Structural Insights Research Articles

Synthesis and Characterization of NiFe₂O₄ Nanoparticles: Structural and Optical Insights

Synthesis and Characterization of NiFe₂O₄ Nanoparticles: Structural and Optical Insights

Structural insights into 1,4-bis(neopentyloxy)pillar[5]arene and the pyridine host–guest system

The crystal structure of 1,4-bis(neopentyloxy)pillar[5]arene, C95H140N2O10 (TbuP), featuring two encapsulated pyridine molecules, reveals significant host–guest interactions. Interestingly, the pyridine guests are positioned near the neopentyloxy substituents instead of the electron-rich aromatic core of the pillar[5]arene. This spatial arrangement suggests a preference for the pyridine molecules to engage with the aliphatic regions of the host. Detailed analysis of the structural characteristics of this host–guest system (TbuP·2Py), as well as its packing pattern within the crystal network, is presented and discussed.

The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase

The dUTPase is a key DNA repair enzyme in Mycobacterium tuberculosis, and it may serve as a novel promising anti-tuberculosis target. Stl repressor from Staphylococcus aureus was shown to bind to and inhibit dUTPases from various sources, and its expression in mycobacterial cells interfered with cell growth. To fine-tune and optimize Stl-induced inhibition of mycobacterial dUTPase, we aimed to decipher the molecular details of this interaction. Structural background of the complex between dUTPase and a truncated Stl lacking the repressor C-terminal homodimerization domain has been described, however, the effects of this truncation of Stl on enzyme binding and inhibition are still not known. Using several independent biophysical, structural and enzyme kinetic methods, here we show that lack of the repressor homodimerization domain strongly perturbs both enzyme binding and inhibition. We also investigated the role of a mycobacteria-specific loop in the Stl-interaction. Our results show that removal of this loop leads to a ten-fold increase in the apparent inhibition constant of Stl. We present a high-resolution three-dimensional structure of mycobacterial dUTPase lacking the genus-specific loop for structural insight. Our present data suggest that potent inhibition of mycobacterial dUTPase by Stl requires the wild-type full-length protein context.

Structural insights into the agonist selectivity of the adenosine A3 receptor

Adenosine receptors play pivotal roles in physiological processes. Adenosine A3 receptor (A3R), the most recently identified adenosine receptor, is expressed in various tissues, exhibiting important roles in neuron, heart, and immune cells, and is often overexpressed in tumors, highlighting the therapeutic potential of A3R-selective agents. Recently, we identified RNA-derived N6-methyladenosine (m6A) as an endogenous agonist for A3R, suggesting the relationship between RNA-derived modified adenosine and A3R. Despite extensive studies on the other adenosine receptors, the selectivity mechanism of A3R, especially for A3R-selective agonists such as m6A and namodenoson, remained elusive. Here, we identify tRNA-derived N6-isopentenyl adenosine (i6A) as an A3R-selective ligand via screening of modified nucleosides against the adenosine receptors. Like m6A, i6A is found in the human body and may be an endogenous A3R ligand. Our cryo-EM analyses elucidate the A3R-Gi complexes bound to adenosine, 5’-N-ethylcarboxamidoadenosine (NECA), m6A, i6A, and namodenoson at overall resolutions of 3.27 Å (adenosine), 2.86 Å (NECA), 3.19 Å (m6A), 3.28 Å (i6A), and 3.20 Å (namodenoson), suggesting the selectivity and activation mechanism of A3R. We further conduct structure-guided engineering of m6A-insensitive A3R, which may aid future research targeting m6A and A3R, providing a molecular basis for future drug discovery.

A Polyphenol Decorated Triplex Hybrid Biomaterial: Structure-Function, Release Profiles, Sorption, and Antipathogenic Effects.

Herein, nonwoven alkali modified flax substrates were coated with incremental levels of chitosan, followed by immobilization of tannic acid, via a facile "dip-coating" strategy to yield a unique hierarchal "triplex" hybrid biomaterial, denoted as "THB". The characterization of the physicochemical properties of THB employed complementary spectroscopic (IR, Raman, and NMR) techniques, which support the role of hydrogen bonding and electrostatic interactions between the components: chitosan as the secondary biopolymer coating and the tertiary adsorbed polyphenols. XRD and SEM techniques provide further structural insight that confirms the unique semicrystalline nature and porous hierarchal structure of the biocomposite. The THBs present a polyphenol kinetic release profile that follows the Korsmeyer-Peppas model that concurs with Fickian diffusion for heterogeneous polymer systems. Furthermore, these systems demonstrate a tailored solvent uptake capacity (up to 4 g/g) in aqueous PBS media. Antipathogenic activity tests revealed 95% elimination of pathogens (E. coli, S. aureus, and C. albicans) at a dose of 50 mg for the THB system. The trend in the structure-property relationships for the THB systems indicates synergistic effects of electrostatic multiform interactions between protonated chitosan and the polyphenol units. Herein, we report the first example of a unique hierarchal biomaterial via a facile design strategy for diversiform roles as responsive adsorbents for environmental remediation to biomedical applications (e.g., controlled release, topical administration, or antimicrobial surface coatings).

StaPep: An Open-Source Toolkit for Structure Prediction, Feature Extraction, and Rational Design of Hydrocarbon-Stapled Peptides.

All-hydrocarbon stapled peptides, with their covalent side-chain constraints, provide enhanced proteolytic stability and membrane permeability, making them superior to linear peptides. However, tools for extracting structural and physicochemical descriptors to predict the properties of hydrocarbon-stapled peptides are lacking. To address this, we present StaPep, a Python-based toolkit for generating 3D structures and calculating 21 features for hydrocarbon-stapled peptides. StaPep supports peptides containing two non-standard amino acids (norleucine and 2-aminoisobutyric acid) and six non-natural anchoring residues (S3, S5, S8, R3, R5, and R8), with customization options for other non-standard amino acids. We showcase StaPep's utility through three case studies. The first generates 3D structures of these peptides with a mean RMSD of 1.62 ± 0.86, offering essential structural insights for drug design and biological activity prediction. The second develops machine learning models based on calculated molecular features to differentiate between membrane-permeable and non-permeable stapled peptides, achieving an AUC of 0.93. The third constructs regression models to predict the antimicrobial activity of stapled peptides against Escherichia coli, with a Pearson correlation of 0.84. StaPep's pipeline spans data retrieval, structure generation, feature calculation, and machine learning modeling for hydrocarbon-stapled peptides. The source codes and data set are freely available on Github: https://github.com/dahuilangda/stapep_package.

Green Synthesis, Structural Insights, and Antimicrobial Potential of Zinc Oxide Nanoparticles Synthesized via Sustainable Method

Background: Green synthesized nanoparticles have gained wide interest in today’s world due to their inherent features like rapidity, eco-friendliness, and costeffectiveness [4].In this study, zinc oxide (ZnO) nanoparticles were synthesized using an aqueous extract of Ixora coccinea leaves. X-ray diffraction (XRD) and Transmission Electron Microscopy (TEM) studies were used to analyze the structural and morphological properties of prepared Zinc Oxide nanoparticles. Methods: The sol-gel method of synthesis via the green route was introduced to synthesize pure Zinc oxide nanoparticles. Silver-doped Zinc Oxide nanoparticles were also prepared using the same method Result: The XRD studies showed the crystalline nature and revealed the purity of Zinc Oxide nanoparticles. The specific functional groups responsible for reduction, stabilization, and capping agents present in the nanoparticles were examined using Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy. The bacterial destruction was better for ZnO nanoparticles than reported for plant extracts and standard drugs. Conclusion: This study proves that Zinc Oxide nanoparticles contain natural antimicrobial agents through green synthesis, which may serve to produce drugs for antimicrobial therapeutics.

Structural insights into human ELAC2 as a tRNA 3' processing enzyme.

Human elaC ribonuclease Z 2 (ELAC2) removes the 3' trailer of precursor transfer ribonucleic acid (pre-tRNA). Mutations in ELAC2 are highly associated with the development of prostate cancer and hypertrophic cardiomyopathy. However, the catalytic mechanism of ELAC2 remains unclear. We determined the cryogenic electron microscopy structures of human ELAC2 in various states, including the apo, pre-tRNA-bound and tRNA-bound states, which enabled us to identify the structural basis for its binding to pre-tRNA and cleavage of the 3' trailer. Notably, conformational rearrangement of the C-terminal helix was related to feeding of the 3' trailer into the cleavage site, possibly explaining why its mutations are associated with disease. We further used biochemical assays to analyse the structural effects of disease-related mutations of human ELAC2. Collectively, our data provide a comprehensive structural basis for how ELAC2 recruits pre-tRNA via its flexible arm domain and guides the 3' trailer of pre-tRNA into the active centre for cleavage by its C-terminal helix.

Exploring structural and biological insights of TEAD through rational design and synthesis of niflumic acid derivatives

Transcriptional enhanced associate domain (TEAD) transcription factors undergo auto-palmitoylation, which is critical to mediate their function and maintain stability. Targeting the palmitate binding pocket of TEAD holds considerable promise for drug discovery, and it can be characterised into three components: a conserved cysteine, a hydrophobic main pocket, and a hydrophilic side pocket. Endogenous palmitate and several known TEAD inhibitors interact with the cysteine and hydrophobic residues in the deep hydrophobic pocket. We anticipate that precise targeting of the polar side pocket could facilitate the discovery of inhibitors with enhanced potencies and properties. Herein, we selected niflumic acid as the core scaffold suitable for targeting the three characteristic components of TEAD palmitate pocket. Reversible and irreversible compounds with substituents capable of directing each part of the palmitate pocket were designed. The newly synthesised compounds inhibited the palmitoylation and transcriptional activity of TEAD and elicited growth-inhibitory effects against several carcinomas, including mesothelioma.

Emerging Trends in Quinoxaline‐based Analogs as Protein Kinase Inhibitors: Structural Developments and SAR Insights

Cancer remains a leading cause of mortality and has been recognized as a significant global health concern. Although numerous effective anticancer agents are available; most of the current drugs lack specificity, leading to common side‐effects associated with chemotherapy. Recent research, however, offers promise for developing more targeted and safer anticancer therapies through protein kinase inhibition. Quinoxaline derivatives represent a notable class of heterocyclic compounds. The extensive spectrum of biological activities demonstrated by quinoxalines has garnered substantial research interest. Quinoxaline and its derivatives have emerged as a novel class of chemotherapeutic agents with significant activity against various tumors through protein kinase inhibition. This review aims to elucidate recent advancements in the quinoxaline derivatives targeting protein kinase along with structural developments and structure‐activity relationships associated with these compounds.

Structural insights, spectroscopic investigation, topological and z-scan analysis of 2-amino-4,6-dimethoxypyrimidine 4-aminobenzoic acid: experimental and theoretical approach

Structural insights, spectroscopic investigation, topological and z-scan analysis of 2-amino-4,6-dimethoxypyrimidine 4-aminobenzoic acid: experimental and theoretical approach

Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists.

This study explores the intricacies of dopamine receptor-ligand interactions, focusing on the D1R and D5R subtypes. Using molecular modeling techniques, we investigated the binding of the pan-agonist rotigotine, revealing a universal binding mode at the orthosteric binding pocket. Additionally, we analyze the stability of antagonist-receptor complexes with SKF83566 and SCH23390. By examining the impact of specific mutations on ligand-receptor interactions through computational simulations and thermostability assays, we gain insights into binding stability. Our research also delves into the structural and energetic aspects of antagonist binding to D1R and D5R in their inactive states. These findings enhance our understanding of dopamine receptor pharmacology and hold promise for drug development in central nervous system disorders, opening doors to future research and innovation in this field.

Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1

Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signalling initiation, which requires binding of BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure, BL was bound to the hydrophobic cavity formed by the transmembrane domain, and triggered local conformational changes. Together, our data provide additional insights into the ABC transporter-mediated BR export.

Structural insights into Influenza A virus RNA polymerase PB1 binding to nuclear import host factor RanBP5

Structural insights into Influenza A virus RNA polymerase PB1 binding to nuclear import host factor RanBP5

Structural and catalytic properties of histidyl-tRNA synthetase: A potential drug target against leishmaniasis

Visceral leishmaniasis is caused by Leishmania donovani which affects the poorer sections of society, and despite the global spread, effective treatment is unavailable. The current study investigates the potential of leishmanial histidyl-tRNA synthetase (LdHisRS) as a drug target. LdHisRS delineated more closeness to other protozoan parasites than its mammalian counterparts and contained relevant differences in the active site residues. The important ATP-binding residues were mutated to alanine and all the proteins, including human HisRS, were purified to homogeneity. LdHisRS exhibited a dimeric state in solution and showed maximal amino acid activation activity in physiological conditions. It also demonstrated a greater affinity for substrate over cofactor, while magnesium and potassium enhanced its activity better than other tested metal ions. Comp-7 m, a benzothiazolo-coumarin derivative, proved to be specific inhibitor of LdHisRS with competitive mode of inhibition for ATP whereas it displayed lower binding affinity towards mutants. LdHisRS majorly contained α-helices and most of the aromatic residues were present in its hydrophobic core. Additionally, Comp-7 m superimposed on ATP adenine ring during docking analysis and LdHisRS-ligand complexes had comparable stability as well as rigidity in molecular dynamics simulation. We thus provide structural and functional insights of LdHisRS which can be useful for devising antileishmanials.

Impact of pH-Dependent Dynamics of Human Serum Proteins on Dialysis Membranes: Cryptographic Structure Assessment, Synchrotron Imaging of Membrane-Protein Adsorption, and Molecular Docking Studies

Proteins are fundamental to biochemical processes and critical in hemodialysis. This study investigates the impact of pH on human serum albumin (HSA), fibrinogen (FB), and transferrin (TRF) interactions with polyarylethersulfone (PAES) hemodialysis membranes. A multi-method approach was utilized, including protein crystallography for structural insights, hydration layer analysis to explore solvation and interaction potentials, molecular docking using AutoDock 4.0 for binding affinity simulations, and in-situ X-ray synchrotron SR-μCT imaging to observe protein deposition dynamics.Molecular docking revealed that PAES demonstrated superior binding energies and interaction patterns with FB and TRF compared to cellulose triacetate (CTA), facilitated by specific hydrogen bonding within a water shell. CTA displayed weaker, hydration-sensitive interactions varying with pH. Imaging studies indicated that FB showed higher adsorption at pH 6 than at pH 7.2, predominantly in the middle membrane regions. Similarly, HSA and TRF exhibited increased adsorption at pH 6, suggesting a stronger affinity under acidic conditions. Mixed protein solutions also indicated higher adsorption at pH 6, emphasizing an increased risk of membrane fouling.These findings highlight the crucial role of pH in modulating protein-membrane interactions and enhancing the efficacy of hemodialysis. A deeper understanding of hydration environments and their effects on protein binding affinities provides valuable insights for optimizing membrane design and performance. Clinically, this research suggests that fine-tuning pH during hemodialysis could mitigate protein fouling on membranes, thereby improving procedural efficiency and potentially leading to better patient outcomes through enhanced dialysis effectiveness.

Strategies for Top-Down Hydrogen Deuterium Exchange-Mass Spectrometry: A Mini Review and Perspective.

Hydrogen deuterium-exchange mass spectrometry (HDX-MS) is commonly used in the study of protein dynamics and protein interactions. By measuring the isotopic exchange of backbone amide hydrogens in solution, HDX-MS offers valuable structural insights into challenging biological systems. Traditional HDX-MS approaches utilize bottom-up (BU) proteomics, in which deuterated proteins are digested before MS analysis. BU-HDX enables the characterization of proteins with various sizes in simple protein mixtures or complex biological samples such as cell lysates. However, BU methods are inherently limited by the inability to resolve protein sub-populations arising from different protein conformations, such as those arising from post-translational modifications (PTMs). Alternatively, top-down (TD) HDX-MS detects the global deuterium uptake at the intact proteoform level, allowing direct probing of structural changes due to protein-protein interactions, PTMs, or conformational changes. Combining TD-HDX-MS with electron-based fragmentation techniques, such as electron capture dissociation (ECD) and electron transfer dissociation (ETD), has demonstrated the feasibility of studying intact protein interactions with amino acid-level resolution. Here, we present a brief overview of methodologies, limitations, and applications of TD-HDX-MS using direct infusion techniques and LC-based approaches. Furthermore, we conclude with a perspective on the future directions for TD-HDX-MS.

3D structural insights into the effect of N-glycosylation in human chitotriosidase variant G102S

BackgroundN-glycosylation is a key post-translational modification critical for protein function and stability. Chitotriosidase-1 (CHIT1), belonging to glycoside hydrolase family 18, is clinically utilized as a biomarker of Gaucher disease. A G102S variant is common in some populations, but the implications of this missense mutation on CHIT1 function and in disease pathology are unknown. We have investigated the effects of the G102S mutation on the N-glycosylation, structure, and activity of CHIT1. MethodsThree recombinant CHIT1 proteins, wild-type (WT), G102S, and N100Q + G102S double mutants, were expressed, purified, and analyzed for glycosylation using SDS-PAGE, MALDI-MS, PNGase F treatment, and lectin blotting. NMR and LC-MS/MS were employed to characterize glycan structures. Enzymatic assays and molecular dynamics simulations were used to assess the effects of mutations on CHIT1 function and dynamics. ResultsThe G102S mutation introduced a new N-glycosylation site at N100, confirmed by SDS-PAGE and MALDI-MS, and the composition of the N-glycan structures was verified by lectin blotting, NMR, and MS. Both G102S and N100Q + G102S proteins exhibited reduced catalytic efficiency compared to WT. Molecular dynamics simulations suggested that G102S mutation induces significant structural changes and reduces stability, particularly without N-glycan, likely impairing substrate binding and enzymatic activity. ConclusionOur findings indicate that the common G102S mutation affects the structure and function of CHIT1, partially by introducing a new N-glycosylation site. They provide a foundation for further research on the impact of N-glycosylation on its hydrolase activity and structural dynamics, with potential implications for understanding the role of CHIT1 in Gaucher disease.

Vanadium-based MXenes: synthesis, structural insights, and electrochemical properties for Zn-ion battery applications: a beginner’s guide

Vanadium-based MXenes: synthesis, structural insights, and electrochemical properties for Zn-ion battery applications: a beginner’s guide

The Inhibition of Serum Amyloid A Protein Aggregation by a Five-Residue Peptidomimetic: Structural and Morphological Insights

The Inhibition of Serum Amyloid A Protein Aggregation by a Five-Residue Peptidomimetic: Structural and Morphological Insights