A review on evolution, structural characteristics, interactions, and regulation of the membrane transport protein: The family of Rab proteins.

Rab proteins are a key family of small GTPases that play crucial roles in vesicular trafficking, membrane dynamics, and maintaining cellular homeostasis. Studying this family of proteins is interesting as having many structural isoforms with variable evolutionary trends and wide distribution in cells. The proteins are renowned for their unique structural characteristics, which support their functional adaptability and specificity.

Estimating protein-ligand interactions with geometric deep learning and mixture density models.

Understanding the interactions between a ligand and its molecular target is crucial in guiding the optimization of molecules for any drug design workflow. Multiple experimental and computational methods have been developed to better understand these intermolecular interactions. With the availability of a large number of structural datasets, there is a need for developing statistical frameworks that improve upon existing physicsbased solutions.

PlQC based highly sensitive and reproducible novel SERS active substrate for biomolecule detection with high specificity.

Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for biomolecule sensing. When combined with a broadband plasmonic structure, label-free, highly sensitive detection of specific molecules is possible. It is non-invasive, sensitive, fast, and can be used for in-situ analysis, unlike enzyme-linked immunosorbent assay, fluorescence immunoassay, and radioimmunoassay.

Artemisinin-resistant Plasmodium falciparum Kelch13 mutant proteins display reduced heme-binding affinity and decreased artemisinin activation.

The potency of frontline antimalarial drug artemisinin (ART) derivatives is triggered by heme-induced cleavage of the endoperoxide bond to form reactive heme-ART alkoxy radicals and covalent heme-ART adducts, which are highly toxic to the parasite. ART-resistant (ART-R) parasites with mutations in the Plasmodium falciparum Kelch-containing protein Kelch13 (PfKekch13) exhibit impaired hemoglobin uptake, reduced yield of hemoglobin-derived heme, and thus decreased ART activation. However, any direct involvement of PfKelch13 in heme-mediated ART activation has not been reported.

Statistical analysis of the unique characteristics of secondary structures in proteins.

Protein folding is a complex process influenced by the primary sequence of amino acids. Early studies focused on understanding whether the specificity or the conservation of properties of amino acids was crucial for folding into secondary structures such as α-helices, β-sheets, turns, and coils. However, with the advent of artificial intelligence (AI) and machine learning (ML), the emphasis has shifted towards the precise nature and occurrence of specific amino acids.

Photoinduced Electron-Transfer-Mediated Differential Recognition of Proteins on Plasmonic Surfaces.

Photoinduced enhanced Raman spectroscopy (PIERS) has emerged as an efficient technique for enhancing the vibrational modes of analyte molecules adsorbed on a plasmonic nanoparticle-semiconductor hybrid material through chemical enhancement governed by electron transfer from the semiconductor to the plasmonic nanoparticles under an additional ultraviolet (UV) preirradiation step. The increase in chemical enhancement is imperative in analyzing and detecting pharmaceutically important moieties, such as amino acids and proteins, with a low Raman scattering cross section, even in complex biological environments. Herein, we demonstrate that UV preirradiation induced the creation of additional oxygen vacancies by introducing a low concentration (≈1%) of Ni as a dopant in the 2D platelike morphology of the BiOCl semiconductor; i.

Identifying High-Quality Leads among Screened Anticancerous Compounds Using SMILES Representations.

Cancer is a lethal disease that affects numerous people worldwide. Chemotherapy stands as one of the most effective treatment regimens to combat cancer. Nevertheless, anticancer drugs face a high failure rate due to safety and efficacy issues.

Overlap in oncogenic and pro-inflammatory pathways associated with areca nut and nicotine exposure.

Background: Betel nut/areca nut/ is one of the most commonly used psychoactive substance, and is also a major preventable cause of cancer. Unlike other psychoactive substances, such as nicotine, the mechanisms underlying addiction to areca nuts and related oncogenesis remain elusive. Recent reports suggest a possible overlap in the mechanisms of action of nicotine and areca nuts in the human body.

Estimating black carbon levels using machine learning models in high-concentration regions.

Black carbon (BC) is emitted into the atmosphere during combustion processes, often in conjunction with emissions such as nitrogen oxides (NO) and ozone (O), which are also by-products of combustion. In highly polluted regions, combustion processes are one of the main sources of aerosols and particulate matter (PM) concentrations, which affect the radiative budget. Despite the high relevance of this air pollution metric, BC monitoring is quite expensive in terms of instrumentation and of maintenance and servicing.

Molecular insights into the binding interactions and energetics of the omicron spike variant with hACE2 and a neutralizing antibody.

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) since 2019 has led to a continuous evolution of viral variants, with the latest concern being the Omicron (B.1.1.

Photocatalytic degradation of parabens: A comprehensive meta-analysis investigating the environmental remediation potential of emerging pollutant.

The increasing prevalence of paraben compounds in the environment has given rise to concerns regarding their detrimental impacts on both ecosystems and human health. Over the past few decades, photocatalytic reactions have drawn significant attention as a method to accelerate the otherwise slow degradation of these pollutants. The current study aims to evaluate the current efficacy of the photocatalytic method for degrading parabens in aqueous solutions.

Field-scale assessment of soil, water, plant, and soil microbiome in and around Rania-Khan Chandpur Chromium contaminated site, India.

Rania-Khan Chandpur site, (Kanpur Dehat, Uttar Pradesh, India), one of the highly Chromium (Cr) contaminated sites in India due to Chromite Ore Processing Residue (COPR), has been investigated at the field-scale. We found that the area around the COPR dumps was hazardously contaminated with the Cr where its concentrations in the surface water and groundwater were > 40 mgL, its maximum contents in the COPRs and in the soils of the adjoining lands were 9.6 wt% and 3.

Anti-COVID-19 Potential of Withaferin-A and Caffeic Acid Phenethyl Ester.

Background: The recent COVID-19 (coronavirus disease 2019) pandemic triggered research on the development of new vaccines/drugs, repurposing of clinically approved drugs, and assessment of natural anti-COVID-19 compounds. Based on the gender difference in the severity of the disease, such as a higher number of men hospitalized and in intense care units, variations in sex hormones have been predicted to play a role in disease susceptibility. Cell surface receptors (Angiotensin-Converting Enzyme 2; ACE2 and a connected transmembrane protease serine 2- TMPSS2) are upregulated by androgens.

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.

Motivation: Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments).

Molecular insights to the anti-COVID-19 potential of α-, β- and γ-cyclodextrins.

SARS-CoV-2 viral infection is regulated by the host cell receptors ACE2 and TMPRSS2, and therefore the effect of various natural and synthetic compounds on these receptors has recently been the subject of investigations. Cyclodextrins, naturally occurring polysaccharides derived from starch, are soluble in water and have a hydrophobic cavity at their center enabling them to accommodate small molecules and utilize them as carriers in the food, supplements, and pharmaceutical industries to improve the solubility, stability, and bioavailability of target compounds. In the current study, computational molecular simulations were used to investigate the ability of α-, β- and γ-Cyclodextrins on human cell surface receptors.

Molecular Insights into the Inhibitory Role of α-Crystallin against γD-Crystallin Aggregation.

Cataracts, a major cause of global blindness, contribute significantly to the overall prevalence of blindness. The opacification of the lens, resulting in cataract formation, primarily occurs due to the aggregation of crystallin proteins within the eye lens. Despite the high concentration of these crystallins, they remarkably maintain the lens transparency and refractive index.

Improved Machine Learning-Based Model for the Classification of Off-Targets in the CRISPR/Cpf1 System.

Targeted nucleases are widely used for altering the specific location of the genome with precision. The endonucleases facilitate efficient genome editing via designing a guide RNA (gRNA) consisting of a 20-nucleotide target sequence. gRNA preferably binds to the target location, but the on- and off-target activities of gRNAs vary widely.

The enhanced electrocatalytic performance of nanoscopic CuPdFe heterometallic molecular box encaged cytochrome c.

Designing molecular cages for atomic/molecular scale guests is a special art used by material chemists to harvest the virtues of the otherwise vile idea known as "the cage". In recent years, there has been a notable surge in research investigations focused on the exploration and utilization of the distinct advantages offered by this art in the advancement of efficient and stable bio-electrocatalysts. This usually is achieved through encapsulation of biologically accessible redox proteins within specifically designed molecular cages and matrices.

Beyond Glucose: The Dual Assault of Oxidative and ER Stress in Diabetic Disorders.

Diabetes mellitus, a prevalent global health concern, is characterized by hyperglycemia. However, recent research reveals a more intricate landscape where oxidative stress and endoplasmic reticulum (ER) stress orchestrate a dual assault, profoundly impacting diabetic disorders. This review elucidates the interplay between these two stress pathways and their collective consequences on diabetes.

A high-fidelity biomechanical modeling framework for injury prediction during frontal car crash.

Injuries arising from car crashes are ubiquitous across the globe and account for over 1.3 million fatalities annually. 93% of mortalities are observed in middle- and low-income countries owing to the lack of infrastructure in the safety assessment of car designs.

Alzheimer's Disease Is Associated with Increased Network Assortativity: Evidence from Metabolic Connectivity.

Unraveling the network pathobiology in neurodegenerative disorders is a popular and promising field in research. We use a relatively newer network measure of assortativity in metabolic connectivity to understand network differences in patients with Alzheimer's Disease (AD), compared with those with mild cognitive impairment (MCI). Eighty-three demographically matched patients with dementia (56 AD and 27 MCI) who underwent positron emission tomography-magnetic resonance imaging (PET-MRI) study were recruited for this exploratory study.

Effect of mutations on the folding and stability of D-crystallin protein.

Interprotein interactions between the partially unfolded states of D-crystallin (D-crys) protein are known to cause cataracts. Therefore, understanding the unfolding pathways of native D-crys is extremely crucial to delineate their aggregation mechanism. In this study, we have performed extensive all-atom Molecular Dynamics simulations with explicit solvent to understand the role of the critical residues that drive the stability of the motifs and domains of D-crys in its wild type and mutant forms.