First-year sea ice leads to an increase in dimethyl sulfide-induced particle formation in the Antarctic Peninsula.

Dimethyl sulfide (DMS) produced by marine algae represents the largest natural emission of sulfur to the atmosphere. The oxidation of DMS is a key process affecting new particle formation that contributes to the radiative forcing of the Earth. In this study, atmospheric DMS and its major oxidation products (methanesulfonic acid, MSA; non-sea-salt sulfate, nss-SO) and particle size distributions were measured at King Sejong station located in the Antarctic Peninsula during the austral spring-summer period in 2018-2020.

Current approaches to flexible loop modeling.

Loops are key components of protein structures, involved in many biological functions. Due to their conformational variability, the structural investigation of loops is a difficult topic, requiring a combination of experimental and computational methods. This paper provides a brief overview of current computational approaches to flexible loop modeling, and presents the main ingredients of the most standard protocols.

SUMOylation Regulates TDP-43 Splicing Activity and Nucleocytoplasmic Distribution.

The nuclear RNA-binding protein TDP-43 forms abnormal cytoplasmic aggregates in the brains of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients and several molecular mechanisms promoting TDP-43 cytoplasmic mislocalization and aggregation have been proposed, including defects in nucleocytoplasmic transport, stress granules (SG) disassembly and post-translational modifications (PTM). SUMOylation is a PTM which regulates a variety of cellular processes and, similarly to ubiquitination, targets lysine residues. To investigate the possible regulatory effects of SUMOylation on TDP-43 activity and trafficking, we first assessed that TDP-43 is SUMO-conjugated in the nuclear compartment both covalently and non-covalently in the RRM1 domain at the predicted lysine 136 and SUMO-interacting motif (SIM, 106-110 residues), respectively.

Effects of Photobiomodulation on the Upper First Molar Intrusion Movement Using Mini-Screws Anchorage: A Randomized Controlled Trial.

The aim of this study was to quantify the changes obtained when the molar intrusion movement is complemented by photobiomodulation (PBM). A common problem in adult patients is the super-eruption of maxillary molars caused by the loss of the antagonist tooth. Super-erupted molars impair oral rehabilitation and can cause both occlusal and functional problems.

Capillary Ionization and Jumps of Capacitive Energy Stored in Mesopores.

We study ionic liquid-solvent mixtures in slit-shaped nanopores wider than a few ion diameters. Using a continuum theory and generic thermodynamic reasoning, we reveal that such systems can undergo a capillary ionization transition. At this transition, the pores spontaneously ionize or deionize upon infinitesimal changes of temperature, slit width, or voltage.

Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical.

Hydroxysulfinyl radical (HOSO) is important due to its involvement in climate geoengineering upon SO injection and generation of the highly hygroscopic HSO. Its photochemical behavior in the upper atmosphere is, however, uncertain. Here we present the ultraviolet-visible photochemistry and photodynamics of this species by simulating the atmospheric conditions with high-level quantum chemistry methods.

Teaching an old dog new tricks: repurposing β-lactams.

Recently, Martelli and colleagues reported on the structural and functional characterization of new antimycobacterials based on N-thio-β-lactams. Surprisingly, the inhibitory mechanism follows a path unexpected for β-lactams, providing an alternative route to defeat drug-resistant strains of Mycobacterium tuberculosis.

Identification of the Dominant T-Cell Epitopes of Lit v 1 Shrimp Major Allergen and Their Functional Overlap with Known B-Cell Epitopes.

Development of efficient peptide-based immunotherapy for shrimp allergy relies on the identification of the dominant T-cell epitopes of its major allergen, tropomyosin. In this study, immunoinformatic tools, T-cell proliferation, cytokine release, IgG/IgE binding, and degranulation assays were used to identify and characterize the T-cell epitopes in Lit v 1 in comparison with previously validated B-cell epitopes. The results showed that of the six in silico predicted T-cell epitopes only one (T2: VQESLLKANIQLVEK, 60-74) promoted T-cell proliferation, the release of IL-2, and upregulated secretion of Th2-associated cytokines in the absence of IgG/IgE binding and degranulation activities.

Fish muscle processing into seafood products reduces β-parvalbumin allergenicity.

Fish is one of the eight major foods causing type-I food allergy, and the prevalence of its allergy is increasing in part due to changes in consumption habits. One of the main drivers for these changes has been the processing developments transforming the fish muscle into seafood products. Most fish allergic patients react to the Ca-binding protein β-parvalbumin (β-PV) abundant in muscle.

Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity.

Endoxylanases active under extreme conditions of temperature and alkalinity can replace the use of highly pollutant chemicals in the pulp and paper industry. Searching for enzymes with these properties, we carried out a comprehensive bioinformatics study of the GH10 family. The phylogenetic analysis allowed the construction of a radial cladogram in which protein sequences putatively ascribed as thermophilic and alkaliphilic appeared grouped in a well-defined region of the cladogram, designated TAK Cluster.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.

The highly infectious disease COVID-19 caused by the SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail.

Penetrating the Blood-Brain Barrier with New Peptide-Porphyrin Conjugates Having anti-HIV Activity.

Passing through the blood-brain barrier (BBB) to treat neurological conditions is one of the main hurdles in modern medicine. Many drugs with promising in vitro profiles become ineffective in vivo due to BBB restrictive permeability. In particular, this includes drugs such as antiviral porphyrins, with the ability to fight brain-resident viruses causing diseases such as HIV-associated neurocognitive disorders (HAND).

Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase.

Our understanding of enzymes with high substrate ambiguity remains limited because their large active sites allow substrate docking freedom to an extent that seems incompatible with stereospecificity. One possibility is that some of these enzymes evolved a set of evolutionarily fitted sequence positions that stringently allow switching substrate ambiguity and chiral specificity. To explore this hypothesis, we targeted for mutation a serine ester hydrolase (EH) that exhibits an impressive 71-substrate repertoire but is not stereospecific ( 50%).

InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.

The InterEvDock3 protein docking server exploits the constraints of evolution by multiple means to generate structural models of protein assemblies. The server takes as input either several sequences or 3D structures of proteins known to interact. It returns a set of 10 consensus candidate complexes, together with interface predictions to guide further experimental validation interactively.

Formation and internal ordering of periodic microphases in colloidal models with competing interactions.

Theory and simulations predict that colloidal particles with short-range attractive and long-range repulsive interactions form periodic microphases if there is a proper balance between the attractive and repulsive contributions. However, the experimental identification of such structures has remained elusive to date. Using molecular dynamics simulations, we investigate the phase behaviour of a model system that stabilizes a cluster-crystal, a cylindrical and a lamellar phase at low temperatures.

Phe-Gly motifs drive fibrillization of TDP-43's prion-like domain condensates.

Transactive response DNA-binding Protein of 43 kDa (TDP-43) assembles various aggregate forms, including biomolecular condensates or functional and pathological amyloids, with roles in disparate scenarios (e.g., muscle regeneration versus neurodegeneration).

Atomic-level evolutionary information improves protein-protein interface scoring.

Motivation: The crucial role of protein interactions and the difficulty in characterizing them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous incorporation of conservation and coevolution information has shown promise for improving protein-protein scoring.

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping.

The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported.

Chemical Interactions Between Ship-Originated Air Pollutants and Ocean-Emitted Halogens.

Ocean-going ships supply products from one region to another and contribute to the world's economy. Ship exhaust contains many air pollutants and results in significant changes in marine atmospheric composition. The role of reactive halogen species (RHS) in the troposphere has received increasing recognition and oceans are the largest contributors to their atmospheric burden.

Glycine rich segments adopt polyproline II helices: Implications for biomolecular condensate formation.

Many intrinsically disordered proteins contain Gly-rich regions which are generally assumed to be disordered. Such regions often form biomolecular condensates which play essential roles in organizing cellular processes. However, the bases of their formation and stability are still not completely understood.

Structural insights into the function of the catalytically active human Taspase1.

Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse models of glioblastoma. Taspase1 is synthesized as an inactive proenzyme, becoming active upon intramolecular cleavage.

Intercomparison Between Surrogate, Explicit, and Full Treatments of VSL Bromine Chemistry Within the CAM-Chem Chemistry-Climate Model.

Many Chemistry-Climate Models (CCMs) include a simplified treatment of brominated very short-lived (VSL) species by assuming CHBr as a surrogate for VSL. However, neglecting a comprehensive treatment of VSL in CCMs may yield an unrealistic representation of the associated impacts. Here, we use the Community Atmospheric Model with Chemistry (CAM-Chem) CCM to quantify the tropospheric and stratospheric changes between various VSL chemical approaches with increasing degrees of complexity (i.

The release of toxic oligomers from α-synuclein fibrils induces dysfunction in neuronal cells.

The self-assembly of α-synuclein (αS) into intraneuronal inclusion bodies is a key characteristic of Parkinson's disease. To define the nature of the species giving rise to neuronal damage, we have investigated the mechanism of action of the main αS populations that have been observed to form progressively during fibril growth. The αS fibrils release soluble prefibrillar oligomeric species with cross-β structure and solvent-exposed hydrophobic clusters.

Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.

A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester.