Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies.

Accurate crystal structure of ice VI from X-ray diffraction with Hirshfeld atom refinement.

Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations have suggested the existence of additional and - to date - unknown phases.

Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths.

Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. It is therefore crucial that we have a way of estimating their extinction risk.

Multifunctional Nanoparticles Based on Iron Oxide and Gold-198 Designed for Magnetic Hyperthermia and Radionuclide Therapy as a Potential Tool for Combined HER2-Positive Cancer Treatment.

Iron oxide nanoparticles are commonly used in many medical applications as they can be easily modified, have a high surface-to-volume ratio, and are biocompatible and biodegradable. This study was performed to synthesize nanoparticles designed for multimodal HER2-positive cancer treatment involving radionuclide therapy and magnetic hyperthermia. The magnetic core (FeO) was coated with a gold-198 layer creating so-called core-shell nanoparticles.

COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments.

The presented methodology is based on coarse-grained representation of biomolecules in implicit environments and is designed for the molecular dynamics simulations of membrane proteins and their complexes. The membrane proteins are not only found in the cell membrane but also in all membranous compartments of the cell: Golgi apparatus, mitochondria, endosomes and lysosomes, and they usually form large complexes. To investigate such systems the methodology is proposed based on two independent approaches combining the coarse-grained MARTINI model for proteins and the effective energy function to mimic the water/membrane environments.

Mitochondria dysfunction in circulating tumor cells.

Circulating tumor cells (CTCs) represent a subset of heterogeneous cells, which, once released from a tumor site, have the potential to give rise to metastasis in secondary sites. Recent research focused on the attempt to detect and characterize these rare cells in the circulation, and advancements in defining their molecular profile have been reported in diverse tumor species, with potential implications for clinical applications. Of note, metabolic alterations, involving mitochondria, have been implicated in the metastatic process, as key determinants in the transition of tumor cells to a mesenchymal or stemness-like phenotype, in drug resistance, and in induction of apoptosis.

Photosynthetic activity in both algae and cyanobacteria changes in response to cues of predation.

A plethora of adaptive responses to predation has been described in microscopic aquatic producers. Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known. One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues.

Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB.

A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules.

Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis.

The multipole model (MM) uses an aspherical approach to describe electron density and can be used to interpret data from X-ray diffraction in a more accurate manner than using the spherical approximation. The MATTS (multipolar atom types from theory and statistical clustering) data bank gathers MM parameters specific for atom types in proteins, nucleic acids, and organic molecules. However, it was not fully understood how the electron density of particular atoms responds to their surroundings and which factors describe the electron density in molecules within the MM.

Label-Free Mass Spectrometry-Based Quantitative Proteomics to Evaluate the Effects of the Calcium-Sensing Receptor Agonist Cinacalcet on Protein Expression in Rat Brains and Livers.

BACKGROUND Cinacalcet is a calcium-sensing receptor agonist that is clinically approved for the treatment of secondary hyperparathyroidism in chronic kidney disease and hypercalcemia in patients with parathyroid carcinoma. This study aimed to use quantitative mass spectrometry-based label-free proteomics to evaluate the effects of cinacalcet on protein expression in rat brains and livers. MATERIAL AND METHODS We randomly assigned 18 Wistar rats to 2 groups: an untreated control group (n=6) and a group treated with cinacalcet at a dose corresponding to the maximum dose used in humans (2 mg/kg/body weight, 5 days/week) divided into 7-day (n=6) and 21-day (n=6) treatment subgroups.

Allosteric modulation of GPCR-induced β-arrestin trafficking and signaling by a synthetic intrabody.

Agonist-induced phosphorylation of G protein-coupled receptors (GPCRs) is a primary determinant of β-arrestin (βarr) recruitment and trafficking. For several GPCRs such as the vasopressin receptor subtype 2 (VR), agonist-stimulation first drives the translocation of βarrs to the plasma membrane, followed by endosomal trafficking, which is generally considered to be orchestrated by multiple phosphorylation sites. We have previously shown that mutation of a single phosphorylation site in the VR (i.

Enzyme-triggered- and tumor-targeted delivery with tunable, methacrylated poly(ethylene glycols) and hyaluronic acid hybrid nanogels.

Enzyme-responsive polymeric-based nanostructures are potential candidates for serving as key materials in targeted drug delivery carriers. However, the major risk in their prolonged application is fast disassembling of the short-lived polymeric-based structures. Another disadvantage is the limited accessibility of the enzyme to the moieties that are located inside the network.

Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank.

The availability of atomic resolution experimental maps of electrostatic potential from 3D electron diffraction (3D ED) extends the possibility of investigating the electrostatic potential beyond the determination of non-H-atom positions. However, accurate tools to calculate this potential for macromolecules, without the use of expensive quantum calculations, are lacking. The University at Buffalo Data Bank (UBDB) gathers atom types that can be used to calculate accurate electrostatic potential maps via structure-factor calculations.

The coupled photocycle of phenyl-p-benzoquinone and Light-Harvesting Complex II (LHCII) within the biohybrid system.

The combination of trimeric form of the light-harvesting complex II (LHCII), a porous graphite electrode (GE), and the application of phenyl-p-benzoquinone (PPBQ), the quinone derivative, allow the construction of a new type of biohybrid photoactive system. The Chl fluorescence decay and voltammetric analyzes revealed that PPBQ impacts LHCII proportionally to accessible quenching sites and that PPBQ forms redox complexes with Chl in both ground and excited states. As a result, photocurrent generation is directly dependent on PPBQ-induced quenching of Chl fluorescence.

Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound.

Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects.

Droplet-based methods for tackling antimicrobial resistance.

Application of droplet-based methods enables (i) faster detection, (ii) increased sensitivity, (iii) characterization of the level of heterogeneity in response to antibiotics by bacterial populations, and (iv) expanded screening of the effectiveness of antibiotic combinations. Hereby, we discuss the key steps and parameters of droplet-based experiments to investigate antimicrobial resistance. We also review recent findings accomplished with these methods and highlight their advantages and capacity to yield new insights into the problem of antimicrobial resistance.

Design of a Sensitive Fluorescent Zn-Based Metal-Organic Framework Sensor for Cimetidine Monitoring in Biological and Pharmaceutical Samples.

A new highly fluorescent zinc-organic framework [Zn(btca)(DMSO)] () was prepared via in situ ligand formation by the solvothermal reaction of Zn(NO)·6HO and pyromellitic dianhydride (PMDA) in DMSO solvent. During the solvothermal reaction, PMDA was gradually hydrolyzed to a pyromellitic acid, 1,2,4,5-benzene tetracarboxylic acid (Hbtca), to provide a tetracarboxylic acid as a linker in the reaction medium. Single-crystal X-ray diffraction analysis exhibits a 3D porous structure with open tetragonal channels running along the crystallographic -axis.

Comparative genomic analysis illustrates evolutionary dynamics of multisubunit tethering complexes across green algal diversity.

The chlorophyte algae are a dominant group of photosynthetic eukaryotes. Although many are photoautotrophs, there are also mixotrophs, heterotrophs, and even parasites. The physical characteristics of green algae are also highly diverse, varying greatly in size, shape, and habitat.

Investigation of electrocatalytic activity of a new mononuclear Mn(II) complex for water oxidation in alkaline media.

Water splitting is a promising way to alleviate the energy crisis. In nature, water oxidation is done by a tetranuclear manganese cluster in photosystem II. Therefore, the study of water oxidation by Mn complexes is attractive in water splitting systems.

Design and Synthesis of Menthol and Thymol Derived Ciprofloxacin: Influence of Structural Modifications on the Antibacterial Activity and Anticancer Properties.

Sixteen new Ciprofloxacin derivatives were designed and successfully synthesized. In an in silico experiment, lipophilicity was established for obtained compounds. All compounds were screened for antimicrobial activity using standard and clinical strains.

The Repeating, Modular Architecture of the HtrA Proteases.

A conserved, 26-residue sequence [AA(X)[A/G][G/L](X)GDV[I/L](X)[V/L]NGE(X)V(X)] and corresponding structure repeating module were identified within the HtrA protease family using a non-redundant set (N = 20) of publicly available structures. While the repeats themselves were far from sequence perfect, they had notable conservation to a statistically significant level. Three or more repetitions were identified within each protein despite being statistically expected to randomly occur only once per 1031 residues.

Monosulfonated dibenzo-24-crown-8 and its properties.

In this paper, we describe a method for preparing a monosulfonated dibenzo-24-crown-8 ether, DB24C8, by direct sulfonation of the parent crown (DB24C8). Since neutral DB24C8 readily interacts with cationic guests, permanently charged DB24C8 is an advantageous candidate for future supramolecular applications. DB24C8 can be isolated as a sulfonic acid to be used as it is or converted to a salt of choice.

Electronic Coupling in 1,2,3-Triazole Bridged Ferrocenes and Its Impact on Reactive Oxygen Species Generation and Deleterious Activity in Cancer Cells.

Mixed-valence (MV) binuclear ferrocenyl compounds have long been studied as models for testing theories of electron transfer and in attempts to design molecular-scale electronic devices (., molecular wires). In contrary to that, far less attention has been paid to MV binuclear ferrocenes as anticancer agents.

Dynamics and disorder: on the stability of pyrazinamide polymorphs.

This article focuses on the structure and relative stability of four pyrazinamide polymorphs. New single crystal X-ray diffraction data collected for all forms at 10 K and 122 K are presented. By combining periodic ab initio DFT calculations with normal-mode refinement against X-ray diffraction data, both enthalpic and entropic contributions to the free energy of all polymorphs are calculated.