Domain Structure Research Articles

Determination of the interactions of a schiff base with different targets via molecular docking and cytotoxic activity studies

The pyrimidine nucleus is a vital pharmacophore that exhibits excellent pharmacological activity. A Schiff base containing a pyrimidine nucleus was obtained in two steps. This compound was assessed on the human prostate (PC3) and liver (HepG2) cancer cell lines using the MTT method. The prepared compound 3 was determined to have a high cytotoxic effect towards prostate cancer with an IC50 value of 9.32 μM. Since experimental prostate and liver cancer studies were examined, the molecular docking study's target structures were determined accordingly. In molecular docking studies, compound 3 interacted in silico with the crystal structure of the human HER2 kinase domain (PDB Id: 3PP0), the crystal structure of VEGFR-2 (PDB Id: 4ASD), and the crystal structure of EGFR tyrosine kinase (PDB Id: 4HJO), respectively. As a result of these interactions, binding energy values were calculated, and binding modes were determined. Additional in vitro and in vivo experiments targeting other cancer cell lines will provide deeper insight into the anticancer spectrum of this compound and new studies on this compound will be planned in the following years. Furthermore, optimizing and studying such pyrimidine-based Schiff base compounds for improved selectivity and potency against prostate cancer is also considered to be valuable as it may increase the potential to capture potential drug candidates.

Exploring the optimal mechanical properties of triply periodic minimal surface structures for biomedical applications: A Numerical analysis

Currently, cutting-edge Additive Manufacturing techniques, such as Selective Laser Melting (SLM) and Electron Beam Melting (EBM), offer manufacturers a valuable avenue, especially in biomedical devices. These techniques produce intricate porous structures that draw inspiration from nature, boast biocompatibility, and effectively counter the adverse issues tied to solid implants, including stress shielding, cortical hypertrophy, and micromotions. Within the domain of such porous structures, Triply Periodic Minimal Surface (TPMS) configurations, specifically the Gyroid, Diamond, and Primitive designs, exhibit exceptional performance due to their bioinspired forms and remarkable mechanical and fatigue properties, outshining other porous counterparts. Consequently, they emerge as strong contenders for biomedical implants. However, assessing the mechanical properties and manufacturability of TPMS structures within the appropriate ranges of pore size, unit cell size, and porosity tailored for biomedical applications remains paramount. This study aims to scrutinize the mechanical behavior of Gyroid, Diamond, and Primitive structures in solid and sheet network iterations within the morphological parameter ranges suitable for tasks like cell seeding, vascularization, and osseointegration. A comparison with the mechanical characteristics of host bones is also undertaken. The methodology revolves around Finite Element Method (FEM) analysis. The six structures are originally modeled with unit cell sizes of 1, 1.5, 2, and 2.5 mm, and porosity levels ranging from 50% to 85%. Subsequently, mechanical properties, such as elasticity modulus and yield strength, are quantified through numerical analysis. The results underscore that implementing TPMS designs enables unit cell sizes between 1 and 2.5 mm, facilitating pore sizes within the suitable range of approximately 300–1500 μm for biomedical implants. Elasticity modulus spans from 1.5 to 33.8 GPa, while yield strength ranges around 20–304.5 MPa across the 50%–85% porosity spectrum. Generally, altering the unit cell size exhibits minimal impact on mechanical properties within the range above; however, it's noteworthy that smaller porosities correspond to heightened defects in additively manufactured structures. Thus, for an acceptable pore size range of 500–1000 μm and a minimum wall thickness of 150 μm, a prudent choice would involve adopting a 2.5 mm unit cell size.

The Creation of a Domain Structure Using Ultrashort Pulse NIR Laser Irradiation in the Bulk of MgO-Doped Lithium Tantalate

The fabrication of stable, tailored domain patterns in ferroelectric crystals has wide applications in optical and electronic industries. All-optical ferroelectric poling by pulse laser irradiation has been developed recently. In this work, we studied the creation of the domain structures in MgO-doped lithium tantalate by focused irradiation with a femtosecond near-infrared laser. Cherenkov-type second harmonic generation microscopy was used for domain imaging of the bulk. We have revealed the creation of enveloped domains around the induced microtracks under the action of the depolarization field. The domain growth is due to a pyroelectric field caused by a nonuniform temperature change. The domains in the bulk were revealed to have a three-ray star-shaped cross-section. It was shown that an increase in the field excess above the threshold leads to consequential changes in domain shape from a three-ray star to a triangular and a circular shape. The appearance of comb-like domains as a result of linear scanning was demonstrated. All effects were considered in terms of a kinetic approach, taking into account the domain wall motion by step generation and kink motion driven by excess of the local field over the threshold. The obtained knowledge is useful for the all-optical methods of domain engineering in ferroelectrics.

Genome-wide identification of the EIN3/EIL transcription factor family and their responses under abiotic stresses in Medicago sativa

BackgroundMedicago sativa, often referred to as the “king of forage”, is prized for its high content of protein, minerals, carbohydrates, and digestible nutrients. However, various abiotic stresses can hinder its growth and development, ultimately resulting in reduced yield and quality, including water deficiency, high salinity, and low temperature. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) transcription factors are key regulators in the ethylene signaling pathway in plants, playing crucial roles in development and in the response to abiotic stresses. Research on the EIN3/EIL gene family has been reported for several species, but minimal information is available for M. sativa.ResultsIn this study, we identified 10 MsEIN3/EIL genes from the M. sativa genome (cv. Zhongmu No.1), which were classified into three clades based on phylogenetic analysis. The conserved structural domains of the MsEIN3/EIL genes include motifs 1, 2, 3, 4, and 9. Gene duplication analyses suggest that segmental duplication (SD) has played a significant role in the expansion of the MsEIN3/EIL gene family throughout evolution. Analysis of the cis-acting elements in the promoters of MsEIN3/EIL genes indicates their potential to respond to various hormones and environmental stresses. We conducted a further analysis of the tissue-specific expression of the MsEIN3/EIL genes and assessed the gene expression profiles of MsEIN3/EIL under various stresses using transcriptome data, including cold, drought, salt and abscisic acid treatments. The results showed that MsEIL1, MsEIL4, and MsEIL5 may act as positive regulatory factors involved in M. sativa’s response to abiotic stress, providing important genetic resources for molecular design breeding.ConclusionThis study investigated MsEIN3/EIL genes in M. sativa and identified three candidate transcription factors involved in the regulation of abiotic stresses. These findings will offer valuable insights into uncovering the molecular mechanisms underlying various stress responses in M. sativa.

Duck circovirus regulates the expression of duck CLDN2 protein by activating the MAPK-ERK pathway to affect its adhesion and infection.

Although duck circovirus (DuCV) poses a widespread infection and a serious hazard to the duck industry, the molecular mechanisms underlying DuCV infection and transmission remain elusive. We initially demonstrated vertical transmission of DuCV through female breeding ducks by simulating natural infection. Furthermore, a differentially expressed membrane protein CLDN2 was identified on the DuCV-infected oviduct of female ducks, and its extracellular loop structural domains EL1 and EL2 were identified as the interaction sites of DuCV Cap proteins. Moreover, the binding of DuCV Cap to CLDN2 triggered the intracellular MAPK-ERK pathway and activated the downstream transcription factor SP5. Importantly, we demonstrated that intracellular Cap also interacts with SP5, leading to upregulation of CLDN2 transcription and facilitating enhanced adherence of DuCV to target tissue, thereby promoting viral infection and transmission. Our study sheds light on the molecular mechanisms underlying vertical transmission of DuCV, highlighting CLDN2 as a promising target for drug development against DuCV infection.

Densification mechanism and structural transformation in glass: molecular dynamic simulation

The structure of GeO2 glass is investigated via molecular dynamic simulation. The influence of pressure to the structure of GeO2 glass is due to the change of short-range order, network structure, domain structure and free volume regions. The obtained results show that the structure of GeO2 was formed by a continuous random network of basic structural units linking to each other via with corner-sharing, edge-sharing, face-sharing bond. At low pressure, the basic structural units are mainly linked via one bridge oxygen (the corner sharing bonds). As pressure increases, the fraction of edge sharing bonds (two bridge oxygen) increases meanwhile the fraction of corner sharing bonds significantly decrease. There is a slight increase with the fraction of face- sharing bonds (three bridge oxygen). The Ge-O bond distance is almost not dependent on pressure, meanwhile the Ge-Ge and O-O bond distances are significantly dependent on pressure. Under compression, the average coordination number of Ge tends to increase from fourfold (at ambient pressure) to six-fold (at high pressure). Moreover, structure of GeO2 glass has two-domain near 15 and 25 GPa. And at ambient pressure or high pressures, the struture of GeO2 glass has single domain. The dependence of the distribution of free volumes on pressure in GeO2 glass has been examined. The distribution of void radius has the Gaussian form and the position of the peak tend to shift to the left under compression.

A Novel Approach for Apical Periodontitis Prevention Through RIPK3 Inhibition Using Organic Flavonoids

Background: Apical periodontitis (AP) entails inflammatory bone resorption facilitated by the induction of necroptosis through receptor-interacting protein kinase 3 (RIPK3). Consequently, the inhibition of RIPK3 holds the potential for favorable effects in addressing AP. A comprehensive investigation, encompassing 44 flavonoids, was undertaken to identify potential inhibitors of RIPK3. Methods: The crystal structure of the RIPK3 catalytic domain (PDB ID: 7MON) underwent meticulous preparation through the removal of ligands and energy optimization. Overall, 44 flavonoids were examined in this study. Utilizing AutoDock 4.0, molecular docking analyses were performed to evaluate the binding energies within the active site of RIPK3 concerning the examined herbal isolates, with subsequent comparison to the results obtained from a positive control inhibitor. Furthermore, the BIOVIA Discovery Studio Visualizer played a crucial role in elucidating the interactions between the top-ranked flavonoids and the residues of RIPK3. Results: Five distinct flavonoids—orientin, rutin, vicenin-2, amentoflavone, and nicotiflorin—manifested notable inhibitory effects on RIPK3, boasting inhibition constant values at either the femtomolar or picomolar scale. Notably, the first three members of this set showcased superior binding affinity to the active site of RIPK3 compared to the reference compound. Conclusion: The proposition arises that flavonoid, particularly orientin, rutin, vicenin-2, amentoflavone, and nicotiflorin, stand as promising herbal isolates for the therapeutic management of AP.

Unusual photodynamic characteristics of the light-oxygen-voltage domain of phototropin linked to terrestrialadaptation of Klebsormidium nitens.

Phototropin (Phot), a blue light-sensing LOV domain protein, mediates blue light responses and is evolutionarily conserved across the green lineage. Klebsormidium nitens, a green terrestrial alga, presents a valuable opportunity to study adaptive responses from aquatic to land habitat transitions. We determined the crystal structure of Klebsormidium nitens Phot LOV1 domain (KnLOV1) in the dark and engineered different mutations (R60K, Q122N, and D33N) to modulate the lifetime of the photorecovery cycle. We observed unusual, slow recovery kinetics in the wild-type KnLOV1 domain (τ = 41 ± 3 min) compared to different mutants (R60K: τ = 2.0 ± 0.1 min, Q122N: τ = 1.7 ± 0.1 min, D33N: τ = 9.6 ± 0.1 min). Crystal structures of wild-type KnLOV1 and mutants revealed subtle but critical changes near the protein chromophore that is responsible for modulating protein dark recovery time. Our findings shed light on the unique structural and biochemical characteristics of the newly studied KnLOV1 and its evolutionary importance for phototropin-mediated physiology.

Genome-Wide Identification and Expression Analysis of GST Genes during Light-Induced Anthocyanin Biosynthesis in Mango (Mangifera indica L.).

Anthocyanins are important secondary metabolites contributing to the red coloration of fruits, the biosynthesis of which is significantly affected by light. Glutathione S-transferases (GSTs) play critical roles in the transport of anthocyanins from the cytosol to the vacuole. Despite their importance, GST genes in mango have not been extensively characterized. In this study, 62 mango GST genes were identified and further divided into six subfamilies. MiGSTs displayed high similarity in their exon/intron structure and motif and domain composition within the same subfamilies. The mango genome harbored eleven pairs of segmental gene duplications and ten sets of tandemly duplicated genes. Orthologous analysis identified twenty-nine, seven, thirty-four, and nineteen pairs of orthologous genes among mango MiGST genes and their counterparts in Arabidopsis, rice, citrus, and bayberry, respectively. Tissue-specific expression profiling highlighted tissue-specific expression patterns for MiGST genes. RNA-seq and qPCR analyses revealed elevated expression levels of seven MiGSTs including MiDHAR1, MiGSTU7, MiGSTU13, MiGSTU21, MiGSTF3, MiGSTF8, and MiGSTF9 during light-induced anthocyanin accumulation in mango. This study establishes a comprehensive genetic framework of MiGSTs in mango fruit and their potential roles in regulating anthocyanin accumulation, which is helpful in developing GST-derived molecular markers and speeding up the process of breeding new red-colored mango cultivars.

Effects of Magnetostatic Interactions in FeNi-Based Multilayered Magnetoimpedance Elements.

Multilayered [Cu(3 nm)/FeNi(100 nm)]5/Cu(150 nm)/FeNi(10 nm)/Cu(150 nm)/FeNi(10 nm)/Cu(150 nm)/[Cu(3 nm)/FeNi(100 nm)]5 structures were obtained by using the magnetron sputtering technique in the external in-plane magnetic field. From these, multilayer magnetoimpedance elements were fabricated in the shape of elongated stripes using the lift-off lithographic process. In order to obtain maximum magnetoimpedance (MI) sensitivity with respect to the external magnetic field, the short side of the rectangular element was oriented along the direction of the technological magnetic field applied during the multilayered structure deposition. MI sensitivity was defined as the change of the total impedance or its real part per unit of the magnetic field. The design of the elements (multilayered structure, shape of the element, etc.) contributed to the dynamic and static magnetic properties. The magnetostatic properties of the MI elements, including analysis of the magnetic domain structure, indicated the crucial importance of magnetostatic interactions between FeNi magnetic layers in the analyzed [Cu(3 nm)/FeNi(100 nm)]5 multilayers. In addition, the uniformity of the magnetic parameters was defined by the advanced technique of the local measurements of the ferromagnetic resonance field. Dynamic methods allowed investigation of the elements at different thicknesses by varying the frequency of the electromagnetic excitation. The maximum sensitivity of 40%/Oe with respect to the applied field in the range of the fields of 3 Oe to 5 Oe is promising for different applications.

The effect of magnesium impurities on the optical and spectral characteristics of calcium orthovanadate single crystals doped with chromium and manganese

The effect of magnesium co-doping on growth conditions, crystal composition, optical and spectral properties of manganese or chromium-doped Ca3(VO4)2 (CVO) crystal was studied. The single crystals were grown by the Czochralski method. Effective segregation coefficients of manganese and chromium in the CVO matrix with magnesium co-doping were calculated. A redistribution of the absorption lines intensities was observed in the absorption spectra of CVO:Mn:Mg and CVO:Cr:Mg. Low (15 K) temperature fluorescence measurements confirmed that co-doping CVO crystal with Mg ions leads to the redistribution of Mn ions concentration in different valence states, but does not cause changes in their spectral properties. In the presence of magnesium, additional annealing of the materials resulted in a slower reduction of the valence state of doping ions and a noticeable change in crystal coloration. All investigated impurities have practically no effect on the specific ferroelectric domain structure of CVO.

Research Progress into the Biological Functions of IFITM3

Interferon-induced transmembrane proteins (IFITMs) are upregulated by interferons. They are not only highly conserved in evolution but also structurally consistent and have almost identical structural domains and functional domains. They are all transmembrane proteins and have multiple heritable variations in genes. The IFITM protein family is closely related to a variety of biological functions, including antiviral immunity, tumor formation, bone metabolism, cell adhesion, differentiation, and intracellular signal transduction. The progress of the research on its structure and related functions, as represented by IFITM3, is reviewed.

Research on the Design of Academic Evaluation Standards of E-commerce Professional Group in Secondary Vocational Schools based on the Integration of Post-course Competition Certificate: Taking Short Video Courses as an Example

Given the subjective and one-sided problems existing in the current evaluation system of e-commerce courses in secondary vocational schools, this paper puts forward the implementation path of “four in one.” Through the integration of big data technology, knowledge graph technology and the PGSD ability analysis model, the evaluation graph is constructed, aiming at achieving comprehensiveness, adaptability, professionalism, scientific and objectivity of the evaluation. The evaluation graph includes a three-tier structure of evaluation system, knowledge domain and skill dimension, and systematically distributes weights to realize the development of multi-dimensional evaluation and personalized learning path.

Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase.

YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer in bacteria. YidC facilitates the insertion and folding of membrane proteins, both in conjunction with the Sec complex and independently. Additionally, YidC acts as a chaperone during the folding of proteins. Multiple investigations have conclusively shown that Gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level all-atom molecular dynamics (MD) simulations, we have carried out an in-depth investigation of the YidC protein originating from Gram-negative bacteria. This research sheds light on the significance of multiple domains of the YidC structure at a detailed molecular level by utilizing equilibrium MD simulations. Specifically, multiple models of YidC embedded in the lipid bilayer were constructed to characterize the critical role of the C2 loop and the periplasmic domain (PD) present in Gram-negative YidC, which is absent in its Gram-positive counterpart. Based on our results, the C2 loop plays a role in the overall stabilization of the protein, most notably in the transmembrane (TM) region, and it also has an allosteric influence on the PD region. We have found critical inter- and intradomain interactions that contribute to the stability of the protein and its function. Finally, our study provides a hypothetical Sec-independent insertion mechanism for Gram-negative bacterial YidC.

An inverse ferroelastic type phase transition and electric properties in bis(ethylenediammonium)tetrachlorozincate chloride crystal

Here we present TGA, DSC, dielectric studies and polarized microscopy observations of bis-ethylenediammonium tetrachlorozinc dichloride. In our studies, we found a high-temperature first-order phase transition at about 478/470 K for the heating/cooling cycle, respectively. The reversibility of the phase transition was detected by DSC and dielectric measurements and also by polarized microscopy observations. The appearance of a ferroelastic-type domain structure phase above the phase transition temperature indicates a reduction in symmetry during the heating cycle. The domain walls observed in the (100) plane are characteristic of a ferroelastic-type phase transition and can be classified as mmmF2/m Aizu species. The reduction in symmetry above the phase transition temperature allows us to classify the phase transition at 476 K as a "reverse" type. Dielectric studies in the frequency range of 40 Hz - 8 MHz allowed to estimate the activation energy for conduction and relaxation processes both with increasing and decreasing temperature. Activation energies obtained both from conductivity (σdc) measured in the temperature range from 445 to 485 K and relaxation process are practically the same both for low- and high-temperature phases as well. Taking into account the results for all directions (a, b, c) and all temperatures, conductivity is 10−7 – 10−4 S/m and is within the range characteristic for semiconductors (10−8 – 106) S/m. The conductivity and relaxation activation energies determined for the directions (a, b, c) have values in the range from 0.58 to 3.7 eV, which are also within the range characteristic for semiconductors. Electrical properties show clearly anisotropic character of the studied material.

CircSEC24B activates autophagy and induces chemoresistance of colorectal cancer via OTUB1-mediated deubiquitination of SRPX2

Circular RNAs (circRNAs) are a type of regulatory RNA that feature covalently closed single-stranded loops. Evidence suggested that circRNAs play important roles in the progression and development of various cancers. However, the impact of circRNA on autophagy-mediated progression of colorectal cancer (CRC) remains unclear. The objective of this project was to investigate the influence of circSEC24B on autophagy and its underlying mechanisms in CRC. To validate the presence and circular structure of circSEC24B in CRC cells and tissues, PCR and Sanger sequencing techniques were employed. Drug resistance and invasive phenotype of CRC cells were evaluated using CCK8, transwell, and Edu assays. Gain- and loss-of-function experiments were conducted to assess the effects of circSEC24B and its protein partner on the growth, invasion, and metastasis of CRC cells in vitro and in vivo. Interactions between circSEC24B, OTUB1, and SRPX2 were analyzed through immunofluorescence, RNA-pulldown, and RIP assays. Mass spectrometry analysis was used to identify potential binding proteins of circRNA in CRC cells. Vectors were constructed to investigate the specific structural domain of the deubiquitinating enzyme OTUB1 that binds to circSEC24B. Results showed that circSEC24B expression was increased in CRC tissues and cell lines, and it enhanced CRC cell proliferation and autophagy levels. Mechanistically, circSEC24B promoted CRC cell proliferation by regulating the protein stability of SRPX2. Specifically, circSEC24B acted as a scaffold, facilitating the binding of OTUB1 to SRPX2 and thereby enhancing its protein stability. Additionally, evidence suggested that OTUB1 regulated SRPX2 expression through an acetylation-dependent mechanism. In conclusion, this study demonstrated that circSEC24B activated autophagy and induced chemoresistance in CRC by promoting the deubiquitination of SRPX2, mediated by the deubiquitinating enzyme OTUB1.

Growth and thickness effect of -oriented ternary 0.06Pb(Mn1/3Nb2/3)O3-0.94Pb(Zr0.48Ti0.52)O3 ferroelectric thin films on silicon substrate by RF sputtering

The development of advanced piezoelectric thin films with large piezoelectric response on silicon substrate is a crucial technology for piezoelectric microelectromechanical systems applications. In this work, high-quality <100>-oriented 0.06Pb(Mn1/3Nb2/3)O3-0.94Pb(Zr0.48Ti0.52)O3 (PMN-PZT) thin films were grown on the Pt/Ti/SiO2/Si substrate by sputtering. X-ray diffraction, scanning electron microscopy, and piezoresponse force microscopy were utilized to characterize the phase, morphologies, and domain structures. The growth parameters were optimized and thickness-dependent electrical properties were established. Well-crystalized micron-thick PMN-PZT films with high remnant polarization of 49 μC/cm2 and giant piezoelectric coefficient (d33) up to 484 pC/N (about twice of the polycrystalline PMN-PZT thin film and thrice of the Pb(Zr0.52Ti0.48)O3 thin film) were obtained. The excellent electrical properties make it highly advantageous for applications in MEMS devices.

Electromagnetic modeling and analysis based on multilayer domain structure for GMI behavior in high frequency

Existing theoretical models on the frequency dependence of the magnetoimpedance (MI) in ferromagnetic microwires primarily describe the MI phenomenon at the limiting cases of lower MHz (<several hundred MHz) or higher GHz (>several GHz) ranges. However, in the intermediate region between these two ranges, known as the transition region, MI curves undergo complex transformations. These transformations have been documented in the literature, but their underlying causes remain poorly understood. Unambiguous knowledge of the domain structure and its correlation with MI properties is essential for elucidating this behavior. In this study, we have, for the first time, observed the inner core magnetic structure of Co-based microwires and revealed its relationship with the high-frequency MI effect. A distinct magnetic structure comprising longitudinal domains in the inner core (IC), circular domains in the outer shell (OS), and a transition region (TR) has been identified. This structure originates from compositional gradients and residual stresses during microwire fabrication. The IC/TR/OS structure manifests in the complex transformations of the MI behavior, exhibiting a turning point at GHz frequencies before the characteristic double MI peak. We developed a multilayer planar model that considers this more realistic magnetic structure, including the TR layer. This model successfully reproduces the key features of the MI curves and provides deeper insights into the high-frequency MI phenomenon. Our findings pave the way for optimizing the sensing capabilities of Co-based ferromagnetic microwires and demonstrate the potential of using high-frequency MI measurements to map their magnetic microstructures.

First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis.

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function ofthe well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9-5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.

Crystal structure of Alzheimer's disease phospholipase D3 provides a molecular basis for understanding its normal and pathological functions.

Human 5'-3' exonuclease PLD3, a member of the phospholipase D family of enzymes, has been validated as a therapeutic target for treating Alzheimer's disease. Here, we have determined the crystal structure of the luminal domain of the enzyme at 2.3 Å resolution, revealing a bilobal structure with a catalytic site located between the lobes. We then compared the structure with published crystal structures of other human PLD family members which revealed that a number of catalytic and lipid recognition residues, previously shown to be key for phospholipase activity, are not conserved or, are absent. This led us to test whether the enzyme is actually a phospholipase. We could not measure any phospholipase activity but the enzyme shows robust nuclease activity. Finally, we have mapped key single nucleotide polymorphisms onto the structure which reveals plausible reasons as to why they have an impact on Alzheimer's disease.