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Structural and supramolecular insights into crystalline multicomponent systems of 2,4-diamino-6-phenyl-1,3,5-triazine with various carboxylic acids

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Acta Crystallographica Section C: Structural Chemistry 2025年第Pt 4期81卷 212-223页

作者： Nidhishree, Murugan Gomathi, Sundaramoorthy Nirmalram, Jeyaraman Selvaraj Yasien, Sayed Ramesh, Pandian Department of Chemistry Periyar Maniammai Institute of Science & Technology Tamilnadu Thanjavur613403 India Department of Chemistry Research and Development Cell PRIST Deemed to be University Tamilnadu Thanjavur613403 India Protein Structure Function Research Laboratory School of Molecular and Cell Biology University of the Witwatersrand Johannesburg2050 South Africa

Three multicomponent systems, namely, 2,4-diamino-6-phenyl-1,3,5-triazine-nicotinic acid (DAPT-NA), C9H9N5·C6H5NO2, (I), 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium hydrogen malonate (DAPT-MMA), C9H10N5+·C3H3O4-, (II), and 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium hydrogen (+)-dibenzoyl-d-tartarate (DAPT-DBTA), C9H10N5+·C18H13O8-, (III), have been synthesized and characterized via single-crystal X-ray diffraction, and their supramolecular interactions have been analysed. The formation of cocrystal (I) and salts (II) and (III) was confirmed through the widening of the C - N - C bond angle of the triazine moiety of 2,4-diamino-6-phenyl-1,3,5-triazine and the difference in the C - O bond distances between the carboxyl and carboxylate groups of the respective carboxylic acids. Cocrystal (I) and salt (II) form robust homomeric and heteromeric R22(8) ring motifs through primary acid-base interactions and complementary base pairing. In cocrystal (I), the complementary base pair exists as wave-like supramolecular strands, whereas in salt (II), it exists as a discrete pair. Salt (II) exhibits DDDAAD sextuple and DADA quadruple hydrogen-bonded arrays (D is donor and A is acceptor) through acid-base interactions and generates a supramolecular rosette-like architecture. In salt (III), the presence of carboxyl-carboxylate interactions and acid-base interactions led to the development of a supramolecular sheet and tunnel-like architecture. Cocrystal (I) and salt (III) are stabilized through offset aromatic π-π stacking interactions and C - H⋯π interactions, and salts (II) and (III) are stabilized via weak carbonyl-π and C - H⋯O hydrogen bonds. Macrocyclic R1212(64) and R33(24) motifs are present in salts (II) and (III), respectively. Hirshfeld surface analysis of (I)-(III) reinforces the fact that N⋯H/H⋯N, O⋯H/H⋯O and C⋯H/H⋯C interactions contribute to the crystal packing and stability. © 2025 International Union of Crystallography. All rights reserved.

关键词： Carboxylation

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Coordination of IFT20 With Other IFT Components Is Required for Ciliogenesis

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Journal of Clinical laboratory Analysis 2025年第9期39卷 e70000页

作者： Wang, Weishu Shan, Ying Liu, Ruming Li, Dengwen Zhou, Jun Lu, Quanlong Zhao, Huijie Department of Genetics and Cell Biology State Key Laboratory of Medicinal Chemical Biology Haihe Laboratory of Cell Ecosystem College of Life Sciences Nankai University Tianjin China Center for Cell Structure and Function Shandong Provincial Key Laboratory of Animal Resistance Biology College of Life Sciences Shandong Normal University Jinan China

Background: Primary cilia are organelles formed on the cell surface. They can act as cellular antennae to sense signals and play important roles in various biological processes. Abnormalities in primary cilia lead to a variety of diseases collectively known as ciliopathies. Intraflagellar transport protein 20 (IFT20) has been implicated in ciliogenesis. Methods: IFT20 knockout cell lines were established using the CRISPR-Cas9 gene editing technology. The GFP-IFT20 plasmid was constructed with the Gateway cloning system. Protein levels were detected via immunoblotting, and the localization of IFT20, acetylated α-tubulin, ARL13B, CP110, MKS3, IFT88, and IFT140 in wild-type and IFT20 knockout cells was examined by immunofluorescence microscopy. The fluorescence intensities were analyzed using ImageJ. Data quantifications and mass spectrometry results were analyzed using GraphPad Prism and Metascape. Results: The IFT20 deficiency impaired ciliogenesis and reduced cilium length. IFT20 depletion did not affect the removal of centriolar coiled-coil protein 110 (CP110) from the mother centriole or the recruitment of Meckel–Gruber syndrome type 3 (MKS3) to the transition zone. Mass spectrometry analysis revealed that proteins interacting with IFT20 were mainly IFT components. IFT20 knockout decreased the levels of both IFT88 and IFT140, and abrogated IFT88 localization at the basal body and ciliary axoneme. IFT20 knockout also impaired IFT140 localization at the ciliary axoneme but did not affect its localization at the basal body. Conclusions: IFT20 is involved in ciliogenesis by regulating the level and localization of other IFT proteins and may have important implications in ciliopathies and related diseases. © 2025 The Author(s). Journal of Clinical laboratory Analysis published by Wiley Periodicals LLC.

关键词： axoneme basal body ciliogenesis cilium IFT20

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UFMylation Modulates OFIP Stability and Centrosomal Localization

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Journal of Clinical laboratory Analysis 2025年第6期39卷 e70004页

作者： Yang, Mulin Zhao, Zihe Di, Jie Dong, Dan Li, Dengwen Ran, Jie Department of Genetics and Cell Biology College of Life Sciences State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin China Center for Cell Structure and Function Shandong Provincial Key Laboratory of Animal Resistance Biology College of Life Sciences Shandong Normal University Jinan China

Background: OFIP, also known as KIAA0753, is a centrosomal and pericentriolar satellite protein implicated in ciliogenesis, centriolar duplication, and microtubule stability. In humans, genetic mutations affecting OFIP have been implicated in the pathogenesis of Oral-Facial-Digital (OFD) Syndrome and Joubert Syndrome. Ubiquitin-fold Modifier 1 (UFM1), the most recently identified ubiquitin-like protein, is covalently transferred to its substrates, in a process known as UFMylation. This modification has recently emerged as a key regulator of various biological processes by altering their stability, activity, or localization. Methods: The interaction between UFL1 and OFIP, as well as the UFMylation of OFIP, were assessed through immunoprecipitation and immunoblotting analyses. The mRNA levels of OFIP were examined using reverse transcription quantitative PCR (RT-qPCR). Immunofluorescence microscopy was employed to examine the localization and distribution patterns of OFIP. Results: Our findings demonstrate that UFL1 interacts with OFIP both in vivo and in vitro. We also found that OFIP undergoes UFMylation, and UFL1 promotes the OFIP UFMylation. Mechanistic studies demonstrate that OFIP UFMylation inhibits its protein stability and maintains its proper centrosomal localization. However, the efficacy of these regulatory mechanisms varies significantly between different cell types, being notably pronounced in HeLa cells but markedly reduced in RPE1 cells. Conclusions: OFIP is identified as a novel substrate for UFMylation. UFL1-mediated OFIP UFMylation is essential for its stability and centrosomal localization in HeLa cells. However, these effects are not observed in RPE1 cells, highlighting cell type-specific heterogeneity in the role of OFIP UFMylation. © 2025 The Author(s). Journal of Clinical laboratory Analysis published by Wiley Periodicals LLC.

关键词： centrosome OFIP protein stability UFL1 UFMylation

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Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling

Results in Chemistry

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Results in Chemistry 2025年 16卷

作者： Mfeka, Mbalenhle Onisuru, Olalekan Pandian, Ramesh Sayed, Yasien Khoza, Thandeka Achilonu, Ikechukwu Department of Biochemistry School of Life Sciences College of Agriculture Engineering & Science University of KwaZulu-Natal Pietermaritzburg 3209 South Africa Protein Structure-Function and Research Laboratory School of Molecular and Cell Biology Faculty of Science University of the Witwatersrand Braamfontein Johannesburg 2000 South Africa

Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schistosome drug target, a careful selection of crystal structure space groups used for CADD is emphasized in this study. Sb28GST was successfully overexpressed and purified to grow protein crystals with a resolution of 2.4 Å in an orthorhombic space group system. High-throughput virtual screening (HTVS) of a flavonoid compound was performed on monoclinic 8ALS and orthorhombic 8BHZ Sb28GST to identify potential ligands. The results showed a diverse selection of hit compounds with apigenin 7-O-(2G-rhamnosyl)gentiobioside (apigenin) being the common ligand. However, quercetin-3-O-Beta-D-Glucose-7-O-Beta-D-Gentiobioside (quercetin) showed the highest affinity to 8ALS with a Glide gscore of −15.66 kcal/mol. Also, 500-ns molecular dynamics simulations (MDS) of the 8ALS-Sb28GST and 8BHZ-Sb28GST apo systems, as well as their corresponding apigenin and quercetin complexes, show two distinct trajectories which reveal significant differences in their dynamic behaviour and also showed varying interactions. This highlights the need for collective assessment of protein polymorphs to comprehensively understand protein dynamics. The inhibitory potency of apigenin and quercetin via a GSH-CDNB conjugation assay confirmed that they significantly reduced the specific enzyme activity of Sb28GST with both ligands having half-maximal inhibitory concentration (IC₅₀) of 0.13 mM. Extrinsic fluorescence studies and thermal shift assay indicated that these compounds bind to the hydrophobic H-site and allosteric L-site at the dimer interface and have a minimal effect on the protein's thermal stability. © 2025 The Authors

关键词： Binding Empirical, ligand High-throughput virtual screening Molecular dynamics simulations Polymorphs Schistosoma bovis

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PROTEIN FACTOR(S) FROM MITOTIC CHO cellS INDUCE MEIOTIC MATURATION IN XENOPUS-LAEVIS OOCYTES

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FEBS LETTERS 1980年第2期109卷 233-238页

作者： NELKIN, B NICHOLS, C VOGELSTEIN, B Cell Structure and Function Laboratory The Johns Hopkins Oncology Center Baltimore MD 21205 USA

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LOCALIZATION OF SV40-GENES WITHIN SUPERCOILED LOOP DOMAINS

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NUCLEIC ACIDS RESEARCH 1980年第23期8卷 5623-5633页

作者： NELKIN, BD PARDOLL, DM VOGELSTEIN, B Cell Structure and Function Laboratory Johns Hopkins Regional Oncology CenterBaltimore MD 21205 USA

Recent studies indicate that eukaryotic DNA is organized into supercoiled loop domains. These loops appear to be anchored at their bases to an insoluble nuclear skeleton or matrix. Most of the DNA in the loops can be released from the matrix by nuclease digestion; the residual DNA remaining with the nuclear matrix represents sequences at the base of the loops, and possibly other sequences which are intimately associated with the nuclear matrix for other reasons. Using a quantitative application of the Southern blotting technique, we have found this residual DNA from SV40 infected 3T3 cells to be enriched in SV40 sequences, indicating that they reside near matrix-DNA attachment points. An enrichment of 3-7 fold relative to total cellular DNA, was found in each of three different lines of SV40 infected 3T3 cells. Control experiments with globin genes showed no such enrichment in this residual matrix DNA. This sequence specificity suggests that the spatial organization of DNA sequences within loops may be related to the functionality of these sequences within the cell.

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SUPERCOILED LOOPS AND EUKARYOTIC DNA-REPLICATION

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cell 1980年第1期22卷 79-85页

作者： VOGELSTEIN, B PARDOLL, DM COFFEY, DS Cell Structure and Function Laboratory The Oncology Center The Johns Hopkins University School of Medicine Baltimore Maryland 21205 USA

Recent studies have indicated that the DNA of the eukaryotic nucleus is organized in the form of supercoiled loops. After depleting interphase nuclei of histones and other nuclear proteins by treatment with nonionic detergent and high salt, intact (unnicked) loops of DNA can be visualized as a halo surrounding a nuclear skeleton or matrix. This halo of DNA loops can be reversibly wound using various concentrations of ethidium bromide and is irreversibly unwound when the DNA is gently nicked with DNase I or exposure to UV light. These structures, comprising a halo of unwound DNA loops anchored to a nuclear matrix, provided a way in which to examine the relationship of DNA replication to the DNA loops. Mouse fibroblast 3T3 cells were pulse-labeled with 3H-thymidine for various periods and autoradiography was performed on the matrix-halo structures. After a 1 min pulse, > 80% of the autoradiographic grains representing newly replicated DNA were found within the nuclear matrix even though the surrounding halo region contained 80% of the total nuclear DNA. With longer pulse times, the autoradiographic grains could be seen to move progressively outward from the nuclear matrix into the halo region. Over 70% of the autoradiographic grains could be chased out of the central matrix into the surrounding halo if the 1 min pulse was followed by a 1 h incubation with excess unlabeled thymidine. DNA replication occurs at fixed sites at the base of the loops. The replicating DNA loops may be motile with respect to their nuclear matrix anchorage sites.

关键词： Animals cell Line cell Nucleus/metabolism Deoxyribonucleases/pharmacology DNA Replication DNA, Superhelical/biosynthesis DNA, Superhelical/biosynthesis Ethidium/pharmacology Mice

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A TECHNIQUE FOR RADIOLABELING DNA RESTRICTION ENDONUCLEASE FRAGMENTS TO HIGH SPECIFIC ACTIVITY

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ANALYTICAL BIOCHEMISTRY 1983年第1期132卷 6-13页

作者： FEINBERG, AP VOGELSTEIN, B Cell Structure and Function Laboratory The Oncology Center Johns Hopkins University School of Medicine Baltimore Maryland 21205 USA

A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described. DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large fragment of DNA polymerase I, using random oligonucleotides as primers. Over 70% of the precursor triphosphate is routinely incorporated into complementary DNA and specific activities of over 109 dpm/.mu.g of DNA can be obtained using relatively small amounts of precursor. These oligolabeled DNA fragments serve as efficient probes in filter hybridization experiments. [Escherichia coli was used.].

关键词： radiolabeling DNA fragments hybridization Southern transfers agarose gels cloned DNA

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HYPOMETHYLATION OF RAS ONCOGENES IN PRIMARY HUMAN CANCERS

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 1983年第1期111卷 47-54页

作者： FEINBERG, AP VOGELSTEIN, B Cell Structure and Function Laboratory The Oncology Center Johns Hopkins University School of Medicine Baltimore Maryland 21205 USA

The methylation status of 2 cellular oncogenes, c-Ha-ras and c-Ki-ras, in primary human carcinomas and the adjacent analogous normal tissues from which the tumors derived. The c-Ha-ras gene was hypomethylated in 6 of 8 carcinomas, including 5 colonic adenocarcinomas and 1 small cell lung carcinoma, when compared to adjacent normal tissues. The c-ki-ras gene was hypomethylated to a lesser extent in 2 colonic adenocarcinomas. This is the 1st demonstration of alterations in methylation of cellular oncogenes in human cancer.

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HYPOMETHYLATION DISTINGUISHES GENES OF SOME HUMAN CANCERS FROM THEIR NORMAL COUNTERPARTS

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NATURE 1983年第5895期301卷 89-92页

作者： FEINBERG, AP VOGELSTEIN, B Cell Structure and Function Laboratory The Oncology Center Johns Hopkins University School of Medicine Baltimore Maryland 21205 USA

It has been suggested that cancer represents an alteration in DNA, heritable by progeny cells, that leads to abnormally regulated expression of normal cellular genes; DNA alterations such as mutations1,2, rearrangements3–5 and changes in methylation6–8 have been proposed to have such a role. Because of increasing evidence that DNA methylation is important in gene expression (for review see refs 7, 9–11), several investigators have studied DNA methylation in animal tumours, transformed cells and leukaemia cells in culture8,12–30. The results of these studies have varied; depending on the techniques and systems used, an increase12–19, decrease20–24, or no change25–29 in the degree of methylation has been reported. To our knowledge, however, primary human tumour tissues have not been used in such studies. We have now examined DNA methylation in human cancer with three considerations in mind: (1) the methylation pattern of specific genes, rather than total levels of methylation, was determined; (2) human cancers and adjacent analogous normal tissues, unconditioned by culture media, were analysed; and (3) the cancers were taken from patients who had received neither radiation nor chemotherapy. In four of five patients studied, representing two histological types of cancer, substantial hypomethylation was found in genes of cancer cells compared with their normal counterparts. This hypomethylation was progressive in a metastasis from one of the patients.

关键词： Science Humanities and Social Sciences multidisciplinary

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