Cross-species comparison of AlphaFold-derived G protein-coupled receptor structures reveals novel melatonin-related receptor in Neurospora crassa.

Melatonin, a molecule with diverse biological functions, is ubiquitously present in living organisms. There is significant interest in understanding melatonin signal transduction pathways in humans, particularly due to its critical role in regulating the sleep-wake cycle. However, a knowledge gap remains in fully elucidating the mechanisms by which melatonin influences circadian regulation.

Mitigating stuttering self-stigma: How do we start and where do we go? Using a Participative Concept Mapping Approach to develop a local framework of principles.

Purpose: This study aims to create a stigma reduction framework for stuttering in the local context of Québec, Canada using the Participative Concept Mapping Approach (PCMA), focusing on both self and societal stigma.

Method: Employing a mixed-methods approach, this study engaged 17 experts-people who stutter, clinicians and health innovation specialists-in PCMA workshops. Via diverse steps, including generation, sorting and rating of ideas in response to the focus prompt, "To effectively address stuttering (self-)stigma, an intervention should…" these sessions led to a framework depicted in visual maps, then refined into actionable principles through qualitative analysis.

Dock2D: Synthetic data for the molecular recognition problem.

Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures extracted from the Protein Data Bank. These training datasets tend to be large and difficult to use for prototyping and, unlike image or natural language datasets, they are not easily interpretable by non-experts.

An Environmental Scan and Appraisal of Patient Online Resources for Managing Rheumatoid Arthritis Flares.

Objective: To conduct an environmental scan and appraisal of online patient resources to support rheumatoid arthritis (RA) flare self-management.

Methods: We used the Google search engine (last search March 2023) using the terms "rheumatoid arthritis" and "flare management." Additional searches targeted major arthritis organizations, as well as regional, national, and international resources.

Enfin, a podcast in French on stuttering! - "Je je je suis un podcast": Impacts of accessing stuttering-related information in one's mother tongue.

Purpose: English-language podcasts on stuttering are numerous. However, stuttering-related podcasts in French are far more rare. In order to create a space to explore stuttering for a French-speaking population, the Association bégaiement communication (ABC), a French-Canadian stuttering organization, produced "Je je je suis un podcast".

Novel one-pot synthesis of a library of 2-aryloxy-1,4-naphthoquinone derivatives. Determination of antifungal and antibacterial activity.

The development of new antibiotics and inexpensive antifungals is an important field of research. Based on the privileged pharmacophore of lawsone, a series of phenolic ether derivatives of 1,4-naphthoquinone were synthesized easily in one step in reasonable yields. All the new compounds were characterized and tested as potential antifungal and antibacterial agents against , and .

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.

Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance.

Salt-Dependent Interactions between the C-Terminal Domain of Osmoregulatory Transporter ProP of and the Lipid Membrane.

Osmosensing transporter ProP detects the increase in cytoplasmic cation concentration associated with osmotically induced cell dehydration and mediates osmolyte uptake into bacteria. ProP is a 12-transmembrane helix protein with an α-helical, cytoplasmic C-terminal domain (CTD) linked to transmembrane helix XII (TM XII). It has been proposed that the CTD helix associates with the anionic membrane surface to lock ProP in an inactive conformation and that the release of the CTD may activate ProP.

The Impact of Composition and Morphology on Ionic Conductivity of Silk/Cellulose Bio-Composites Fabricated from Ionic Liquid and Varying Percentages of Coagulation Agents.

Blended biocomposites created from the electrostatic and hydrophobic interactions between polysaccharides and structural proteins exhibit useful and unique properties. However, engineering these biopolymers into applicable forms is challenging due to the coupling of the material's physicochemical properties to its morphology, and the undertaking that comes with controlling this. In this particular study, numerous properties of the silk and microcrystalline cellulose biocomposites blended using ionic liquid and regenerated with various coagulation agents were investigated.

Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies.

Objective: The TMEM175/GAK/DGKQ locus is the 3rd strongest risk locus in genome-wide association studies of Parkinson disease (PD). We aimed to identify the specific disease-associated variants in this locus, and their potential implications.

Methods: Full sequencing of TMEM175/GAK/DGKQ followed by genotyping of specific associated variants was performed in PD (n = 1,575) and rapid eye movement sleep behavior disorder (RBD) patients (n = 533) and in controls (n = 1,583).

Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains.

Cation-π interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation-π interactions presents a challenge to both additive and polarizable force fields, which are rarely designed to account for the complexation of charged groups with aromatic moieties. We calibrate the Drude polarizable force field for complexes of alkali metal ions (Li , Na , K , Rb , Cs ), ammonium (NH ), tetramethylammonium (TMA ), and tetraethylammonium (TEA ) with aromatic amino acid side chain model compounds (benzene, toluene, 4-methylphenol, 3-methylindole) using high-level ab initio quantum chemical properties of these complexes.

Crystal structure of 4-[(adamantan-1-yl)amino]-naphthalene-1,2-dione.

The title compound, CHNO, an example of a stable 1,2-naphtho-quinone, was determined by single-crystal X-ray diffraction analysis at 100 K. This structure illustrates steric buttressing of the adamantanyl group, forcing the N-H group into the coplanar aromatic C-H. The presence of strong delocalization between the planar N atom at the 4-position and the carbonyl group at the 2-position is indicated.

Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP.

ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.

Crystal structure of ()-2-(-butyl-amino)-4-(-butyl-imino)-naphthalen-1(4)-one.

The title compound, CHNO, is the first example of a naphtho-quinone imine derivative isolated in the 4-imine/2-amine tautomeric form having bulky alkyl substituents at the N atoms. The mol-ecular conformation is stabilized by an intra-molecular hydrogen bond between the amine and a carbonyl group and by London attraction between the two -butyl groups. Only van der Waals inter-actions were identified in the crystal packing.

Deep convolutional networks for quality assessment of protein folds.

Motivation: The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined as complex functions of the atomic coordinates. However, very few methods have attempted to learn these features directly from the data.

Gold nanoparticles in ophthalmology.

Many research projects are underway to improve the diagnosis and therapy in ophthalmology. Indeed, visual acuity deficits affect 285 million people worldwide and different strategies are being developed to strengthen patient care. One of these strategies is the use of gold nanoparticles (GNP) for their multiple properties and their ability to be used as both diagnosis and therapy tools.

Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution.

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH and RN(CH)) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA) and tetraethylammonium (TEA). Polarizable molecular models are calibrated for NH, TMA, and TEA interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes.

Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Hemoglobin N.

Many globins convert NO to innocuous NO through their nitric oxide dioxygenase (NOD) activity. Mycobacterium tuberculosis fights the oxidative and nitrosative stress imposed by its host (the toxic effects of O and NO species and their OONO and NO derivatives) through the action of truncated hemoglobin N (trHbN), which catalyzes the NOD reaction with one of the highest rates among globins. The general NOD mechanism comprises the following steps: binding of O to the heme, diffusion of NO into the heme pocket and formation of peroxynitrite (OONO), isomerization of OONO, and release of NO.

Loss of hepatic DEPTOR alters the metabolic transition to fasting.

Objective: The mechanistic target of rapamycin (mTOR) is a serine/threonine kinase that functions into distinct protein complexes (mTORC1 and mTORC2) that regulates growth and metabolism. DEP-domain containing mTOR-interacting protein (DEPTOR) is part of these complexes and is known to reduce their activity. Whether DEPTOR loss affects metabolism and organismal growth has never been tested.

mTORC1 is Required for Brown Adipose Tissue Recruitment and Metabolic Adaptation to Cold.

In response to cold, brown adipose tissue (BAT) increases its metabolic rate and expands its mass to produce heat required for survival, a process known as BAT recruitment. The mechanistic target of rapamycin complex 1 (mTORC1) controls metabolism, cell growth and proliferation, but its role in regulating BAT recruitment in response to chronic cold stimulation is unknown. Here, we show that cold activates mTORC1 in BAT, an effect that depends on the sympathetic nervous system.

Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining (2)H NMR Spectroscopy and Molecular Dynamics Simulations.

Little is known about the interaction of very long-chain saturated fatty acids (VLCFAs) with biological membranes. However, this could play an important role on interleaflet interactions and signal transduction mechanisms in cells. The aim of this work is to determine how VLCFA structurally adapts in fluid phospholipid bilayers, since both species must exhibit a significant hydrophobic mismatch.

Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2.

Background: RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group.

Mechanism of NH4(+) Recruitment and NH3 Transport in Rh Proteins.

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases like NH3, the role of such proteins remains a paradox.

Molecular model of hemoglobin N from Mycobacterium tuberculosis bound to lipid bilayers: a combined spectroscopic and computational study.

A singular aspect of the 2-on-2 hemoglobin structures of groups I and II is the presence of tunnels linking the protein surface to the distal heme pocket, supporting the storage and the diffusion of small apolar ligands to/from the buried active site. As the solubility of apolar ligands is greater in biological membranes than in solution, the association of these proteins with biological membranes may improve the efficiency of ligand capture. As very little is known on this subject, we have investigated the interactions between hemoglobin N (HbN), a group I 2-on-2 hemoglobin from the pathogenic Mycobacterium tuberculosis (Mtb), and biological membranes using both experimental techniques and MD simulations.