Article
Biochemistry & Molecular Biology
Tatsuya Kondo, Miyu Kichijo, Makoto Nakaya, Shigeo Takenaka, Takatoshi Arakawa, Toshihisa Kotake, Shinya Fushinobu, Tatsuji Sakamoto
Summary: In this study, a novel enzyme FoBGlcA with unique catalytic activity was isolated and characterized. The crystal structure of FoBGlcA revealed a high structural divergence compared to other GH79 beta-glucuronidases, and its unique substrate specificity may be attributed to distinct loop structure near the catalytic site. Evaluating the mutant enzymes based on the crystal structure of FoBGlcA reaction product complex determined the amino acid residues involved in the catalytic activity of the enzyme.
Article
Multidisciplinary Sciences
Min Zhang, Anna Jungblut, Franziska Kunert, Luis Hauptmann, Thomas Hoffmann, Olga Kolesnikova, Felix Metzner, Manuela Moldt, Felix Weis, Frank DiMaio, Karl-Peter Hopfner, Sebastian Eustermann
Summary: In this study, the authors reveal the structural mechanism for ATP-dependent chromatin remodeling of hexasomes by the INO80 complex. They demonstrate how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. The researchers also find that the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.
Article
Chemistry, Multidisciplinary
Andrea Mascherpa, Nozomii Ishii, Ayelen Tayagui, Jiang Liu, Matthieu Sollogoub, Antony J. J. Fairbanks
Summary: Beta-cyclodextrin and its derivatives have been approved for therapeutic use in over 30 clinical settings. They show promise as therapeutics for lysosomal storage disorders and other diseases involving metabolite accumulation in the lysosome. In this study, a synthetic glycan terminated with mannose-6-phosphate residues was attached to beta-cyclodextrin and its effect on cellular internalization and transport to the lysosome was investigated.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Todd A. Anzelon, Saikat Chowdhury, Siobhan M. Hughes, Yao Xiao, Gabriel C. Lander, Ian J. MacRae
Summary: PIWI proteins use piRNAs to silence transposable elements and maintain genome integrity. Like Argonaute, PIWI identifies targets using the piRNA seed region, but creates a weaker seed, making piRNAs less promiscuous than miRNAs. Additionally, PIWI facilitates piRNA-target pairing in a tolerant manner, leading to long-lived interactions that defend against evolving genomic threats.
Article
Multidisciplinary Sciences
Andre T. Graca, Michael Hall, Karina Persson, Wolfgang P. Schroder
Summary: Arabidopsis thaliana, the first higher plant with a fully sequenced genome, lacks a high-resolution structure of Photosystem II; our study presents the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex. The digitonin extracted PSII complexes elucidate key structural and stabilizing factors of Photosystem II.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Kazumasa Oda, Takashi Nomura, Takanori Nakane, Keitaro Yamashita, Keiichi Inoue, Shota Ito, Johannes Vierock, Kunio Hirata, Andres D. Maturana, Kota Katayama, Tatsuya Ikuta, Itsuki Ishigami, Tamaki Izume, Rie Umeda, Ryuun Eguma, Satomi Oishi, Go Kasuya, Takafumi Kato, Tsukasa Kusakizako, Wataru Shihoya, Hiroto Shimada, Tomoyuki Takatsuji, Mizuki Takemoto, Reiya Taniguchi, Atsuhiro Tomita, Ryoki Nakamura, Masahiro Fukuda, Hirotake Miyauchi, Yongchan Lee, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Michihiro Sugahara, Tetsunari Kimura, Tatsuro Shimamura, Takaaki Fujiwara, Yasuaki Yamanaka, Shigeki Owada, Yasumasa Joti, Kensuke Tono, Ryuichiro Ishitani, Shigehiko Hayashi, Hideki Kandori, Peter Hegemann, So Iwata, Minoru Kubo, Tomohiro Nishizawa, Osamu Nureki
Summary: Channelrhodopsins (ChRs) are microbial light-gated ion channels used in optogenetics for controlling neural activity with light. Time-resolved crystallographic analyses revealed conformational changes in ChR following photoactivation, suggesting early changes in the pore-forming helices trigger the opening of the ion conducting pore.
Article
Chemistry, Analytical
Xianzhe Wei, Juan Li, Xiaofeng Yang, Baoli Dong, Bing Geng, Zengjun Li, Xiaoxiao Hu, Biyan Ding, Jing Zhang, Mei Yan
Summary: This paper presents the design of an enzyme-activated two-photon fluorescent probe (RN-GLU) for rapid and selective detection of beta-glucuronidase (GLU) in colon cancer. The probe exhibits good lysosome targetability and penetration ability, making it a potential method for evaluating GLU functions in colon cancer diagnosis and complex biosystems.
ANALYTICA CHIMICA ACTA
(2022)
Article
Materials Science, Multidisciplinary
A. Martinelli
Summary: The structural and microstructural properties of Mn substituted β-FeSe were studied using high-resolution synchrotron X-ray powder diffraction. It was found that the thermal increase of structural strain in the tetragonal phase leads to the progressive breaking of 4-fold symmetry at the local scale, which qualitatively traces the development of anisotropy in physical properties, commonly attributed to nematicity. This implies a close relationship and interplay between structural strain and physical properties, suggesting that structural strain may be the origin of unexpected anisotropy in some physical properties. Interestingly, incommensurate satellite peaks were observed in the diffraction pattern collected in the low-temperature orthorhombic phase field, possibly indicating the occurrence of a charge-density-wave instability.
MATERIALS RESEARCH BULLETIN
(2023)
Article
Chemistry, Medicinal
Yujie Wang, Keshi Xu, Hongchun Liu, Wei Zhang, Chun Hu, Yingxia Li
Summary: Auristatins-glucuronide conjugates designed to target beta-Glucuronidase in the tumor microenvironment were synthesized and evaluated. The conjugates showed remarkable stability and selectivity in vitro antiproliferative activities against beta-glucuronidase pretreated and untreated cancer cells. Conjugate 20 exhibited potent antitumor efficacy in a mouse model without inducing side effects.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
M. Rhyan Puno, Christopher D. Lima
Summary: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation. Cryogenic electron microscopy structures of human nuclear exosome targeting complexes reveal mechanistic insights to substrate recognition and early steps before RNA handover. ZCCHC8 serves as a scaffold, mediating homodimerization and facilitating RNA capture by MTR4, while RBM7 anchors to the helicase core. These interactions coordinate RNA capture, translocation, and decay.
Article
Cell Biology
Chih-Chia Su, Meinan Lyu, Zhemin Zhang, Masaru Miyagi, Wei Huang, Derek J. Taylor, Edward W. Yu
Summary: In this study, cryo-electron microscopy was used to explore the composition and high-resolution structure of human liver enzymes. Ten unique human liver enzymes involved in diverse cellular processes were identified and their structures were determined. The interactions between enzymes involved in protein quality control were also observed. These results highlight the importance of cryo-EM in elucidating human organ proteomics at the atomic level.
Article
Chemistry, Medicinal
Juanjuan Wang, Zebin Liu, Xiaowei Pan, Ning Wang, Legong Li, Yuguang Du, Jianjun Li, Mei Li
Summary: Fucoidans are polyanionic fucose-containing sulfated polysaccharides that can be cleaved by fucoidan-degrading enzymes to produce low-molecular-weight fucoidans suitable for pharmaceutical use. FdlA is an endo-type fucoidan-degrading enzyme that cleaves sulfated fuco-glucuronomannan through a lytic mechanism. The crystal structures of FdlA-NTD reveal a right-handed parallel beta-helix fold with unique substrate binding site and potentially representing a novel polysaccharide lyase family with different catalytic residues.
Article
Biochemistry & Molecular Biology
Hui Sun, Ning Cui, Shu-Jing Han, Zhi-Peng Chen, Ling-Yun Xia, Yuxing Chen, Yong-Liang Jiang, Cong-Zhao Zhou
Summary: Carboxysome is a self-assembled microcompartment that sequesters enzymes inside a protein shell. The research suggests that CcmM and CcmN may act as adaptors to facilitate the recruitment of shell proteins and the assembly of intact beta-carboxysome.
Article
Materials Science, Ceramics
Elisa Boanini, Massimo Gazzano, Katia Rubini, Paolo P. Mazzeo, Adriana Bigi
Summary: The study investigated the substitution of strontium for calcium in alpha-CaHPO4 and beta-SrHPO4, as well as the influence of synthesis methods on the structures. The results showed that strontium substitution in alpha-CaHPO4 can reach up to 100%, while in beta-SrHPO4 it is limited to about 20%. Additionally, powder X-ray analysis revealed that beta-SrHPO4 crystallizes with a monoclinic cell in the space group P21/c.
CERAMICS INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Qu Chen, Rajesh Menon, Lesley J. Calder, Pavel Tolar, Peter B. Rosenthal
Summary: This study used cryo-EM to investigate the structure of the human full-length IgM pentamer, uncovering flexible antigen binding domains attached to an asymmetric and rigid core. The motion of the Fab arms in IgM is different from IgG and IgA, which may influence its binding to antigens and complement pathway activation.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Artificial Intelligence
Jianfeng Cui, Lixin Wang, Xiangmin He, Victor Hugo C. De Albuquerque, Salman A. AlQahtani, Mohammad Mehedi Hassan
Summary: Feature extraction plays a crucial role in arrhythmia classification. This paper presents a feature extraction method that combines traditional approaches and 1D-CNN to improve the accuracy of arrhythmia classification. Experimental results show that the proposed method achieves an average classification accuracy of 98.35%, surpassing the latest methods.
NEURAL COMPUTING & APPLICATIONS
(2023)
Article
Plant Sciences
Maria Batool, Ali Mahmoud El-Badri, Muhammad Umair Hassan, Yang Haiyun, Wang Chunyun, Yan Zhenkun, Kuai Jie, Bo Wang, Guangsheng Zhou
Summary: Drought poses serious threats to global crop production, including oilseed crops like Brassica napus L. Various approaches have been used to increase drought tolerance, but there is room for further improvement. Future research should focus on developing genetically engineered rapeseed plants with enhanced drought tolerance.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Biochemistry & Molecular Biology
Bader Saud Alotaibi, Jatin Joshi, Mohammad Raghibul Hasan, Mohd Shahnawaz Khan, Salem Hussain Alharethi, Taj Mohammad, Fahad A. Alhumaydhi, Abdelbaset Mohamed Elasbali, Md Imtaiyaz Hassan
Summary: In this study, potential inhibitors of ROCK1 were identified through structure-based virtual screening of natural compounds. Isoononin and Candidissiol showed appreciable binding affinity and selectivity towards ROCK1, and molecular dynamics simulations confirmed their stability.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Computer Science, Information Systems
Mohamed Hassaoui, Mohamed Hanini, Said El Kafhali
Summary: The use of C2 servers in cyberattacks has increased significantly, with attackers using DGA technique to hide their servers. Existing techniques for binary classification of domain names have issues with real-time detection and sensitivity to data. This paper proposes the DTFS-DGA model, which combines neural networks and traditional machine learning models to detect DGA in real-time without relying on reverse engineering and being insensitive to data size.
JOURNAL OF COMPUTER SECURITY
(2023)
Article
Biochemistry & Molecular Biology
Ahmad Abu Turab Naqvi, Syed Afzal Murtaza Rizvi, Md. Imtaiyaz Hassan
Summary: The expression of CBX genes was found to be significantly altered in various cancers, suggesting their potential as biomarkers for therapeutic intervention. Machine learning models showed excellent performance in cancer classification.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Mohd Adnan, Saleha Anwar, Debarati DasGupta, Mitesh Patel, Abdelbaset Mohamed Elasbali, Hassan H. Alhassan, Alaa Shafie, Arif Jamal Siddiqui, Fevzi Bardakci, Mejdi Snoussi, Md. Imtaiyaz Hassan
Summary: In this study, the alkaloid Harmaline (HAR) was investigated for its potential as a MARK4 inhibitor. Molecular docking and fluorescence binding studies showed a strong binding affinity between HAR and MARK4, and HAR significantly inhibited the kinase activity of MARK4. Structural investigations revealed that HAR binds to the active site pocket of MARK4 and forms multiple non-covalent interactions with biologically important residues. These findings suggest that HAR could be a potential therapeutic agent for MARK4-related diseases, including Alzheimer's disease.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Fatima Khatoon, Sabeeha Ali, Vijay Kumar, Abdelbaset Mohamed Elasbali, Hassan H. Alhassan, Salem Hussain Alharethi, Asimul Islam, Md Imtaiyaz Hassan
Summary: Honokiol is a natural polyphenolic compound extracted from Magnolia grandiflora, with various pharmacological properties and potential therapeutic implications, including antimicrobial and anti-tumorigenic effects. Recent studies have also suggested its potential role in COVID-19 therapy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Aiman Mushtaq, Prithvi Singh, Gulnaz Tabassum, Taj Mohammad, Md Imtaiyaz Hassan, Mansoor Ali Syed, Ravins Dohare
Summary: This study identified key genes in lung cancer and their potential as biomarkers for disease prognosis and targeted therapy. Several potential drug candidates were also identified.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Rashid Waseem, Neetu Singh Yadav, Tanzeel Khan, Faizan Ahmad, Syed Naqui Kazim, Md Imtaiyaz Hassan, Amresh Prakash, Asimul Islam
Summary: In this study, urea-induced denaturation was used to investigate the conformational changes of irisin. The results showed that the unfolding of irisin occurs in a biphasic manner, with an intermediate state (I) populated at 2.5 M urea concentration. Molecular dynamics (MD) simulations confirmed the presence of a molten globule state during the unfolding process of irisin.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Review
Polymer Science
Guravtar Singh Mann, Naved Azum, Anish Khan, Malik Abdul Rub, Md Imtaiyaz Hassan, Kisa Fatima, Abdullah M. Asiri
Summary: Global climate change has already caused various environmental effects and led to a shift in focus towards sustainable materials. Green composites, which combine renewable fibers with polymers, offer a wide range of applications and superior features compared to conventional materials.
Review
Nutrition & Dietetics
Md. Khabeer Azhar, Saleha Anwar, Gulam Mustafa Hasan, Anas Shamsi, Asimul Islam, Suhel Parvez, Md. Imtaiyaz Hassan
Summary: Rosmarinic acid (RA) is an abundant phytochemical with anti-inflammatory and antioxidant properties, playing significant roles in cancer, neuroprotection, and diabetes.
Review
Chemistry, Multidisciplinary
Gulam Mustafa Hasan, Md. Imtaiyaz Hassan, Sukhwinder Singh Sohal, Anas Shamsi, Manzar Alam
Summary: Non-small cell lung carcinoma (NSCLC) is the most common cancer globally, and phytochemicals and small molecule inhibitors have been found to effectively prevent NSCLC and other types of cancers by regulating signaling pathways. This review focuses on the bioactive compounds and small-molecule inhibitors, such as EGCG, Perifosine, ABT-737, Thymoquinine, Quercetin, Venetoclax, Gefitinib, and Genistein, and discusses their potential in NSCLC therapy.
Article
Chemistry, Medicinal
Maria Voura, Saleha Anwar, Ioanna Sigala, Eleftheria Parasidou, Souzanna Fragoulidou, Md. Imtaiyaz Hassan, Vasiliki Sarli
Summary: In this study, derivatives of 2-methylacridone were synthesized and tested for their MARK4 kinase inhibitory activity. The derivatives with piperazine and tryptophan moieties showed high antiproliferative activity against cancer cells.
ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE
(2023)
Article
Engineering, Civil
Prabhat Kumar, Govind P. Gupta, Rakesh Tripathi, Sahil Garg, Mohammad Mehedi Hassan
Summary: The recent growth of IoT technologies in the maritime industry has digitalized Maritime Transportation Systems (MTS), but also introduced cybersecurity threats. Cyber Threat Intelligence (CTI) is an effective security strategy, but existing solutions have low detection rates and high false alarm rates. To address these challenges, an automated framework called DLTIF has been proposed, which can accurately identify threat types.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2023)
Article
Engineering, Civil
Xiaoding Wang, Sahil Garg, Hui Lin, Georges Kaddoum, Jia Hu, Mohammad Mehedi Hassan
Summary: This paper proposes a hierarchical trust evaluation strategy based on heterogeneous blockchain, utilizing federated deep learning technology for Intelligent Transportation Systems (ITS) security.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2023)