Pathogenicity and virulence of Helicobacter pylori: A paradigm of chronic infection

Infection with Helicobacter pylori is one of the most common infections of mankind. Infection typically occurs in childhood and persists for the lifetime of the host unless eradicated with antimicrobials. The organism colonizes the stomach and causes gastritis. Most infected individuals are asymptomatic, but infection also causes gastric and duodenal ulceration, and gastric cancer. H. pylori possesses an arsenal of virulence factors, including a potent urease enzyme for protection from acid, flagella that mediate motility, an abundance of outer membrane proteins that can mediate attachment, several immunomodulatory proteins, and an ability to adapt to specific conditions in individual human stomachs. The presence of a type 4 secretion system that injects effector molecules into gastric cells and subverts host cell signalling is associated with virulence. In this review we discuss the interplay of H. pylori colonization and virulence factors with host and environmental factors to determine disease outcome in infected individuals.

Highly versatile small virus-encoded proteins in cellular membranes: A structural perspective on how proteins' inherent conformational plasticity couples with host membranes' properties to control cellular processes

We investigated several small viral proteins that reside and function in cellular membranes. These proteins belong to the viroporin family because they assemble into ion-conducting oligomers. However, despite forming similar oligomeric structures with analogous functions, these proteins have diverse amino acid sequences. In particular, the amino acid compositions of the proposed channel-forming transmembrane (TM) helices are vastly different-some contain residues (e.g., His, Trp, Asp, Ser) that could facilitate cation transport. Still, other viroporins' TM helices encompass exclusively hydrophobic residues; therefore, it is difficult to explain their channels' activity, unless other mechanisms (e.g., involving a negative lipid headgroups and/or membrane destabilization) take place. For this study, we selected the M2, Vpu, E, p13II, p7, and 2B proteins from the influenza A, HIV-1, human T-cell leukemia, hepatitis C, and picorna viruses, respectively. We provide a brief overview of the current knowledge about these proteins' structures as well as remaining questions about more comprehensive understanding of their structures, conformational dynamics, and function. Finally, we outline strategies to utilize a multi-prong structural and computational approach to overcome current deficiencies in the knowledge about these proteins.

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. Cell-based experimental approaches, including expression analyses at mRNA and protein levels and virus replication, were used to assess the effect on receptor expression and virus infection, respectively. We found that none of the three CDs could dock effectively to human cell surface receptor ACE2 and viral protease Mpro (essential for virus replication). On the other hand, α- and β-CD showed strong and stable interactions with TMPRSS2, and the expression of both ACE2 and TMPRSS2 was downregulated at the mRNA and protein levels in cyclodextrin (CD)-treated cells. A cell-based virus replication assay showed ∼20% inhibition by β- and γ-CD. Taken together, the study suggested that (i) downregulation of expression of host cell receptors may not be sufficient to inhibit virus infection (ii) activity of the receptors and virus protein Mpro may play a critical and clinically relevant role, and hence (iii) newly emerging anti-Covid-19 compounds warrant multimodal functional analyses.

Quantification of Pectolinarin in Rat Plasma Using UPLC-MS/MS and Its Pharmacokinetic Analysis

Pectolinarin is a flavonoid compound known for its wound-healing properties, including anti-inflammatory and antibacterial effects. In this study, we employed UPLC-MS/MS to quantify pectolinarin in rat plasma and investigate its pharmacokinetics. Plasma samples were processed using an acetonitrile precipitation method. Chromatographic separation was performed on a UPLC BEH column with a gradient mobile phase of acetonitrile-water (containing 0.1% formic acid). Detection was carried out using electrospray ionization (ESI) tandem mass spectrometry in multiple reaction monitoring (MRM) mode with positive ionization, targeting transitions of m/z 623.3 → 315.3 for pectolinarin and m/z 370.5 → 125.0 for the IS. The results demonstrated that pectolinarin exhibited acceptable linearity in rat plasma within the concentration range of 1.2 to 2300 ng/mL (r > 0.995). The intraday and interday precision, expressed as relative standard deviation (RSD), was below 9.2%. Accuracy ranged from 97.3% to 108.3%, with average recovery exceeding 94.7%. The matrix effect was between 97.8% and 105.3%. The method was successfully applied to evaluate the pharmacokinetics of pectolinarin in rats following both oral and intravenous administration. The absolute bioavailability of pectolinarin in rats was determined to be 0.28%.

Bias in, bias out - AlphaFold-Multimer and the structural complexity of protein interfaces

A structural understanding of protein-protein interactions is a key component of many facets of applied molecular biology research. AlphaFold-Multimer (AF-MM) provided a breakthrough in the ability to predict protein-protein interface structure. However, the available training data for this model and the resulting benchmarking and validation efforts show a bias toward interactions between more ordered regions of proteins. Here we highlight some of the successes and limitations of AF-MM and discuss available methods and future directions to enable balanced prediction of all interface types.

α/β Hydrolases: Toward Unraveling Entangled Classification

α/β Hydrolase-like enzymes form a large and functionally diverse superfamily of proteins. Despite retaining a conserved structural core consisting of an eight-stranded, central β-sheet flanked with six α-helices, they display a modular architecture allowing them to perform a variety of functions, like esterases, lipases, peptidases, epoxidases, lyases, and others. At the same time, many α/β hydrolase-like families, even enzymatically distinct, share a high degree of sequence similarity. This imposes several problems for their annotation and classification, because available definitions of particular α/β hydrolase-like families overlap significantly, so the unambiguous functional assignment of these superfamily members remains a challenging task. For instance, two large and important peptidase families, namely S9 and S33, blend with lipases, epoxidases, esterases, and other enzymes unrelated to proteolysis, which hinders automatic annotations in high-throughput projects. With the use of thorough sequence and structure analyses, we newly annotate three protein families as α/β hydrolase-like and revise current classifications of the realm of α/β hydrolase-like superfamily. Based on manually curated structural superimpositions and multiple sequence and structure alignments, we comprehensively demonstrate structural conservation and diversity across the whole superfamily. Eventually, after detailed pairwise sequence similarity assessments, we develop a new clustering of the α/β hydrolases and provide a set of family profiles allowing for detailed, reliable, and automatic functional annotations of the superfamily members.

The roles of intrinsically disordered proteins in neurodegeneration

Neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, and Huntington's disease share a common pathological hallmark: the accumulation of misfolded proteins, particularly involving intrinsically disordered proteins (IDPs) like TDP-43, FUS, Tau, α-synuclein, and Huntingtin. These proteins undergo pathological aggregation, forming toxic inclusions that disrupt cellular function. The dysregulation of proteostasis mechanisms, including the ubiquitin-proteasome system (UPS), ubiquitin-independent proteasome system (UIPS), autophagy, and molecular chaperones, exacerbates these proteinopathies by failing to clear misfolded proteins effectively. Emerging therapeutic strategies aim to restore proteostasis through proteasome activators, autophagy enhancers, and chaperone-based interventions to prevent the toxic accumulation of IDPs. Additionally, understanding liquid-liquid phase separation (LLPS) and its role in stress granule dynamics offers novel insights into how aberrant phase transitions contribute to neurodegeneration. By targeting the molecular pathways involved in IDP aggregation and proteostasis regulation, and better understanding the specificity of each component, research in this area will pave the way for innovative therapeutic approaches to combat these neurodegenerative diseases. This review discusses the molecular mechanisms underpinning IDP pathology, highlights recent advancements in drug discovery, and explores the potential of targeting proteostasis machinery to develop effective therapies.

Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski's rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound 211 exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of -8.95 kcal/mol, -8.60 kcal/mol, -10.33 kcal/mol, and -9.90 kcal/mol, respectively. During MD simulation, compound 211 and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.

Improvements in large-scale production of tobacco etch virus protease

Tobacco-etch-virus (TEV) protease is the workhorse of many laboratories in which protein expression is the linchpin of downstream experiments. TEV protease is remarkable in its sequence specificity as the cleavage sequence rarely appears in higher organisms and its ability to cleave fusion tag proteins from proteins of interest. Herein we report work done on large-scale production of TEV protease using different promotors, media, fusion tags, and expression platforms. During our work we detected post-translational modification (gluconoylation and phosphogluconoylation) of TEV protease and the subsequent effects this has on the purity of the protein. Subsequently we made our pgl plus bacteria that negates these modifications and their effects. We also introduce a GFP-based assay for measurement of activity and ultimately a new set of protocols for producing 400-500 mg/L TEV protease.

Single-point mutations in disordered proteins: Linking sequence, ensemble, and function

Mutations in genomic DNA often result in single-point missense mutations in proteins. For folded proteins, the functional effect of these missense mutations can often be understood by their impact on structure. However, missense mutations in intrinsically disordered protein regions (IDRs) remain poorly understood. In IDRs, function can depend on the structural ensemble- the collection of accessible, interchanging conformations that is encoded in their amino acid sequence. We argue that, analogously to folded proteins, single-point mutations in IDRs can alter their structural ensemble, and consequently alter their biological function. To make this argument, we first provide experimental evidence from the literature showcasing how single-point missense mutations in IDRs affect their ensemble dimensions. Then, we use genomic data from patients to show that disease-linked missense mutations occurring in IDRs can, in many cases, significantly alter IDR structural ensembles. We hope this analysis prompts further study of disease-linked, single-point mutations in IDRs.

Structure and Dynamics of Macrophage Infectivity Potentiator Proteins from Pathogenic Bacteria and Protozoans Bound to Fluorinated Pipecolic Acid Inhibitors

Macrophage infectivity potentiator (MIP) proteins, found in pro- and eukaryotic pathogens, influence microbial virulence, host cell infection, pathogen replication, and dissemination. MIPs share an FKBP (FK506 binding protein)-like prolyl-cis/trans-isomerase domain, making them attractive targets for inhibitor development. We determined high-resolution crystal structures of Burkholderia pseudomallei and Trypanosoma cruzi MIPs in complex with fluorinated pipecolic acid inhibitors. The inhibitor binding profiles in solution were compared across B. pseudomallei, T. cruzi, and Legionella pneumophila MIPs using 1H, 15N, and 19F NMR spectroscopy. Demonstrating the versatility of fluorinated ligands for characterizing inhibitor complexes, 19F NMR spectroscopy identified differences in ligand binding dynamics across MIPs. EPR spectroscopy and SAXS further revealed inhibitor-induced global structural changes in homodimeric L. pneumophila MIP. This study demonstrates the importance of integrating diverse methods to probe protein dynamics and provides a foundation for optimizing MIP-targeted inhibitors in this structurally conserved yet dynamically variable protein family.

Construction and characterization of cloning vector and temperature sensitive vectors for Gordonia sp. IITR100

Gordonia spp. are Gram-positive, non-sporulating bacteria which have several industrial as well as environmental applications. In order to enhance their potential, metabolic engineering is required which often involves genome manipulation. For this purpose, temperature sensitive plasmids are useful as the desired genes for integrases or recombinases can be supplied transiently, followed by curing of the plasmid. Here, we report the construction of a cloning vector and temperature sensitive vectors based upon the pKB1 replicon from Gordonia westfalica. The amino acid residues or regions for creating temperature sensitive mutants were predicted based on in silico methods, and the dynamics of these mutant proteins were studied using docking and molecular dynamic simulations. The desired mutations were incorporated in the replication protein by site directed mutagenesis. The results were validated by growth kinetics of the wild type and mutants at permissive and non-permissive temperatures. This is the first report on temperature sensitive vectors based on native replicon from a plasmid originating from Gordonia.

Water occupancy in the Acinetobacter baumannii F-ATP synthase c-ring and its implications as a novel inhibitor target

The Acinetobacter baumannii F1FO-ATP synthase is essential for the opportunistic human pathogen. Its membrane-embedded FO domain consists of the c-ring and subunit a. The c-ring translocates protons via a conserved carboxylate across the membrane via two half-channels in subunit a, and its revolution enables the F1 domain to carry out ATP formation. Here, we used molecular dynamics simulations, free energy calculations, and in vivo mutational experiments to assess the likely existence of water molecules in the binding site of the A. baumannii c-ring. We first predicted its binding site structure in the ion-locked conformation and extrapolated the presence of two water molecules in the ion-binding site. Based on our predictions, amino acid point mutations confirmed the critical role of key residues involved in the water-binding site upon ATP synthesis ability and cell growth. We discuss the implications of our findings in the context of rational drug design to target the A. baumannii FO domain.

Attenuation of viral replication foci in nuclei by 1,6 Hexanediol implicates phase separation in the assembly of baculoviral replication factories

The assembly of replication factors into functional complexes is crucial for the initiation of viral genome replication and processing of nascent viral DNA. Binding to viral DNA and interaction of protein domains presumably guide compartmentalization of replication factors. The phase separation due to hydrophilicity and hydrophobicity of components may also contribute to the assembling process. However, phase separation effects are poorly investigated in the infection cycle of baculoviruses, large DNA viruses infecting Diptera, Hymenoptera, and Lepidoptera insects. Herein, we describe an investigation on a possible role of phase separation in the assembly of nuclear replication factories in Spodoptera frugiperda Sf9 cells infected with the Autographa californica multiple nucleopolyhedrovirus (AcMNPV). The inhibitory effect of 1,6-Hexanediol on the translocation of a viral DNA binding protein (DBP) to the replicative centers has revealed the involvement of liquid phases separation in the assembly of these centers. DBP is a structural component of the virogenic stroma, a sub-nuclear membrane-less compartment involved in viral DNA replication and the production of nucleocapsids. This sub-nuclear structure is presumably assembled via a biomolecular condensation mechanism.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives

Protein allostery is a fundamental biological regulatory mechanism that allows communication between distant locations within a protein, modifying its function in response to signals. Experimental techniques, such as NMR spectroscopy and cryo-electron microscopy (cryo-EM), are critical validation tools for computational predictions and provide valuable insights into dynamic conformational changes. Combining these approaches has greatly improved our understanding of classical conformational allostery and complex dynamic coupling mechanisms. Recent advances in machine learning and enhanced sampling methods have broadened the scope of allostery research, identifying cryptic allosteric sites and directing new drug discovery approaches. Despite progress, bridging static structural data with dynamic functional states remains challenging. This review underscores the importance of combining experimental and computational approaches to comprehensively understand protein allostery and its diverse applications in biology and medicine.

ATP1A3 Variants, Variably Penetrant Short QT Intervals, and Lethal Ventricular Arrhythmias

Importance

Alternating hemiplegia of childhood (AHC) is a disorder that can result from pathogenic variants in ATP1A3-encoded sodium-potassium adenosine triphosphatase alpha 3 (ATP1A3). While AHC is primarily a neurologic disease, some individuals experience sudden unexplained death (SUD) potentially associated with cardiac arrhythmias.

Objective

To determine the impact of ATP1A3 variants on cardiac electrophysiology and whether lethal ventricular arrhythmias are associated with SUD in patients with AHC.

Design, Setting, and Participants

In this international, multicenter case-control study from 12 centers across 10 countries, patients with AHC were grouped by ATP1A3 variant status (positive vs negative) and into subgroups with the most common AHC variants (D801N, E815K, G947R, and other). A healthy control cohort was established for comparison. Blinded, manual measurements of QT intervals and corrected QT interval (QTc) were performed independently by 2 pediatric cardiac electrophysiologists. Induced pluripotent stem cell cardiomyocytes were derived from patients with AHC who were positive for the D801N variant of ATP1A3 (iPSC-CMD801N cells). Data analysis was performed from April to June 2022.

Exposure

Presence of ATP1A3 variant.

Main Outcomes and Measures

The primary outcome was QTc. Outcomes, including survival, were abstracted and variants were mapped on cryogenic electron microscopy structure maps. iPSC-CMD801N cells were used to validate ventricular repolarization and arrhythmic susceptibility in vitro.

Results

Among the 222 individuals included (148 with AHC and 74 control), the mean (SD) age at diagnostic electrocardiography was 11.0 (9.4) years and 119 (54%) were female. The cohort with AHC consisted of 148 largely unrelated probands (mean [SD] age at diagnostic electrocardiography, 11.5 [10.5] years). Of these, 123 individuals were ATP1A3 genotype positive, including 35 (28%) with the D801N variant, 21 (17%) with the E815K variant, 8 (7%) with the G947R variant, and 8 (7%) with a loss-of-function variant. Probands with the D801N variant had shorter mean (SD) QTcs (381.8 [36.6] milliseconds; 24 [69%] with QTc <370 milliseconds) compared with those who had the E815K variant (393.6 [43.1] milliseconds; P = .001; 4 [19%] with QTC <370 milliseconds), the G947R variant (388.4 [26.5] milliseconds; P = .02; 1 [13%] with QTc <370 milliseconds), a loss-of-function variant (403.0 [33.5] milliseconds; P < .001; 1 [13%] with QTc <370 milliseconds), all other variants (387.8 [37.1] milliseconds; P < .001; 44 [86%] with QTc <370 milliseconds), and healthy controls (415.4 [21.0] milliseconds; P < .001; 0 with QTc <370 milliseconds). Three D801N-positive individuals had a major cardiac event, compared with 0 major cardiac events in all other individuals (P = .02). The D801N variant and 4 rare variants (D805N, P323S, S772R, and C333F) found in individuals with the shortest QTcs localized to the potassium-binding domain of ATP1A3. IPSC-CMD801N lines demonstrated shortened action potential duration, higher mean diastolic potential, and delayed afterdepolarizations compared with controls.

Conclusions and Relevance

Nearly 70% of individuals with D801N variants of ATP1A3 had short QTcs (<370 milliseconds), with an association between ventricular arrhythmias and cardiac arrest. This may underlie the SUD etiology in AHC.

No structure, no problem: Protein stabilization by Hero proteins and other chaperone-like IDPs

In order for a protein to function, it must fold into its proper three-dimensional structure. Otherwise, improperly folded proteins are typically prone to aggregate through a process that is detrimental to cellular health. It is widely known that a diverse group of proteins, called molecular chaperones, function to promote proper folding of other proteins and prevent aggregation. In contrast, intrinsically disordered proteins (IDPs) lack substantial tertiary structures, but nonetheless serve important functional roles. In some cases, IDPs have been observed to display remarkably chaperone-like activities, where they stabilize the activities of client proteins and prevent their aggregation. While it was previously thought that chaperone-like IDPs were mainly utilized by extremophilic organisms in their survival of extreme stress, we recently showed that a group of chaperone-like IDPs, we named heat-resistant obscure (Hero) proteins, are also widespread in non-extremophile animals, including humans and flies. Thus, we should consider the possibility that IDPs serve significant chaperone-like functions in protein stabilization relevant to physiological conditions. However, as most of our understanding of how chaperones function is based on insights from their structured domains, it is unclear how chaperone-like IDPs elicit chaperone-like effects without these structures. Here we summarize our understanding of Hero proteins to date, and based on experimental evidence, outline the features that are likely important for their protein stabilizing activities. We draw on concepts from the studies of chaperones and chaperone-like IDPs, in order to draft potential models of how chaperone-like IDPs achieve chaperone-like effects in the absence of well-defined structures.

Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach

BACKGROUND

Acquired Immunodeficiency Syndrome (AIDS) is a critical global health issue caused by the human immunodeficiency virus (HIV). It has different strains and subtypes; among these, Subtype C accounts for higher infection rates than others. Despite its high prevalence, the molecular interactions with host receptors, specifically CD4, have not yet been explored.

METHODS

This study investigates the molecular interactions between HIV subtype C and the CD4 receptor via docking and dynamics approach. Four HIV targets were examined, and their structure was modelled. Subsequently, these models were docked with the CD4 to analyze their binding interaction. The stability was examined over 200 simulations via Desmond software, and trajectories were analyzed, followed by Root mean square deviation (RMSD), root mean square fluctuation (RMSF), and the radius of gyration (Rg), PCA (principal component analysis), etc., to assess their stability and interaction dynamics.

RESULTS

The four target structures were modelled, and their quality was validated. Further, the docking analysis with CD4 revealed that the Envelope glycoprotein has -13.6 kcal/mol, protease has -11.2 kcal/mol, Reverse transcriptase has -12.4 kcal/mol, and integrase has -13.1 kcal/mol binding affinity towards it, followed by the number of hydrogen bond, such as 9, 6, 11, 6. The simulation over 200 ns demonstrated that the average RMSD for each complex started stabilizing within the 0.9 Å - 3.4 Å, followed by 25-50 ns, whereas the RMSF, Rg and PCA revealed the relative compactness and flexibility varied across different viral targets.

CONCLUSIONS

The study successfully identified the interactive residues of HIV subtype C toward the CD4 receptor. The binding affinities and stability data provide valuable insights into Subtype C's molecular interactions with the host, and these findings underscore the potential for developing treatments that disrupt these interactions to combat HIV more effectively.

ExploreTurns: A web tool for the exploration, analysis, and classification of beta turns and structured loops in proteins; application to beta-bulge and Schellman loops, Asx helix caps, beta hairpins, and other hydrogen-bonded motifs

The most common type of protein secondary structure after the alpha helix and beta sheet is the four-residue beta turn, which plays many key structural and functional roles. Existing tools for the study of beta turns operate in backbone dihedral-angle (Ramachandran) space, which presents challenges for the visualization, comparison and analysis of the wide range of turn conformations. In this work, a new turn-local coordinate system and structural alignment, together with a set of geometric descriptors for turn backbone shape, are incorporated into ExploreTurns, a web facility for the exploration, analysis, geometric tuning and retrieval of beta turns and their contexts which combines the advantages of Ramachandran- and Euclidean-space representations. Due to the prevalence of beta turns in proteins, this facility, supported by its interpreter for a new general nomenclature which classifies H-bonded loop motifs and beta hairpins, serves as an exploratory browser and analysis tool for most loop structure. The tool is applied to the detection of new H-bonded loops, including short and "double" Schellman loops, a large family of beta-bulge loops with a range of geometries and H-bond topologies, and other motifs. Other applications presented here include the mapping of sequence preferences in Asx helix N-caps and an investigation of the depth dependence of beta-turn geometry. ExploreTurns, available at www.betaturn.com, should prove useful in research, education, and applications such as protein design, in which an enhanced Euclidean-space picture of turn and motif structure and the ability to identify and tune structures suited to particular requirements may improve performance.

Conformationally adaptive therapeutic peptides for diseases caused by intrinsically disordered proteins (IDPs). New paradigm for drug discovery: Target the target, not the arrow

The traditional model of protein structure determined by the amino acid sequence is today seriously challenged by the fact that approximately half of the human proteome is made up of proteins that do not have a stable 3D structure, either partially or in totality. These proteins, called intrinsically disordered proteins (IDPs), are involved in numerous physiological functions and are associated with severe pathologies, e.g. Alzheimer, Parkinson, Creutzfeldt-Jakob, amyotrophic lateral sclerosis (ALS), and type 2 diabetes. Targeting these proteins is challenging for two reasons: i) we need to preserve their physiological functions, and ii) drug design by molecular docking is not possible due to the lack of reliable starting conditions. Faced with this challenge, the solutions proposed by artificial intelligence (AI) such as AlphaFold are clearly unsuitable. Instead, we suggest an innovative approach consisting of mimicking, in short synthetic peptides, the conformational flexibility of IDPs. These peptides, which we call adaptive peptides, are derived from the domains of IDPs that become structured after interacting with a ligand. Adaptive peptides are designed with the aim of selectively antagonizing the harmful effects of IDPs, without targeting them directly but through selected ligands, without affecting their physiological properties. This "target the target, not the arrow" strategy is promised to open a new route to drug discovery for currently undruggable proteins.

A Structural Voyage Toward the Landscape of Humoral and Cellular Immune Escapes of SARS-CoV-2

The genome-based surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the past nearly 5 years since its emergence has refreshed our understanding of virus evolution, especially on convergent co-evolution with the host. SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations that affect the functional properties of the virus by altering its infectivity, virulence, transmissibility, and interactions with host immunity. This poses a huge challenge to global prevention and control measures based on drug treatment and vaccine application. As one of the key evasion strategies in response to the immune profile of the human population, there are overwhelming amounts of evidence for the reduced antibody neutralization of SARS-CoV-2 variants. Additionally, data also suggest that the levels of CD4+ and CD8+ T-cell responses against variants or sub-variants decrease in the populations, although non-negligible cross-T-cell responses are maintained. Herein, from the perspectives of structural immunology, we outline the characteristics and mechanisms of the T cell and antibody responses to SARS-CoV and its variants/sub-variants. The molecular bases for the impact of the immune escaping variants on the interaction of the epitopes with the key receptors in adaptive immunity, that is, major histocompatibility complex (MHC), T-cell receptor (TCR), and antibody are summarized and discussed, the knowledge of which will widen our understanding of this pandemic-threatening virus and assist the preparedness for Pathogen X in the future.

Application of cryo-FIB-SEM for investigating ultrastructure in guard cells of higher plants

Stomata are vital for CO2 and water vapor exchange, with guard cells' aperture and ultrastructure highly responsive to environmental cues. However, traditional methods for studying guard cell ultrastructure, which rely on chemical fixation and embedding, often distort cell morphology and compromise membrane integrity. In contrast, plunge-freezing in liquid ethane rapidly preserves cells in a near-native vitreous state for cryogenic electron microscopy. Using this approach, we applied Cryo-Focused Ion Beam-Scanning Electron Microscopy (cryo-FIB-SEM) to study the guard cell ultrastructure of Vicia faba, a higher plant model chosen for its sensitivity to external factors and ease of epidermis isolation, advancing beyond previous cryo-FIB-SEM applications in lower plant algae. The results firstly introduced cryo-FIB-SEM volume imaging, enabling subcellular ultrastructure visualization of higher plants like V. faba in a vitrified, unaltered state. 3D models of organelles such as stromules, chloroplast protrusions, chloroplasts, starch granules, mitochondria, and vacuoles were reconstructed from cryo-FIB-SEM volumetric data, with their surface area and volume initially determined using manual segmentation. Future studies using this near-native volume imaging technique hold promise for investigating how environmental factors like drought or salinity influence stomatal behavior and the morphology of guard cells and their organelles.

Unraveling atomic-scale mechanisms of GDP extraction catalyzed by SOS1 in KRAS-G12 and KRAS-D12 oncogenes

The guanine exchange factor SOS1 plays a pivotal role in the positive feedback regulation of the KRAS signaling pathway. Recently, the regulation of KRAS-SOS1 interactions and KRAS downstream effector proteins has emerged as a key focus in the development of therapies targeting KRAS-driven cancers. However, the detailed dynamic mechanisms underlying SOS1-catalyzed GDP extraction and the impact of KRAS mutations remain largely unexplored. In this study, we unveil and describe in atomic detail the primary mechanisms by which SOS1 facilitates GDP extraction from KRAS oncogenes. For GDP-bound wild-type KRAS (KRAS-G12), four critical amino acids (Lys811, Glu812, Lys939, and Glu942) are identified as essential for the catalytic function of SOS1. Notably, the KRAS-G12D mutation (KRAS-D12) significantly accelerates the rate of GDP extraction. The molecular basis of this enhancement are attributed to hydrogen bonding interactions between the mutant residue Asp12 and a positively charged pocket in the intrinsically disordered region (residues 807-818), comprising Ser807, Trp809, Thr810, and Lys811. These findings provide novel insights into SOS1-KRAS interactions and offer a foundation for developing anti-cancer strategies aimed at disrupting these mechanisms.

Platelet inhibition by hypochlorous acid involves cAMP signalling

Hypochlorous acid (HOCl), made by neutrophil-derived myeloperoxidase, has been suggested to inhibit platelets, however, the mechanisms involved have not been described. Here we confirm that HOCl exposure changes platelet morphology and inhibits platelet spreading and aggregation. HOCl effects could be reversed by glutathione suggesting a role for cysteine oxidation. Mass spectrometry-based proteomics of HOCl-exposed platelets revealed oxidised cysteine residues in 37 proteins including adenylate cyclase 6 and Rap1B. Adenylate cyclase is involved in the inhibitory cAMP pathway triggered by endothelium-derived prostacyclin and Rap1 is a small G protein required for integrin αIIbβ3 activation and platelet aggregation. We show that HOCl exposure stimulates cAMP production and phosphorylation of the cAMP-dependent protein kinase substrate VASP in platelets and transfected HEK293T cells. In addition, HOCl inhibited Rap1-GTP formation. These data suggest that HOCl inhibits platelets at least in part through the cAMP pathway and by regulating Rap1. Thus, this study provides new insights into HOCl mediated crosstalk between neutrophils and platelets.

The Roles of Forkhead Box O3a (FOXO3a) in Bone and Cartilage Diseases - A Narrative Review

Bone and cartilage diseases are significantly associated with musculoskeletal disability. However, no effective drugs are available to cure them. FOXO3a, a member of the FOXO family, has been implicated in cell proliferation, ROS detoxification, autophagy, and apoptosis. The biological functions of FOXO3a can be modulated by post-translational modifications (PTMs), such as phosphorylation and acetylation. Several signaling pathways, such as MAPK, NF-κB, PI3K/AKT, and AMPK/Sirt1 pathways, have been implicated in the development of bone and cartilage diseases by mediating the expression of FOXO3a. In particular, FOXO3a acts as a transcriptional factor in mediating the expression of various genes, such as MnSOD, CAT, BIM, BBC3, and CDK6. FOXO3a plays a critical role in the metabolism of bone and cartilage. In this article, we mainly discussed the biological functions of FOXO3a in bone and cartilage diseases, such as osteoporosis (OP), osteoarthritis (OA), rheumatoid arthritis (RA), ankylosing spondylitis (AS), and intervertebral disc degeneration (IDD). FOXO3a can promote osteogenic differentiation, induce osteoblast proliferation, inhibit osteoclast activity, suppress chondrocyte apoptosis, and reduce inflammatory responses. Collectively, up-regulation of FOXO3a expression shows beneficial effects, and FOXO3a has become a potential target for bone and cartilage diseases.

Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM

One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interactions, HIV-2 CA assembly remains poorly understood. By templating the assembly of HIV-2 CA on functionalized liposomes, we report high-resolution structures of the HIV-2 CA lattice, including both CA hexamers and pentamers, alone and with peptides of host phenylalanine-glycine (FG)-motif proteins Nup153 and CPSF6. While the overall fold and mode of FG-peptide binding is conserved with HIV-1, this study reveals distinctive features of the HIV-2 CA lattice, including differing structural character at regions of host factor interactions and divergence in the mechanism of formation of CA hexamers and pentamers. This study extends our understanding of HIV capsids and highlights an approach facilitating the study of lentiviral capsid biology.

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.

PD1-TLR10 fusion protein enhances the antitumor efficacy of CAR-T cells in colon cancer

BACKGROUND

The immunosuppressive microenvironment negatively affects the efficacy of chimeric antigen receptor T (CAR-T) cells in solid tumors. Fusion protein that combining extracellular domain of inhibitory checkpoint protein and the cytoplasmic domain of stimulatory molecule may improve the efficacy of CAR-T cells by reversing the suppressive signals.

METHODS

To generate optimal PD1-TLR10 fusion proteins, PD1 extracellular domain and TLR10 intracellular domain were connected by transmembrane domain from PD1, CD28, or TLR10, respectively. The fusion protein was co-expressed with second generation anti-CEA CAR in the same retroviral vector. The effector function and the efficacy of fusion protein armored CAR-T cells was evaluated in vitro and in vivo.

RESULTS

PD1-TLR10 armored CEA CAR-T cells showed stronger cytotoxicity and cytokine release against CEA-positive tumor cells. Specifically, CAR-T cells with fusion protein containing TLR10 transmembrane domain demonstrated better anti-tumor activity in xenograft mouse model.

CONCLUSION

Our study demonstrated that CEA CAR-T armored with rational designed PD1-TLR10 fusion protein had improved efficacy in colon cancer.

Dihydropyrimidine-2-thione derivatives as SARS-CoV-2 main protease inhibitors: synthesis, SAR and in vitro profiling

Despite the passage of approximately five years since the outbreak, an efficacious remedy for SARS-CoV-2 remains elusive, highlighting the urgent imperative for developing SARS-CoV-2 potent inhibitors. In our current study, we have unmasked the hitherto unrealized potential of dihydropyrimidine-2-thiones against the Main Protease (Mpro) of SARS-CoV-2. Employing a predictive docking tool, we identified promising lead compounds and optimized them via comprehensive Structural Activity Relationship (SAR) studies. Key design elements included proton donor/acceptor groups, six-membered rings, and fluorinated moieties to enhance interactions. These leads underwent in vitro inhibition assays to enhance their interaction with key Mpro amino acid residues. Our findings indicated that all synthesized compounds exhibited significant inhibition of the Mpro. Compounds 12j (IC50 = 0.063 μM), and 12l (IC50 = 0.054 μM) displayed exceptional in vitro binding affinities. In addition to their string inhibitory activity, CC50 values were assessed, confirming acceptable cytotoxicity profiles for potent compounds. Molecular dynamic simulation substantiated the binding mechanism revealing that compound 12l maintains robust stability with the target protein. Furthermore, compounds predicted to have minimal oral toxicity and high intestinal absorption make them promising candidates for drug development. These findings paved the way for the potent clinical application of these dihydropyrimidine-2-thiones as efficient SARS-CoV-2 therapeutics.

Cholinesterase Inhibitors from Plants and Their Potential in Alzheimer's Treatment: Systematic Review

INTRODUCTION

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by memory loss and cognitive decline, primarily due to dysfunction of acetylcholine caused by acetylcholinesterase and butyrylcholinesterase. While synthetic cholinesterase inhibitors like donepezil, rivastigmine, and galantamine are commonly used, they have notable side effects, prompting interest in natural alternatives. Medicinal plants, rich in bioactive compounds like flavonoids and alkaloids, have shown potential as cholinesterase inhibitors with additional antioxidants and anti-inflammatory benefits. This study aimed to evaluate the cholinesterase-inhibiting effects of various plant species and their compounds to identify new therapeutic candidates and reduce side effects.

METHOD

A PRISMA-compliant review was conducted, screening studies from multiple databases, with a final inclusion of 64 in vivo studies.

RESULTS

These studies highlighted plant extracts such as Ferula ammoniacum, Elaeagnus umbellata, Bacopa monnieri, and Centella asiatica, which improved memory, reduced oxidative stress, and provided neuroprotection. Some extracts also reduced amyloid plaques, enhanced neuronal integrity, and restored cholinesterase activity, indicating their potential as therapeutic agents for AD and other neurodegenerative diseases.

CONCLUSIONS

The findings underscore the promise of plant-based compounds in treating cognitive decline and cholinergic dysfunction in AD, advocating for further research into their therapeutic potential.

Comprehensive Bioactive Compound Profiling of Artocarpus heterophyllus Leaves: LC-MS/MS Analysis, Antioxidant Potential, and Molecular Insights

Purpose

Artocarpus heterophyllus leaves, rich in phytochemicals, present a promising source of natural bioactive compounds for therapeutic and cosmetic applications. This study evaluated the phytochemical composition, antioxidant potential, and tyrosinase inhibition activities of leaf extracts while assessing the enzyme inhibition properties of key compounds through molecular docking and dynamics simulations.

Patients and Methods

Ethanol and ethyl acetate extracts were analyzed using Thin Layer Chromatography (TLC) and Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). Antioxidant activity was determined via DPPH radical scavenging and tyrosinase inhibition was compared against kojic acid. Molecular docking and molecular dynamics simulations explored binding interactions of Artocarpin and Sitosterol with matrix metalloproteinases (MMPs) and tyrosinase.

Results

Artocarpin and Sitosterol were identified as primary bioactive compounds. Ethanol extracts exhibited stronger tyrosinase inhibition (IC50: 177.24 ppm), while ethyl acetate extracts showed superior antioxidant activity (IC50: 117.64 ppm). Molecular docking highlighted high binding affinities of Artocarpin and Sitosterol with MMP-13 and tyrosinase. MD simulations confirmed stable interactions, particularly between Artocarpin and MMP-13, supporting its potential as a therapeutic agent.

Conclusion

Artocarpin and Sitosterol from Artocarpus heterophyllus leaf extracts demonstrate potent antioxidant, enzyme inhibitory, and tyrosinase inhibition activities. These findings underscore their potential for managing oxidative stress, inflammation, and pigmentation disorders, warranting further investigation into their bioavailability and formulation for therapeutic and cosmetic uses.

A novel Zn (II)/Cd (II)/Pb (II)-translocating PIB-type ATPase mediates metal resistance in Chryseobacterium sp. strain PMSZPI in metal-enriched soil of uranium ore deposit

Transition metals at higher concentrations are toxic to the cells. Membrane bound, ATP-driven efflux pumps belonging to the P-type ATPase superfamily maintain metal homeostasis by transporting metals/ions across the biological membranes. A soil bacterium, Chryseobacterium sp. strain PMSZPI, residing in metal enriched environment of uranium ore deposit exhibited high tolerance to multiple heavy metals. In an attempt to unveil one of the molecular determinants of metal resistance in PMSZPI, we characterized an unannotated, novel metal exporting PIB-2-ATPase that was categorized as Zn (II)/Cd (II)/Pb(II) PIB-2-ATPase based on amino-acid sequence alignment and the substrate specificities. The heterologously expressed and purified PIB-2-ATPase exhibited zinc/cadmium dependent ATP hydrolysis activity, ATP dependent phosphorylation and activity inhibition in the presence of vanadate. In-vivo metal tolerance assays and analysis of intracellular metal contents indicated involvement of PIB-2-ATPase in metal efflux. The disordered N-terminal metal binding domain of PIB-2-ATPase was found to be inconsequential for its function. Mutagenesis studies revealed the role of the conserved transmembrane (TM) residues (cysteine, aspartate and lysine) in metal translocation. Overall, our data establishes the vital role of Zn(II)/Cd(II)/Pb(II) PIB-2-ATPase in conferring metal resistance in PMSZPI.

Afobazole: a potential drug candidate which can inhibit SARS CoV-2 and mimicry of the human respiratory pacemaker protein

In COVID-19 patients, respiratory failure was reported due to damage to the respiratory centers of the brainstem. Molecular mimicry of three brainstem pre-Botzinger complex proteins (DAB1, AIFM and SURF1) was regarded as the underlying reason for respiratory failure and the autoimmune neurological sequelae. Of the three brainstem proteins mimicked by SARS CoV-2, corresponding sequences to two of the mimicry peptides were located in the N-protein of SARS CoV-2. N-protein is important for viral RNA synthesis and genome packaging. Here, we have used molecular modeling, docking and MD simulations to discern potential drugs which can inhibit molecular mimicry of DAB1 by SARS CoV-2 and also eliminate it by interfering in genome packaging. The binding site (drug target) for molecular docking was defined as the amino acid sequence extending from position 168-185 of the N-protein which was a SLiM region and also included the mimicry hexapeptide. Molecular docking after MD simulations was used to discern probable inhibitors of the drug-target from FDA-approved neurological drugs in the Broad Institute's Drug Repurposing Hub. Our results revealed that an anti-anxiety drug afobazole qualified the ADMET parameters, formed a stable complex with the drug-target and exhibited the highest binding energy (-88.21 kJ/mol). This suggests that afobazole can be repurposed against SARS CoV-2 for disrupting molecular mimicry of human DAB1 protein and also eliminate the etiopathological agent by interfering in viral genome packaging.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00316-6.

Hellenia speciosa: A comprehensive review of traditional applications, phytonutrients, health benefits and safety

Hellenia speciosa (H. speciosa) is not only recognized for its nutritional benefits, but is also revered as a traditional medicinal plant with diverse biological activities. H. speciosa is a perennial herb that is abundant in phytonutrients, including important nutrients such as proteins, amino acids, and vitamins, as well as potent bioactive components like steroids, terpenes, and volatile oils. Among them, steroids and terpenoids are the main bioactive components in H. speciosa, and they are also the two most abundant compounds in it. H. speciosa has a variety of pharmacological effects, such as anti-inflammatory, antidiabetic, and antimicrobial, which is consistent with its traditional use as a folk medicine. Based on its traditional uses, phytonutrients, and health benefits, H. speciosa is considered a valuable medicinal and edible plant. This review provides a comprehensive overview and critical analysis of recent advancements in research on H. speciosa, serving as a valuable reference for future investigations and rational exploitation of this plant.

AlphaFold prediction of structural ensembles of disordered proteins

Deep learning methods of predicting protein structures have reached an accuracy comparable to that of high-resolution experimental methods. It is thus possible to generate accurate models of the native states of hundreds of millions of proteins. An open question, however, concerns whether these advances can be translated to disordered proteins, which should be represented as structural ensembles because of their heterogeneous and dynamical nature. To address this problem, we introduce the AlphaFold-Metainference method to use AlphaFold-derived distances as structural restraints in molecular dynamics simulations to construct structural ensembles of ordered and disordered proteins. The results obtained using AlphaFold-Metainference illustrate the possibility of making predictions of the conformational properties of disordered proteins using deep learning methods trained on the large structural databases available for folded proteins.

Development of a Novel Human Serum Albumin-Based Tool for Effective Drug Discovery: The Investigation of Protein Quality and Immobilization

The binding ability of human serum albumin (HSA) on active pharmaceutical ingredients (APIs) is one of the most important parameters in the early stages of drug discovery. In this study, an immobilized HSA-based tool was developed for the rapid and easy in vitro screening of API binding. The work explored the serious incompleteness in the identification of HSA used for in vitro screening published in the last five years. To mitigate this problem, a comprehensive analysis and immobilization studies were performed on the most used HSA types. Serious differences in the colloidal stability of HSAs and their API binding ability on a selected set of APIs were observed. HSAs were immobilized on magnetic nanoparticles with glutardialdehyde (GDA) or cyclohexyl-diglycidyl ether (CDGE) linkers, which have never been used for HSA immobilization before. The HSA-MNP-CDGE complexes achieved a higher immobilization yield and preserved API binding ability; however, the esterase-like enzymatic activity of HSA reduced significantly.

Recent Developments in 14-3-3 Stabilizers for Regulating Protein-Protein Interactions: An Update

14-3-3 proteins play a crucial role in the regulation of protein-protein interactions, impacting various cellular processes and disease mechanisms. Recent advancements have led to the development of stabilizers that enhance the binding of 14-3-3 proteins to clients, presenting promising therapeutic potentials. This perspective provides an updated overview of the latest developments in the field of 14-3-3 stabilizers, with a focus on their design, synthesis, and biological evaluation. We discuss the structural basis for the interaction between 14-3-3 proteins and their ligands, highlighting key modifications that enhance binding affinity and selectivity. Additionally, we explore the therapeutic applications of 14-3-3 stabilizers across major therapeutic areas such as cancer, metabolic disorders, and neurodegenerative diseases. By summarizing recent research findings and technological advancements, this perspective aims to shed light on the current state of 14-3-3 stabilizer developments and outline future directions for optimizing these compounds as effective therapeutic agents.

Investigating the Therapeutic Ability of Novel Antimicrobial Peptide Dendropsophin 1 and Its Analogues through Membrane Disruption and Monomeric Pore Formation

Antimicrobial peptides (AMPs) are an alternative source of antibiotics that fight worldwide antibiotic-resistant catastrophes. Dendropsophin 1 (Dc1) is a recently invented novel AMP with 17 amino acid residues obtained from the screen secretion of a frog named Dendropsophus columbianus. Dc1 has two slightly mutated analogues, namely, Dc1.1 and Dc1.2, with improved cationicity and mean amphipathic moment to enhance the selective toxicity against microorganisms. Experimental results indicate that Dc1 and Dc1.1 have similar antimicrobial activity against Gram-negative bacteria Escherichia coli and Gram-positive bacteria Staphylococcus aureus, whereas the synthesized peptide Dc1.2 has shown antimicrobial activity against a wide range of microorganisms. However, the molecular level details of the peptide-membrane interaction and the corresponding changes in the peptide structure remain elusive. In this study, we investigate the bacterial membrane disruption capability of these AMPs by running a total of 14.2 μs long molecular dynamics (MD) simulations. Our findings suggest that all three peptides affect the upper layer of the membrane with different degrees of disruption. After penetration, Dc1 and Dc1.2 retain stable α-helices in the core region, indicating the potential to disrupt the second layer. However, secondary structure analysis shows that Dc1.2 attains extended helical regions on the C-terminus, suggesting it as the superior candidate among the analogues to have the potential of stable pore formation, leading to bacterial cell death. To speed up our study, we adopt a one-transmembrane configuration of Dc1, Dc1.1, and Dc1.2 and find toroidal pores with subsequent water leakage for Dc1.2.

Crystallographic Structure and Antiglioma Potential of Centrolobium microchaete Seed Lectin

The genus Centrolobium comprises species of Neotropical trees with seeds that possess medicinal and bioactive applications. Lectins from this genus exhibit anti-inflammatory and immunomodulatory effects, influencing the activation of the immune system. This study focuses on characterizing the structure and carbohydrate-binding properties of the lectin from Centrolobium microchaete (CML) and evaluating its potential against gliomas. The structure of the lectin in complex with methyl-mannose-α1,3-mannose (MDM) was resolved using X-ray crystallography at 1.3 Å resolution, with its interactions further analyzed through molecular dynamics simulations. Structurally, CML adopts a β-sandwich motif and assembles into canonical dimers. In vitro assays revealed that CML reduced the viability of C6 glioma cells, although only at high concentrations, without impacting cell migration or morphology. CML activated autophagic processes, albeit with lower efficacy compared with other mannose-specific lectins. The limited antiglioma activity of CML may be linked to its inability to form tetramers and unusual specificity toward asymmetric glycans, both crucial features for interactions with cellular glycans and the activation of signaling pathways. This study represents the first investigation of the antiglioma potential of a mannose-specific lectin from the Dalbergieae tribe, highlighting both its structural characteristics and functional limitations.

Oxygen K-edge inner-shell calculations of polymers in solutions realized by the extraction of local structures from molecular dynamics simulations

Inner-shell quantum chemical calculations of large molecular systems, such as polymers and soft matter in solution, were performed to understand the phase transition dynamics of these systems using soft x-ray absorption spectroscopy (XAS). The molecular structures of 40-mer poly(N-isopropylacrylamide) (PNIPAM) chains in solutions were obtained using molecular dynamics simulations. The 5-mer PNIPAM chains with terminated H atoms, including the second coordination shells of the solvent methanol and water molecules, were extracted from the 40-mer PNIPAM chains in solutions. The O K-edge inner-shell spectra of the 5-mer PNIPAM chains were obtained by averaging the inner-shell spectra of 9700 extracted polymer structures. This calculation method can be used to precisely evaluate the energy shifts of the C=O π* peaks of PNIPAM caused by the structural changes of the polymer chains, the substitutions of the hydrogen bonds of the C=O groups in PNIPAM from methanol to water molecules, and the increase in the coordination numbers of solvent molecules with the C=O groups, which were observed in the O K-edge XAS experiments.

Atomistic Mechanism of Lipid Membrane Binding for Blood Coagulation Factor VIII with Molecular Dynamics Simulations on a Microsecond Time Scale

During the blood coagulation cascade, coagulation factor VIII (FVIII) is activated by thrombin to form activated factor VIII (FVIIIa). FVIIIa associates with platelet surfaces at the site of vascular damage to form an intrinsic tenase complex with activated factor IX. A working model for FVIII membrane binding involves the association of positively charged FVIII residues with negatively charged lipid headgroups and the burial of hydrophobic residues into the membrane interior. Currently, the atomic details of the FVIII lipid binding interactions and membrane orientation are lacking. This study reports residue-specific FVIII C domain interactions with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) in atomistic detail. Contact maps between residues in the C domains with different lipid moieties support prior structural data describing how the C domains associate with membranes through electrostatic and hydrophobic interactions. Solvent-accessible surface area analysis quantified the extent to which residues in the C1 and C2 domains bury into the membrane. Calculations of the potential energy between the C domains and DOPC and DOPS revealed an FVIII membrane-binding orientation that agrees with previous experimental data. This study expands our knowledge of the structural basis of FVIII membrane association, which may be critical for the development of next-generation FVIII replacement constructs with improved activity.

Semirational Engineering of a Distal Loop Region to Enhance the Catalytic Activity and Stability of Leucine Dehydrogenase

Enzymatic asymmetric synthesis of l-phenylglycine by amino acid dehydrogenases has potential for industrial applications; however, this is hindered by their low catalytic efficiency toward high-concentration substrates. We identified and characterized a novel leucine dehydrogenase (MsLeuDH) with a high catalytic efficiency for benzoylformic acid via directed metagenomic approaches. Further, we obtained a triple-point mutant MsLeuDH-EER (D332E/G333E/L334R) with improved stability and catalytic efficiency through the rational design of distal loop 13. A coexpression system of MsLeuDH-EER and formate dehydrogenase completely converted a 300 mM substrate within 4 h with >99.9% enantiomeric excess. Molecular dynamics simulations revealed that mutations on loop 13 enhanced the overall structural rigidity of the protein to improve its stability but also stabilized the "closed" conformation through rigidifying the hinge region loop by distant modulation. Our results show that distal loop 13 can serve as a new hotspot region for enhancing the catalytic performance of leucine dehydrogenases.

Enzymes in a human cytoplasm model organize into submetabolon complexes

Enzyme-enzyme interactions are fundamental to the function of cells. Their atomistic mechanisms remain elusive mainly due to limitations of in-cell measurements. We address this challenge by atomistically modeling, for a total of ≈80 μs, a slice of the human cell cytoplasm that includes three successive enzymes along the glycolytic pathway: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), and phosphoglycerate mutase (PGM). We tested the model for nonspecific protein stickiness, an artifact of current atomistic force fields in crowded environments. The simulations reveal that the human enzymes co-organize in-cell into transient submetabolon complexes, consistent with previous experimental results. Our data both reiterate known specificity between GAPDH and PGK and reveal extensive direct interactions between GAPDH and PGM. Our simulations further reveal, through force field benchmarking, the critical role of protein solvation in facilitating these enzyme-enzyme interactions. Transient interenzyme interactions with μs lifetime occur repeatedly in our simulations via specific sticky protein surface patches, with interactions often mediated by charged patch residues. Some of the residues that interact frequently with one another lie in or near the active site of the enzymes. We show that some of these patches correspond to a general mode to interact with several partners for promiscuous enzymes like GAPDH. We further show that the non-native yeast PGK is stickier than human PGK in our human cytoplasm model, supporting the idea of evolutionary pressure to reduce sticking. Our cytoplasm modeling paves the way toward capturing the atomistic dynamics of an entire enzymatic pathway in-cell.

Clinical and microbiological characteristics of high-level daptomycin-resistant Corynebacterium species: A systematic scoping review

INTRODUCTION

Corynebacterium species potentially develop high-level daptomycin resistance (HLDR) shortly after daptomycin (DAP) administration. We aimed to investigate the clinical and microbiological characteristics of HLDR Corynebacterium infections.

METHODS

We first presented a clinical case accompanied by the results of a comprehensive genetic analysis of the isolate, and then performed a systematic scoping review. Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews, we searched for articles with related keywords, including "Corynebacterium", "Daptomycin", and "Resistance", in the MEDLINE and Web of Science databases from the database inception to October 25, 2024. Clinical case reports and research articles documenting the isolation of HLDR Corynebacterium species, defined by a minimum inhibitory concentration of DAP at ≥256 μg/mL, were deemed eligible for this review.

RESULTS

Of 80 articles screened, seven case reports detailing eight cases of HLDR Corynebacterium infections, as well as five research articles, were included. C. striatum was the most common species (7/9 cases, 77.8 %), and prosthetic device-associated infections accounted for 66.7 % of the cases. Duration of DAP administration before the emergence of HLDR isolates ranged from 5 days to 3 months; three-quarters of the cases developed within 17 days. Three HLDR isolates were genetically confirmed to have an alteration in pgsA2. The majority of the patients were treated with either glycopeptides or linezolid, with favorable outcomes. In vitro experiments confirmed that C. striatum strains acquire the HLDR phenotype at higher rates (71 %-100 %) within 24 h of incubation, compared to other Corynebacterium strains.

CONCLUSION

DAP monotherapy, especially for prosthetic device-associated infections, can result in the development of HLDR Corynebacterium. Additional research is warranted to investigate the clinical implications of this potentially proliferating antimicrobial resistant pathogen.

Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions

The mRNA splicing machinery has been estimated to generate 100,000 known protein-coding transcripts for 20,000 human genes (Ensembl, Sept. 2024). However, this set is expanding with the massive and rapidly growing data coming from high-throughput technologies, particularly single-cell and long-read sequencing. Yet, the implications of splicing complexity at the protein level remain largely uncharted. In this review, we describe the current advances toward systematically assessing the contribution of alternative splicing to proteome function diversification. We discuss the potential and challenges of using artificial intelligence-based techniques in identifying alternative splicing proteoforms and characterising their structures, interactions, and functions.

Runcaciguat activates soluble guanylyl cyclase via the histidine essential for heme binding and nitric oxide activation

Soluble guanylyl cyclase (sGC) is a well-established pharmacological target for the treatment of acute angina pectoris, pulmonary hypertension and heart failure. Histidine 105 in the heme binding pocket of sGC is a crucial residue for heme binding and natural enzyme activation by NO. It was assumed that the heme-free sGC mutants α1/β1H105F and α1/β1H105A were valuable research tools for studying NO independent sGC activators. These mutants have been used in drug screening and animal models. We confirm that the first generation of sGC activators cinaciguat and BAY 60-2770 activate the α1/β1H105F and α1/β1H105A mutants. In contrast, we show that the second generation sGC activators runcaciguat and BAY 543 only activate heme-free sGC when the β1H105 residue is present. By testing runcaciguat in β1 H105F knock-in mice, we confirm this histidine-dependency in vivo. We propose a novel classification of sGC activators, distinguishing between the histidine-dependent activators runcaciguat and BAY 543 and the histidine-independent activators cinaciguat, BAY 60-2770 and BI703704. The histidine-dependency of some of the sGC activators provides a compelling rationale for a re-evaluation of previous research and drug development programs based on sGC histidine mutants. Whether the classification of sGC activators based on the activation mechanism also makes a therapeutic difference needs to be clarified in the future.

Effects of chopping and salting on the properties of pre-rigor silver carp muscle: Metabolic process, protein functionality, and ultrastructure

Chopping and salting are two important processing steps in emulsified meat products. Effects of chopping and salting on metabolic process, protein functionality, and ultrastructure of pre-rigor silver carp muscle, and how these three aspects changed during rigor transformation were explored. Chopping caused an accelerated loss of adenosine triphosphate (ATP) from 1.16 μmol/g to 0.16 μmol/g, and salt addition inhibited accumulation of hypoxanthine nucleoside (HxR) and hypoxanthine (Hx). Similarly, chopping led to faster decrease of glycogen from 4.59 mg/g to 1.50 mg/g and increase in lactic acid from 0.52 mmol/g protein to 0.82 mmol/g protein, and salt exerted an inhibition effect. In agreement with ATP and glycogen breakdown, metabolic profiling revealed that chopping and salting altered the metabolism in fatty acids and amino acids during rigor transformation. After rigor transformation, chopping with salt led to significant reduction in radical scavenging ability, accompanied by greater loss of sulfhydryl groups. Salt also promoted protein denaturation, evidenced by increased surface hydrophobicity and decreased intrinsic fluorescence. The ultrastructure of fish muscle after chopping or chopping with salt was similar between pre- and post-rigor stages. The abovementioned findings can provide valuable insight into the production of fish products.

The structure of FCGBP is formed as a disulfide-mediated homodimer between its C-terminal domains

Mucus in the colon is crucial for intestinal homeostasis by forming a barrier that separates microbes from the epithelium. This is achieved by the structural arrangement of the major mucus proteins, such as MUC2 and FCGBP, both of which are comprised of several von Willebrand D domains (vWD) and assemblies. Numerous disulfide bonds stabilise these domains, and intermolecular bonds generate multimers of MUC2. The oligomeric nature of FCGBP is not known. Human hFCGBP contains 13 vWD domains whereas mouse mFCGBP consists of only 7. We found unpaired cysteines in the vWD1 (human and mouse) and vWD5 (mouse)/vWD11 (human) assemblies which were not involved in disulfide bonds. However, the most C-terminal vWD domains, vWD7 (mouse)/vWD13 (human), formed disulfide-linked dimers. The intermolecular bond between C5284 and C5403 of human hFCGBP was observed by using mass spectrometry to generate the dimer. Cryo-EM structure analysis of recombinant mouse mFCGBP revealed a compact dimer with two symmetric intermolecular disulfide bonds between C2462 and C2581, corresponding to the dimerising cysteines in the human hFCGBP. This compact conformation involves interactions between the vWD assemblies, but although the domains involved at the interface are the same, the nature of the interactions differ. Mouse mFCGBP was also found to exist in a semi-extended conformation. These different interactions offer insights into the dynamic nature of the FCGBP homodimer.