powder X-ray diffraction method shows that it partially transforms into form 1a with time. The latter form is characterized by a less dense molecular packing in the crystal

Towards universal stimuli-responsive drug delivery systems: Pillar[5]arenes synthesis and self-assembly into nanocontainers with tetrazole polymers

In this work, we have proposed a novel universal stimulus-sensitive nanosized polymer system based on decasubstituted macrocyclic structures—pillar[5]arenes and tetrazole-containing polymers. Decasubstituted pillar[5]arenes containing a large, good leaving tosylate, and phthalimide groups were first synthesized and characterized. Pillar[5]arenes containing primary and tertiary amino groups, capable of interacting with tetrazole-containing polymers, were obtained with high yield by removing the tosylate and phthalimide protection. According to the fluorescence spectroscopy data, a dramatic fluorescence enhancement in the pillar[5]arene/fluorescein/polymer system was observed with decreasing pH from neutral (pH = 7) to acidic (pH = 5). This indicates the destruction of associates and the release of the dye at a pH close to 5. The presented results open a broad range of opportunities for the development of new universal stimulus-sensitive drug delivery systems containing macrocycles and nontoxic tetrazole-based polymers

2D monomolecular nanosheets based on thiacalixarene derivatives: Synthesis, solid state self-assembly and crystal polymorphism

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Synthetic organic 2D materials are attracting careful attention of researchers due to their excellent functionality in various applications, including storage batteries, catalysis, thermoelectricity, advanced electronics, superconductors, optoelectronics, etc. In this work, thiacalix[4]arene derivatives functionalized by geranyl fragments at the lower rim in cone and 1,3-alternate conformations, that are capable of controlled self-assembly in a 2D nanostructures were synthesized. X-ray diffraction analysis showed the formation of 2D monomolecular-layer nanosheets from synthesized thiacalix[4]arenes, the distance between which depends on the stereoisomer used. It was established by DSC, FSC, and PXRD methods that the obtained macrocycles are capable of forming different crystalline polymorphs, moreover dimethyl sulphoxide (DMSO) is contributing to the formation of a more stable polymorph for cone stereoisomer. The obtained crystalline 2D materials based on synthesized thiacalix[4]arenes can find application in material science and medicine for the development of modern pharmaceuticals and new generation materials

NMR signal assignments afnd secondary structure determination of the N-terminal domain of the ribosome maturation factor M from Staphylococcus aureus

The ribosome maturation factor M (RimM) is a protein with a molecular mass of 19.072 kDa involved in assembling of the 30S ribosome subunit. The RimM is necessary for the efficient processing of 16S rRNA. However, the mechanism of interaction of the RimM N-terminal domain with 16S rRNA remains poorly studied. The synthesis of the N-terminal domain of RimM from Staphylococcus aureus enriched in 13C and 15N isotopes and subsequent analysis of chemical shifts of the 1H, 13C, and 15N signals from the backbone and side chains are described. An analysis of chemical shifts suggests that the N-terminal domain of RimM contains six β-chains and three α-helices with the topology β1-β2-α1-β3-β4-β5-α2-β6-β3. The secondary structure of the N-terminal domain of RimM contains a KH domain between the β1 and β2 fold with a strongly conserved segment with the GXXG sequence. The further structural studies by integrated structural biology approach (NMR spectroscopy, X-ray diffraction analysis, and cryoelectron microscopy) of RimM and its complex with ribosome will allow screening of highly selective inhibitors of Staphylococcus aureus translation

In vitro Reconstitution of the S. aureus 30S Ribosomal Subunit and RbfA Factor Complex for Structural Studies

© 2020, Pleiades Publishing, Ltd. Abstract: Ribosome-binding factor A (RbfA) from Staphylococcus aureus is a cold adaptation protein that is required for the growth of pathogenic cells at low temperatures (10-15°C). RbfA is involved in the processing of 16S rRNA, as well as in the assembly and stabilization of the small 30S ribosomal subunit. Structural studies of the 30S–RbfA complex will help to better understand their interaction, the mechanism of such complexes, and the fundamental process such as 30S subunit assembly that determines and controls the overall level of protein biosynthesis. This article describes protocols for preparation of RbfA and the small 30S ribosomal subunits and reconstitution and optimization of the 30S–RbfA complex to obtain samples suitable for cryo-electron microscopy studies

Trialkyl(vinyl)phosphonium Chlorophenol Derivatives as Potent Mitochondrial Uncouplers and Antibacterial Agents

Trialkyl phosphonium derivatives of vinyl-substituted p-chlorophenol were synthesized here by a recently developed method of preparing quaternary phosphonium salts from phosphine oxides using Grignard reagents. All the derivatives with a number (n) of carbon atoms in phosphonium alkyl substituents varying from 4 to 7 showed pronounced uncoupling activity in isolated rat liver mitochondria at micromolar concentrations, with a tripentyl derivative being the most effective both in accelerating respiration and causing membrane potential collapse, as well as in provoking mitochondrial swelling in a potassium-acetate medium. Remarkably, the trialkyl phosphonium derivatives with n from 4 to 7 also proved to be rather potent antibacterial agents. Methylation of the chlorophenol hydroxyl group suppressed the effects of P555 and P444 on the respiration and membrane potential of mitochondria but not those of P666, thereby suggesting a mechanistic difference in the mitochondrial uncoupling by these derivatives, which was predominantly protonophoric (carrier-like) in the case of P555 and P444 but detergent-like with P666. The latter was confirmed by the carboxyfluorescein leakage assay on model liposomal membranes

Amphiphilic Pd^II-NHC Complexes on 1,3-Alternate p-tert-Butylthiacalix[4]arene Platform: Synthesis and Catalytic Activities in Coupling and Hydrogenation Reactions

© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Herein we report the first example of amphiphilic PdII–NHC complexes on the thiacalix[4]arene backbone in 1,3-alternate configuration. Relative catalytic activity of synthesized PdII–NHC complexes in Suzuki–Miyaura coupling of haloarenes with phenylboronic acid was studied. A combination of micellar and metallocomplex catalysis was observed in Suzuki–Miyaura coupling upon going from pure DMF to water/DMF 3:1: the 2-fold increase of conversion of 4-bromoanisole unlike pure DMF was found. Interesting feature was found using chloroarene in DMF/water: the reaction selectivity changed from heterocoupling to homo coupling of phenylboronic acid. PdII–NHC complexes demonstrated a high activity in model hydrogenation reaction of p-nitrophenol using sodium borohydride. The most lipophilic PdII–NHC complex was found to be most active, which can be attributed with additional p-nitrophenol preconcentration in the aggregates due to larger hydrophobic capacity of macrocycle