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1.
Article in English | MEDLINE | ID: mdl-38949083

ABSTRACT

Mixed metal oxides (MMOs) are a promising class of electrocatalysts for the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). Despite their importance for sustainable energy schemes, our understanding of relevant reaction pathways, catalytically active sites, and synergistic effects is rather limited. Here, we applied synchrotron-based X-ray absorption spectroscopy (XAS) to explore the evolution of the amorphous Co-Cu-W MMO electrocatalyst, shown previously to be an efficient bifunctional OER and HER catalyst for water splitting. Ex situ XAS measurements provided structural environments and the oxidation state of the metals involved, revealing Co2+ (octahedral), Cu+/2+ (tetrahedral/square-planar), and W6+ (octahedral) centers. Operando XAS investigations, including X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), elucidated the dynamic structural transformations of Co, Cu, and W metal centers during the OER and HER. The experimental results indicate that Co3+ and Cu0 are the active catalytic sites involved in the OER and HER, respectively, while Cu2+ and W6+ play crucial roles as structure stabilizers, suggesting strong synergistic interactions within the Co-Cu-W MMO system. These results, combined with the Tafel slope analysis, revealed that the bottleneck intermediate during the OER is Co3+ hydroperoxide, whose formation is accompanied by changes in the Cu-O bond lengths, pointing to a possible synergistic effect between Co and Cu ions. Our study reveals important structural effects taking place during MMO-driven OER/HER electrocatalysis and provides essential experimental insights into the complex catalytic mechanism of emerging noble-metal-free MMO electrocatalysts for full water splitting.

2.
Front Oncol ; 14: 1420213, 2024.
Article in English | MEDLINE | ID: mdl-38952551

ABSTRACT

Purpose: To construct and validate a computed tomography (CT) radiomics model for differentiating lung neuroendocrine neoplasm (LNEN) from lung adenocarcinoma (LADC) manifesting as a peripheral solid nodule (PSN) to aid in early clinical decision-making. Methods: A total of 445 patients with pathologically confirmed LNEN and LADC from June 2016 to July 2023 were retrospectively included from five medical centers. Those patients were split into the training set (n = 316; 158 LNEN) and external test set (n = 129; 43 LNEN), the former including the cross-validation (CV) training set and CV test set using ten-fold CV. The support vector machine (SVM) classifier was used to develop the semantic, radiomics and merged models. The diagnostic performances were evaluated by the area under the receiver operating characteristic curve (AUC) and compared by Delong test. Preoperative neuron-specific enolase (NSE) levels were collected as a clinical predictor. Results: In the training set, the AUCs of the radiomics model (0.878 [95% CI: 0.836, 0.915]) and merged model (0.884 [95% CI: 0.844, 0.919]) significantly outperformed the semantic model (0.718 [95% CI: 0.663, 0.769], p both<.001). In the external test set, the AUCs of the radiomics model (0.787 [95% CI: 0.696, 0.871]), merged model (0.807 [95%CI: 0.720, 0.889]) and semantic model (0.729 [95% CI: 0.631, 0.811]) did not exhibit statistical differences. The radiomics model outperformed NSE in sensitivity in the training set (85.3% vs 20.0%; p <.001) and external test set (88.9% vs 40.7%; p = .002). Conclusion: The CT radiomics model could non-invasively, effectively and sensitively predict LNEN and LADC presenting as a PSN to assist in treatment strategy selection.

3.
Front Immunol ; 15: 1363156, 2024.
Article in English | MEDLINE | ID: mdl-38953028

ABSTRACT

Introduction: Human Herpesvirus 6B (HHV-6B) impedes host immune responses by downregulating class I MHC molecules (MHC-I), hindering antigen presentation to CD8+ T cells. Downregulation of MHC-I disengages inhibitory receptors on natural killer (NK) cells, resulting in activation and killing of the target cell if NK cell activating receptors such as NKG2D have engaged stress ligands upregulated on the target cells. Previous work has shown that HHV-6B downregulates three MHC-like stress ligands MICB, ULBP1, and ULBP3, which are recognized by NKG2D. The U20 glycoprotein of the related virus HHV-6A has been implicated in the downregulation of ULBP1, but the precise mechanism remains undetermined. Methods: We set out to investigate the role of HHV-6B U20 in modulating NK cell activity. We used HHV-6B U20 expressed as a recombinant protein or transduced into target cells, as well as HHV-6B infection, to investigate binding interactions with NK cell ligands and receptors and to assess effects on NK cell activation. Small-angle X-ray scattering was used to align molecular models derived from machine-learning approaches. Results: We demonstrate that U20 binds directly to ULBP1 with sub-micromolar affinity. Transduction of U20 decreases NKG2D binding to ULBP1 at the cell surface but does not decrease ULBP1 protein levels, either at the cell surface or in toto. HHV-6B infection and soluble U20 have the same effect. Transduction of U20 blocks NK cell activation in response to cell-surface ULBP1. Structural modeling of the U20 - ULBP1 complex indicates some similarities to the m152-RAE1γ complex.


Subject(s)
GPI-Linked Proteins , Herpesvirus 6, Human , Killer Cells, Natural , Lymphocyte Activation , NK Cell Lectin-Like Receptor Subfamily K , Humans , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , Herpesvirus 6, Human/immunology , GPI-Linked Proteins/metabolism , GPI-Linked Proteins/immunology , NK Cell Lectin-Like Receptor Subfamily K/metabolism , NK Cell Lectin-Like Receptor Subfamily K/immunology , Lymphocyte Activation/immunology , Protein Binding , Viral Proteins/immunology , Viral Proteins/metabolism , Glycoproteins/immunology , Glycoproteins/metabolism , Intracellular Signaling Peptides and Proteins
5.
Abdom Radiol (NY) ; 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38954000

ABSTRACT

PURPOSE: To evaluate the diagnostic performance of bowel wall enhancement for diagnosing concomitant bowel ischemia in patients with parietal pneumatosis (PI) diagnosed at abdominal CT. MATERIALS AND METHODS: From January 1, 2012 to December 31, 2021, 226 consecutive patients who presented with PI on abdominal CT from any bowel segment were included. Variables at the time of the CT were retrospectively extracted from medical charts. CT examinations were blindly analyzed by two independent radiologists. The third reader classified all disagreement of bowel enhancement in three categories: (1) normal bowel enhancement; (2) doubtful bowel wall enhancement; (3) absent bowel wall enhancement. Multivariable logistic regression analysis was performed. Concomitant bowel ischemia was defined as requirement of bowel resection specifically due to ischemic lesion in operated patients and death from bowel ischemia in non-operated patients. RESULTS: Overall, 78/226 (35%) patients had PI associated with concomitant bowel ischemia. At multivariate analysis, Only absence or doubtful bowel wall enhancement was associated with concomitant bowel ischemia (OR = 167.73 95%CI [23.39-4349.81], P < 0,001) and acute mesenteric ischemia associated with PP (OR = 67.94; 95%CI [5.18-3262.36], P < 0.009). Among the 82 patients who underwent a laparotomy for suspected bowel ischemia, rate of non-therapeutic laparotomy increased from 15/59 (25%), 2/6 (50%) and 16/17 (94%) when bowel wall enhancement was absent, doubtful and normal respectively. CONCLUSION: Absence of enhancement of the bowel wall is the primary feature associated with concomitant bowel ischemia. It should be carefully assessed when PI is detected to avoid non-therapeutic laparotomy.

6.
Proc Natl Acad Sci U S A ; 121(28): e2321193121, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38954549

ABSTRACT

Iron antimonide (FeSb2) has been investigated for decades due to its puzzling electronic properties. It undergoes the temperature-controlled transition from an insulator to an ill-defined metal, with a cross-over from diamagnetism to paramagnetism. Extensive efforts have been made to uncover the underlying mechanism, but a consensus has yet to be reached. While macroscopic transport and magnetic measurements can be explained by different theoretical proposals, the essential spectroscopic evidence required to distinguish the physical origin is missing. In this paper, through the use of X-ray absorption spectroscopy and atomic multiplet simulations, we have observed the mixed spin states of 3d 6 configuration in FeSb2. Furthermore, we reveal that the enhancement of the conductivity, whether induced by temperature or doping, is characterized by populating the high-spin state from the low-spin state. Our work constitutes vital spectroscopic evidence that the electrical/magnetical transition in FeSb2 is directly associated with the spin-state excitation.

7.
Eur Spine J ; 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38955868

ABSTRACT

OBJECTIVE: This study aimed to develop and validate a predictive model for osteoporotic vertebral fractures (OVFs) risk by integrating demographic, bone mineral density (BMD), CT imaging, and deep learning radiomics features from CT images. METHODS: A total of 169 osteoporosis-diagnosed patients from three hospitals were randomly split into OVFs (n = 77) and Non-OVFs (n = 92) groups for training (n = 135) and test (n = 34). Demographic data, BMD, and CT imaging details were collected. Deep transfer learning (DTL) using ResNet-50 and radiomics features were fused, with the best model chosen via logistic regression. Cox proportional hazards models identified clinical factors. Three models were constructed: clinical, radiomics-DTL, and fusion (clinical-radiomics-DTL). Performance was assessed using AUC, C-index, Kaplan-Meier, and calibration curves. The best model was depicted as a nomogram, and clinical utility was evaluated using decision curve analysis (DCA). RESULTS: BMD, CT values of paravertebral muscles (PVM), and paravertebral muscles' cross-sectional area (CSA) significantly differed between OVFs and Non-OVFs groups (P < 0.05). No significant differences were found between training and test cohort. Multivariate Cox models identified BMD, CT values of PVM, and CSAPS reduction as independent OVFs risk factors (P < 0.05). The fusion model exhibited the highest predictive performance (C-index: 0.839 in training, 0.795 in test). DCA confirmed the nomogram's utility in OVFs risk prediction. CONCLUSION: This study presents a robust predictive model for OVFs risk, integrating BMD, CT data, and radiomics-DTL features, offering high sensitivity and specificity. The model's visualizations can inform OVFs prevention and treatment strategies.

8.
Orthop Rev (Pavia) ; 16: 120304, 2024.
Article in English | MEDLINE | ID: mdl-38957743

ABSTRACT

Background: Dega osteotomy is becoming more widely used for the treatment of developmental dysplasia of the hip (DDH). Objective: A thorough description of this procedure is needed as many of the technical aspects are not fully defined. Moreover, more follow-up series are also needed to evaluate its outcomes. Methods: In this study, we gave a detailed anatomic description for this procedure and also presented our experience as a retrospective radiographic and case-note study. We examined the clinical and radiographic records of 44 patients (48 hips) with varying degrees of DDH. Results: The average age of the patients was 2 months and 7 months while the average follow up period was 41 months. Clinical and radiographic assessment including CT with 3D reconstruction to examine the anatomic characteristics of the osteotomy were undertaken. We found that concentric reduction was achieved in 93.7% with excellent clinical and radiographic outcomes. Only 3 cases needed revision of the Dega osteotomy. The re-operation rate was 12.5%. CT scan revealed that the arcuate line was crossed by the osteotomy in the majority of cases. In 20.7% of cases, a bone cut that was intended to be a Dega osteotomy was found to have been inadvertently implemented as another osteotomy variant. However, this bore no significant effect on the outcome. Conclusion: We found that a well-implemented Dega osteotomy is a reliable tool to cope with the acetabular changes in DDH.

9.
Adv Colloid Interface Sci ; 331: 103237, 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38959812

ABSTRACT

Adsorption of surfactants to fluid interfaces occurs in numerous technological and daily-life contexts. The coverage at the interface and other properties of the formed adsorption layers determine the performance of a surfactant with regard to the desired application. Given the importance of these applications, there is a great demand for the comprehensive characterization and understanding of surfactant adsorption layers. In this review, we provide an overview of suitable experimental and simulation-based techniques and review the literature in which they were used for the investigation of surfactant adsorption layers. We come to the conclusion that, while these techniques have been successfully applied to investigate Langmuir monolayers of water-insoluble surfactants, their application to the study of Gibbs adsorption layers of water-soluble surfactants has not been fully exploited. Finally, we emphasize the great potential of these methods in providing a deeper understanding of the behavior of soluble surfactants at interfaces, which is crucial for optimizing their performance in various applications.

10.
Nanotechnology ; 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38959868

ABSTRACT

We present a spectroscopic study of the magnetic properties of Fe3-δGeTe2 single crystals with varying Fe content, achieved by tuning the stoichiometry of the crystals. We carried out x-ray absorption spectroscopy and analyzed the x-ray circular magnetic dichroism spectra using the sum rules, to determine the orbital and spin magnetic moments of the materials. We find a clear reduction of the spin and orbital magnetic moment with increasing Fe deficiency. Magnetic susceptibility measurements show that the reduction in magnetization is accompanied by a reduced Curie temperature. Multiplet calculations reveal that the Fe2+ state increasingly mixes with a higher valence state when the Fe deficiency is increased. This effect is correlated with the weakening of the magnetic moment. As single crystals are the base material for exfoliation processes, our results are relevant for the assembly of 2D magnetic heterostructures. .

11.
Structure ; 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38959899

ABSTRACT

LoaP is a member of the universal NusG protein family. Previously, we reported that unlike other characterized homologs, LoaP binds RNA sequence-specifically, recognizing a stem-loop in the 5'-untranslated region of operons it regulates. To elucidate how this NusG homolog acquired this ability, we now determined the co-crystal structure of Thermoanaerobacter pseudethanolicus LoaP bound to its cognate 26-nucleotide dfn RNA element. Our structure reveals that the LoaP C-terminal KOW domain recognizes the helical portion of the RNA by docking into a broadened major groove, while a protruding ß-hairpin of the N-terminal NusG-like domain binds the UNCG tetraloop capping the stem-loop. Major-groove RNA recognition is unusual and is made possible by conserved features of the dfn hairpin. Superposition with structures of other NusG proteins implies that LoaP can bind concurrently to the dfn RNA and the transcription elongation complex, suggesting a new level of co-transcriptional regulation by proteins of this conserved family.

12.
Genes Dev ; 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38960718

ABSTRACT

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

13.
J Mol Model ; 30(8): 247, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38960900

ABSTRACT

BACKGROUND: Cubic perovskite titanium stannous oxide (TiSnO3) is a promising material for various applications due to its functional properties. However, understanding how these properties change under external stress is crucial for its development and optimization. METHOD: This study employed density functional theory calculations to investigate the structural, electronic, optical, thermal, and mechanical properties of TiSnO3 under varying degrees of external static isotropic stress (0-120 GPa). RESULTS: The study reveals a significant decrease in the bandgap of TiSnO3 with increasing stress due to lattice modifications and the formation of delocalized electrons. Partial density of states analysis indicates that Sn and O states play a key role in shaping the electronic band structure. TiSnO3 exhibits increased light absorption with stress, accompanied by a blue shift in absorption peaks, whereas, both polarizability and refractive index decrease with increasing stress. Mechanically, all elastic moduli (bulk, shear, and Young's) show an increase under stress, signifying a stiffening response of the material under stress. Similarly, the Pugh ratio suggests a transition from ductile to brittle behaviour at elevated stress levels. Phonon dispersion calculations indicate the instability of the cubic phase at 0 K. However, a phonon gap emerges at 30 GPa and widens with increasing stress. X-ray diffraction further supports these findings by demonstrating a shift in diffraction peaks towards higher angles with increasing stress, consistent with the applied stress. CONCLUSION: In conclusion, this computational study offers a thorough understanding of how external stress influences the properties of TiSnO3, providing valuable insights for potential applications in various fields.

14.
Article in English | MEDLINE | ID: mdl-38961051

ABSTRACT

Thick polycrystalline perovskite films synthesized by using solution processes show great potential in X-ray detection applications. However, due to the evaporation of the solvent, many pinholes and defects appear in the thick films, which deteriorate their optoelectronic properties and diminish their X-ray detection performance. Therefore, the preparation of large area and dense perovskite thick films is desired. Herein, we propose an effective strategy of filling the pores with a saturated precursor solution. By adding the saturated perovskite solution to the polycrystalline perovskite thick film, the original perovskite film will not be destroyed because of the solution-solute equilibrium relationship. Instead, it promotes in situ crystal growth within the thick film during the annealing process. The loosely packed grains in the original thick perovskite film are connected, and the pores and defects are partially filled and fixed. Finally, a much denser perovskite thick film with improved optoelectronic properties has been obtained. The optimized thick film exhibits an X-ray sensitivity of 1616.01 µC Gyair-1 cm-2 under an electric field of 44.44 V mm-1 and a low detection limit of 28.64 nGyair s-1 under an electric field of 22.22 V mm-1. These values exceed the 323.86 µC Gyair-1 cm-2 and 40.52 nGyair s-1 of the pristine perovskite thick film measured under the same conditions. The optimized thick film also shows promising working stability and X-ray imaging capability.

15.
Acta Crystallogr F Struct Biol Commun ; 80(Pt 7): 154-163, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38958188

ABSTRACT

The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form ß-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Šresolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.


Subject(s)
Complementarity Determining Regions , Immunoglobulin Fab Fragments , Immunoglobulin Heavy Chains , Immunoglobulin Light Chains , Models, Molecular , Animals , Cattle , Immunoglobulin Heavy Chains/chemistry , Crystallography, X-Ray , Immunoglobulin Light Chains/chemistry , Immunoglobulin Light Chains/genetics , Complementarity Determining Regions/chemistry , Immunoglobulin Fab Fragments/chemistry , Amino Acid Sequence , Protein Conformation
16.
Cochlear Implants Int ; : 1-8, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38958389

ABSTRACT

OBJECTIVES: Proper electrode placement is essential for favorable hearing outcomes following cochlear implantation. Though often used, traditional intraoperative X-ray imaging is time consuming, exposes patients and staff to radiation, and poses interpretational challenges. The Nucleus® SmartNav System, utilizes electrode voltage telemetry (EVT) to analyze the positioning of the electrode array intraoperatively. This study investigates the efficacy of SmartNav in optimizing the efficiency and accuracy of assessing electrode placement. METHODS: This prospective clinical study analyzed placement of 50 consecutive Cochlear Corporation cochlear implants conducted at a single institution between March of 2022 and June of 2023. Placement check of electrode array using SmartNav and X-ray was completed and individually assessed. A comparative analysis of SmartNav and X-ray completion times for electrode placement assessment was conducted. RESULTS: Subjects included nine ears with abnormal anatomy and three reimplants. SmartNav placement check required a total time of 2.12 min compared to X-ray imaging at 14.23 min (p = 1.6E-16, CI 95%). Both SmartNav and X-ray had excellent sensitivity of 100% in identifying appropriate electrode position (p = 1.0). Tip fold-over was identified using both modalities in 3 cases with noted easier interpretation using SmartNav. CONCLUSION: The Nucleus® SmartNav System significantly outperformed traditional X-ray imaging, offering a faster and more straightforward approach to assessing electrode positioning during cochlear implant surgery, thereby enhancing surgical efficiency and patient safety.

17.
Mol Pharm ; 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38958508

ABSTRACT

Crystalline suspensions of monoclonal antibodies (mAbs) have great potential to improve drug substance isolation and purification on a large scale and to be used for drug delivery via high-concentration formulations. Crystalline mAb suspensions are expected to have enhanced chemical and physical properties relative to mAb solutions delivered intravenously, making them attractive candidates for subcutaneous delivery. In contrast to small molecules, the development of protein crystalline suspensions is not a widely used approach in the pharmaceutical industry. This is mainly due to the challenges in finding crystalline hits and the suboptimal physical properties of the resulting crystallites when hits are found. Modern advances in instrumentation and increased knowledge of mAb crystallization have, however, resulted in higher probabilities of discovering crystal forms and improving their particle properties and characterization. In this regard, physical, analytical characterization plays a central role in the initial steps of understanding and later optimizing the crystallization of mAbs and requires careful selection of the appropriate tools. This contribution describes a novel crystal structure of the antibody pembrolizumab and demonstrates the usefulness of small-angle X-ray scattering (SAXS) for characterizing its crystalline suspensions. It illustrates the advantages of SAXS when used to (i) confirm crystallinity and crystal phase of crystallites produced in batch mode; (ii) confirm crystallinity under various conditions and detect variations in crystal phases, enabling fine-tuning of the crystallizations for phase control across multiple batches; (iii) monitor the physical response and stability of the crystallites in suspension with regard to filtration and washing; and (iv) monitor the physical stability of the crystallites upon drying. Overall, this work highlights how SAXS is an essential tool for mAb crystallization characterization.

18.
Chemistry ; : e202400785, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38958609

ABSTRACT

Organic halogen compounds are cornerstones of applied chemical sciences. Halogen substitution is a smart molecular design strategy adopted to influence reactivity, membrane permeability and receptor interaction. Chiral bioreceptors may restrict the stereochemical requirements in the halo-ligand design. Straightforward (but expensive) catalyzed stereospecific halogenation has been reported. Historically, PCl5 served access to uncatalyzed stereoselective chlorination although the stereochemical outcomes were influenced by steric parameters. Nonetheless, stereochemical investigation of PCl5 reaction mechanism with carbamoyl (RCONHX) compounds has never been addressed. Herein, we provide the first comprehensive stereochemical mechanistic explanation outlining halogenation of carbamoyl compounds with PCl5; the key regioselectivity-limiting nitrilimine intermediate (8-Z.HCl); how substitution pattern influences regioselectivity; why oxadiazole byproduct (P1) is encountered; stereo-electronic factors influencing the hydrazonoyl chloride (P2) production; and discovery of two stereoselectivity-limiting parallel mechanisms (stepwise and concerted) of elimination of HCl and POCl3. DFT calculations, synthetic methodology optimization, X-ray evidence and experimental reaction kinetics study evidence all supported the suggested mechanism proposal (Scheme 2). Finally, we provide mechanism-inspired future recommendations for directing the reaction stereoselectivity toward elusive and stereochemically inaccessible (E)-bis-hydrazonoyl chlorides along with potentially pivotal applications of both (E/Z)-stereoisomers especially in medicinal chemistry and protein modification.

19.
Proc Natl Acad Sci U S A ; 121(28): e2407066121, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38959038

ABSTRACT

Mammalian transglutaminases, a family of Ca2+-dependent proteins, are implicated in a variety of diseases. For example, celiac disease (CeD) is an autoimmune disorder whose pathogenesis requires transglutaminase 2 (TG2) to deamidate select glutamine residues in diet-derived gluten peptides. Deamidation involves the formation of transient γ-glutamyl thioester intermediates. Recent studies have revealed that in addition to the deamidated gluten peptides themselves, their corresponding thioester intermediates are also pathogenically relevant. A mechanistic understanding of this relevance is hindered by the absence of any structure of Ca2+-bound TG2. We report the X-ray crystallographic structure of human TG2 bound to an inhibitory gluten peptidomimetic and two Ca2+ ions in sites previously designated as S1 and S3. Together with additional structure-guided experiments, this structure provides a mechanistic explanation for how S1 regulates formation of an inhibitory disulfide bond in TG2, while also establishing that S3 is essential for γ-glutamyl thioester formation. Furthermore, our crystallographic findings and associated analyses have revealed that i) two interacting residues, H305 and E363, play a critical role in resolving the thioester intermediate into an isopeptide bond (transamidation) but not in thioester hydrolysis (deamidation); and ii) residues N333 and K176 stabilize preferred TG2 substrates and inhibitors via hydrogen bonding to nonreactive backbone atoms. Overall, the intermediate-state conformer of TG2 reported here represents a superior model to previously characterized conformers for both transition states of the TG2-catalyzed reaction.


Subject(s)
Calcium , GTP-Binding Proteins , Protein Glutamine gamma Glutamyltransferase 2 , Transglutaminases , Transglutaminases/metabolism , Transglutaminases/chemistry , Protein Glutamine gamma Glutamyltransferase 2/metabolism , Humans , Calcium/metabolism , GTP-Binding Proteins/metabolism , GTP-Binding Proteins/chemistry , Crystallography, X-Ray , Glutens/metabolism , Glutens/chemistry , Models, Molecular , Protein Conformation , Celiac Disease/metabolism , Protein Binding
20.
Subcell Biochem ; 104: 101-117, 2024.
Article in English | MEDLINE | ID: mdl-38963485

ABSTRACT

Yeast COMPASS (complex of proteins associated with Set1) and human MLL (mixed-lineage leukemia) complexes are histone H3 lysine 4 methyltransferases with critical roles in gene regulation and embryonic development. Both complexes share a conserved C-terminal SET domain, responsible for catalyzing histone H3 K4 methylation on nucleosomes. Notably, their catalytic activity toward nucleosomes is enhanced and optimized with assembly of auxiliary subunits. In this review, we aim to illustrate the recent X-ray and cryo-EM structures of yeast COMPASS and human MLL1 core complexes bound to either unmodified nucleosome core particle (NCP) or H2B mono-ubiquitinated NCP (H2Bub.NCP). We further delineate how each auxiliary component of the complex contributes to the NCP and ubiquitin recognition to maximize the methyltransferase activity.


Subject(s)
Histone-Lysine N-Methyltransferase , Myeloid-Lymphoid Leukemia Protein , Nucleosomes , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Humans , Nucleosomes/metabolism , Histone-Lysine N-Methyltransferase/chemistry , Histone-Lysine N-Methyltransferase/metabolism , Histone-Lysine N-Methyltransferase/genetics , Myeloid-Lymphoid Leukemia Protein/metabolism , Myeloid-Lymphoid Leukemia Protein/chemistry , Myeloid-Lymphoid Leukemia Protein/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Histones/metabolism , Histones/chemistry , Histones/genetics , Cryoelectron Microscopy/methods
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