Article
Multidisciplinary Sciences
Luyao Bao, Juan Hu, Bowen Zhan, Mingzhe Chi, Zhengyang Li, Sen Wang, Chan Shan, Zhaozhao Zhao, Yanchao Guo, Xiaoming Ding, Chaoneng Ji, Shengce Tao, Ting Ni, Xuelian Zhang, Guoping Zhao, Jixi Li
Summary: This study reports the crystal structures of RNase J from Mycobacterium tuberculosis in apo-state and complex with single strand RNA, revealing its physiological function in RNA metabolism.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Nelly Morellet, Pierre Hardouin, Nadine Assrir, Carine van Heijenoort, Beatrice Golinelli-Pimpaneau
Summary: This study investigates the structural organization of Bacillus subtilis RNase Y using NMR and AlphaFold models. The N-terminal domain of RNase Y is found to have a long coiled-coil structure connected to a C-terminal region composed of helices. The structural organization of the N-terminal domain is maintained in the full-length model of RNase Y, and the C-terminal region is likely involved in the dimerization of RNase Y.
Article
Chemistry, Physical
Aditya K. Padhi, Timir Tripathi
Summary: Dimerization of SARS-CoV-2 main protease is essential for its activity, and mutations in the dimeric interface may further stabilize it. Through protein design strategies, potential mutations that can stabilize the protein have been identified in the circulating SARS-CoV-2 genomes, providing insights into viral adaptation and mutational surveillance.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Jixian Wang, Xin-Xin Tian, Lei Yu, David J. Young, Wen-Bao Wang, Hai-Yan Li, Hong-Xi Li
Summary: Defect engineering is a promising strategy to enhance the photocatalytic hydrogen production performance of semiconductive materials by modulating structural defects. A series of covalent organic frameworks, TAPT-COF-X, with controlled proportion of defects showed improved hydrogen evolution rates, with TAPT-COF-7 achieving a H2 evolution rate 2.3 times higher than the parent TAPT-COF. Time-resolved fluorescence measurements and electrochemical impedance spectroscopy indicated that TAPT-COF-7 also had the highest charge separation efficiency.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Hematology
Louris J. Feitsma, Harma C. Brondijk, Gavin E. Jarvis, Dominique Hagemans, Dominique Bihan, Natasia Jerah, Marian Versteeg, Richard W. Farndale, Eric G. Huizinga
Summary: Glycoprotein VI (GPVI) plays a crucial role in collagen-induced platelet activation and is essential in the development of thrombosis, heart attack, and stroke. This study reveals the crystal structures of GPVI bound to collagen peptides and identifies the binding site and essential residues for collagen binding. The study also demonstrates the binding of GPVI to collagen chains containing the sequence motif OGPOGP. These findings provide insights for the development of receptor-specific therapeutics targeting GPVI.
Review
Biochemistry & Molecular Biology
Amita R. Sahoo, Matthias Buck
Summary: This review focuses on the interaction between Eph receptors and ephrin ligands in regulating various processes from embryonic development to tissue homeostasis. It also highlights the importance of the transmembrane domain of Eph receptors in signal transduction and introduces techniques such as NMR and molecular modeling used to study them. Additionally, the use of transmembrane peptides to manipulate Eph receptor signaling is discussed, along with future directions for research in this field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nirupa Nagaratnam, Silvia L. Delker, Rebecca Jernigan, Thomas E. Edwards, Janey Snider, Darren Thifault, Dewight Williams, Brent L. Nannenga, Mary Stofega, Lidia Sambucetti, James J. Hsieh, Andrew J. Flint, Petra Fromme, Jose M. Martin-Garcia
Summary: Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, with its activity closely related to the proliferation, invasion, and metastasis of cancer cells. This study reveals the structure and function of the active site of Taspase1, providing a potential target for the development of anticancer therapeutics.
Article
Multidisciplinary Sciences
Gyunghee Jo, Jeomil Bae, Ho Jeong Hong, Ah-reum Han, Do-Kyun Kim, Seon Pyo Hong, Jung A. Kim, Sangkyu Lee, Gou Young Koh, Ho Min Kim
Summary: Angiopoietin (Angpt)-Tie receptor 2 (Tie2) plays a key role in regulating vascular stability and is a potential therapeutic target in vascular diseases. A new Tie2-agonistic antibody has been developed, targeting a site distinct from the Angpt1-binding site, influencing Tie2 clustering and activation in an Angpt2 inhibition-resistant manner.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Licong He, Qiaoyu Zhao, Jianzhong Qi, Yifan Wang, Wenyu Han, Zhangcheng Chen, Yao Cong, Sheng Wang
Summary: The cryo-EM structure of human 5-HT6R-Gs heterotrimer reveals key structural determinants for its constitutive activity, which can be targeted for the design of more effective medications for neuropsychiatric disorders. This study provides valuable insights into the molecular basis of constitutive activity and its therapeutic potential.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Budheswar Dehury, Sarbani Mishra, Sanghamitra Pati
Summary: The spread of different SARS-CoV-2 variants highlights the importance of understanding the structural properties of its proteins. This study reveals the structural dynamics of M-PRO, an attractive drug target for antiviral treatments, and identifies stable and compact conformations with intact catalytic sites and structural integrity.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yujing Ren, Beiming Yu, Lihui Zhou, Feng Wang, Yanfeng Wang
Summary: This study analyzed the phosphorylation mechanism of UCHL3 in its deubiquitinating activity and provided in vitro evidence of UCHL3's cleavage activity towards specific types of polyubiquitin chains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Florian Bleffert, Joachim Granzin, Muttalip Caliskan, Stephan N. Schott-Verdugo, Meike Siebers, Bjoern Thiele, Laurence Rahme, Sebastian Felgner, Peter Doermann, Holger Gohlke, Renu Batra-Safferling, Karl-Erich Jaeger, Filip Kovacic
Summary: Cells adapt their membrane composition to changing conditions by regulating GPL synthesis and degradation. This study identified a cytoplasmic membrane-bound phospholipase A(1) (PlaF) from Pseudomonas aeruginosa that might be involved in GPL remodeling. PlaF is an important virulence factor and its structure and activation mechanism were revealed, offering insights for the development of therapeutics targeting PlaF.
Article
Chemistry, Multidisciplinary
Hanggara Sudrajat, Sri Hartuti, Sandhya Babel, Truong Khang Nguyen, Hien Duy Tong
Summary: Constructing a SnO2-ZnO heterostructure enhances the photocatalytic activity by restricting electron-hole recombination, increasing the electron population by up to 17 times. XPS, XANES, and EXAFS analyses confirm changes in the chemical state and local structure of Zn cations upon heterostructuring.
JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS
(2021)
Article
Multidisciplinary Sciences
Huirong Yang, Zishuo Yu, Xizi Chen, Jiabei Li, Ningning Li, Jiaxuan Cheng, Ning Gao, Hai-Xin Yuan, Dan Ye, Kun-Liang Guan, Yanhui Xu
Summary: The Tuberous sclerosis complex (TSC) consists of TSC1, TSC2, and TBC1D7 in a 2:2:1 stoichiometry, forming an arch-shaped structure. The complex includes two TSC1 coiled-coils and one TBC1D7 bridging over the TSC2 dimer, showing asymmetry. The TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1, revealing mechanisms of TSC complex assembly and GAP activity.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sudhaker Dharavath, Gary X. Shaw, Xinhua Ji
Summary: RNase III family is a class of dsRNA-specific endonucleases that recognizes substrates in a sequence-specific manner. This study reveals the reaction trajectory of two-Mg2+-ion catalysis by prokaryotic and eukaryotic RNase III enzymes and identifies the functional role of a third Mg2+ ion in bacterial RNase III.
Article
Biochemistry & Molecular Biology
Huizhi Lu, Liangyan Wang, Shengjie Li, Chaoming Pan, Kaiying Cheng, Yuxia Luo, Hong Xu, Bing Tian, Ye Zhao, Yuejin Hua
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemical Research Methods
Congli Zhou, Jingli Dai, Huizhi Lu, Zijing Chen, Miao Guo, Yuan He, Kaixuan Gao, Tong Ge, Jiayu Jin, Liangyan Wang, Bing Tian, Yuejin Hua, Ye Zhao
Article
Nanoscience & Nanotechnology
Yulan Weng, Jiulong Li, Xingcheng Ding, Binqiang Wang, Shang Dai, Yulong Zhou, Renjiang Pang, Ye Zhao, Hong Xu, Bing Tian, Yuejin Hua
INTERNATIONAL JOURNAL OF NANOMEDICINE
(2020)
Article
Microbiology
Yuan He, Yiyi Wang, Chen Qin, Ying Xu, Kaiying Cheng, Hong Xu, Bing Tan, Ye Zhao, Liangyan Wang, Yuejin Hua
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Xingru Zhou, Xuanyi Chen, Ying An, Huizhi Lu, Liangyan Wang, Hong Xu, Bing Tian, Ye Zhao, Yuejin Hua
Summary: Deinococcus radiodurans can survive under extreme conditions of ionizing radiation and desiccation. The DNA polymerase A of D. radiodurans, DrPolA, exhibits unique biochemical characteristics such as high fidelity and gap endonuclease activity, which contribute to its outstanding DNA repair capacity.
Article
Genetics & Heredity
Jingli Dai, Zijing Chen, Jinfeng Hou, Yudong Wang, Miao Guo, Jiajia Cao, Liangyan Wang, Hong Xu, Bing Tian, Ye Zhao
Summary: Deinococcus radiodurans exhibits significant resistance to various DNA-damaging agents. A toxin-antitoxin system, MazEF, responds to DNA damage stress in D. radiodurans. Analysis revealed regulation of genes involved in membrane trafficking and metal ion transportation by MazEF in response to DNA damage stress. Additionally, the MazEF system may mediate cell death by reducing ROS accumulation upon DNA damage stress.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Miao Guo, Yina Wang, Yuyue Tang, Zijing Chen, Jinfeng Hou, Jingli Dai, Yudong Wang, Liangyan Wang, Hong Xu, Bing Tian, Yuejin Hua, Ye Zhao
Summary: Pol mu can perform gap-filling repair synthesis in NHEJ and has a mutagenic role under certain conditions. Crystal structures and kinetics of Pol mu reveal insights into its molecular mechanism during dGTP misincorporation, with two residues playing a crucial role in the active site microenvironment.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Yinping Tian, Qiang Zhu, Zeyu Sun, Didi Geng, Bingyi Lin, Xiaoling Su, Jiahui He, Miao Guo, Hong Xu, Ye Zhao, Weijie Qin, Peng George Wang, Liuqing Wen, Wen Yi
Summary: This study identifies a novel O-GlcNAcylated protein and reveals its regulatory role in cell cycle progression and DNA damage response.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Microbiology
Jianling Cai, Chaoming Pan, Ye Zhao, Hong Xu, Bing Tian, Liangyan Wang, Yuejin Hua
Summary: DRJAMM, a protein with efficient catalytic activity, shows strong adaptability to different metal ions and temperatures. It plays a crucial role in oxidative resistance and is required for the normal functioning of the dimethyl sulfoxide respiratory system in D. radiodurans.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ying Xu, Lingyi Xu, Chen Qin, Liangyan Wang, Jiangtao Guo, Yuejin Hua, Ye Zhao
Summary: This study reports the structure of a bacterial HerA-NurA complex from Deinococcus radiodurans, revealing the barrel-like hexameric structure of HerA and the unique dimer subcomplex structure of NurA. In addition, the study also finds that the extended N-terminal region (ENR) of NurA is involved in bacterial NurA dimerization and activation, and the flexible ENR is close to the HerA-NurA interface, dividing the central channel of the DrNurA dimer into two halves, potentially involved in DNA end processing.
Article
Microbiology
Chen Qin, Wanchun Han, Ying Xu, Ye Zhao, Hong Xu, Bing Tian, Liangyan Wang, Yuejin Hua
Summary: In this study, the biochemical properties and crystal structure of RuvC enzyme from Deinococcus radiodurans were described. DrRuvC exhibited specific binding and cleavage abilities towards HJ DNA, with a preference for Mn2+ as the co-factor. The crystal structure of DrRuvC revealed important amino acid sites for its activities, indicating its typical resolvase characteristics with a specific choice for metal co-factor.
Article
Biochemistry & Molecular Biology
Jinfeng Hou, Jingli Dai, Zijing Chen, Yudong Wang, Jiajia Cao, Jing Hu, Shumai Ye, Yuejin Hua, Ye Zhao
Summary: This study investigates the phosphorylation regulation role of a histone-like HU protein from Deinococcus radiodurans. The results show that phosphorylation modulates the DNA-binding capabilities of the histone-like HU protein, contributing to the environmental adaptation of this organism.
PROTEIN AND PEPTIDE LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Jianling Cai, Maoxu Zhang, Zijing Chen, Ye Zhao, Hong Xu, Bing Tian, Liangyan Wang, Yuejin Hua
Summary: In this study, the essential role of MoaE protein in the extreme resistance of Deinococcus radiodurans was demonstrated through in vitro and in vivo experiments. The crystal structure of DrMoaE was determined to be a dimer, which disappeared after mutation. Deletion of drmoaE gene resulted in sensitivity to DNA damage stress and slower growth rate in D. radiodurans. Increased transcript levels of drmoaE and accumulation of intracellular reactive oxygen species under oxidative stress suggested its involvement in antioxidant process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zijing Chen, Yuyue Tang, Yuejin Hua, Ye Zhao
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Article
Microbiology
Jingli Dai, Kaixuan Gao, Tao Yao, Huizhi Lu, Congli Zhou, Miao Guo, Shang Dai, Liangyan Wang, Hong Xu, Bing Tian, Yuejin Hua, Ye Zhao
MICROBIOLOGICAL RESEARCH
(2020)