Article
Biology
Zhuangfeng Weng, Jiefu Zheng, Yiyi Zhou, Zuer Lu, Yixi Wu, Dongyi Xu, Huanhuan Li, Huanhuan Liang, Yingfang Liu
Summary: This study reports the structural characterization of the MCM8/9 complex using cryo-electron microscopy. The complex is arranged as a heterohexamer with a central channel for DNA binding. The N-terminal OB domains of MCM8/9 have hairpin structures that unwind duplex DNA. Activation by HROB leads to a change in symmetry and rotational motion of the C-tier ring, which is important for the unwinding ability of MCM8/9.
Article
Multidisciplinary Sciences
Han Pan, Ruifang Guan, Ruixue Zhao, Guangshuo Ou, Zhucheng Chen
Summary: The central spindle in animal cells regulates the formation of the division plane during cytokinesis. The molecular backbone of centralspindlin has the propensity to undergo liquid-liquid phase separation, and the synergy between ZEN-4 and CYK-4 subunits is critical for its function in microtubule bundling and central spindle assembly. Charge-driven macromolecular condensation mediates the assembly of the central spindle by centralspindlin.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Maulin M. Patel, Leonidas Tsiokas
Summary: The primary cilium is an important organelle present in most cell types, serving as a signaling center for various cellular processes. Abnormal cilia length can lead to a range of human diseases, known as ciliopathies. While cilia assembly is well understood, the process of cilia disassembly and its biological roles remain less clear and require further investigation for potential therapeutic targets.
Article
Chemistry, Multidisciplinary
Gourab Mukherjee, Gunasekaran Velmurugan, Marion Kerscher, Jagnyesh Kumar Satpathy, Chivukula V. Sastri, Peter Comba
Summary: This study reports the synthesis and spectroscopic characterization of a relatively stable mononuclear high-spin FeIII-alkylperoxido complex supported by an engineered bispidine framework. Contrary to previous studies, this complex exhibits versatile reactivity in both electrophilic and nucleophilic reactions. Detailed mechanistic studies and computational calculations reveal a novel reaction mechanism, where a putative superoxido intermediate orchestrates the amphoteric property of the oxidant. These findings are of great significance for the design of more stable and highly active iron-oxygen adducts.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Haiming Zhuang, Dong Ji, Jigang Fan, Mingyu Li, Ran Tao, Kui Du, Shaoyong Lu, Zongtao Chai, Xiaohua Fan
Summary: Hepatitis C virus (HCV) recruits host miRNA to form a complex with Ago2 protein for self-protection against exonucleolytic attacks. Structural features and nucleotide sequence of HCV RNA can affect the binding between the complex and Ago2 protein, leading to the destabilization of target RNA.
Article
Multidisciplinary Sciences
Zeyuan Guan, Qunxia Zhang, Zhifei Zhang, Jiaqi Zuo, Juan Chen, Ruiwen Liu, Julie Savarin, Larissa Broger, Peng Cheng, Qiang Wang, Kai Pei, Delin Zhang, Tingting Zou, Junjie Yan, Ping Yin, Michael Hothorn, Zhu Liu
Summary: In this study, the authors investigate the regulation of PHR2 by SPX2 based on crystal structure analysis. They propose that SPX2 prevents the DNA binding and oligomerisation of PHR2 to inactivate it. These findings provide insights into how PP-InsPs activate SPX receptor proteins to target PHR family transcription factors.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
E. Read, B. Lonetti, S. Gineste, A. T. Sutton, E. Di Cola, P. Castignolles, M. Gaborieau, A. -F. Mingotaud, M. Destarac, J. -D. Marty
Summary: The study focuses on investigating the structural changes of polyion complexes (PICs) composed of thermoresponsive polymers with temperature variations, and suggests that the polymer structure and PICs composition play a crucial role in the observed modifications.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Multidisciplinary Sciences
Komal Soni, Anusree Sivadas, Attila Horvath, Nikolay Dobrev, Rippei Hayashi, Leo Kiss, Bernd Simon, Klemens Wild, Irmgard Sinning, Tamas Fischer
Summary: In this study, the interaction between the MTREC core protein Red1 and Pla1 is characterized and its functional relevance in vivo is assessed. The authors found that the Red1-Pla1 interaction leads to hyperadenylation of CUTs, facilitating their degradation. Additionally, this interaction is required for the efficient assembly of facultative heterochromatic islands in fission yeast.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Sicong Li, Priscila dos Santos Bury, Fanglu Huang, Junhong Guo, Guo Sun, Anna Reva, Chuan Huang, Xinyun Jian, Yuan Li, Jiahai Zhou, Zixin Deng, Finian J. Leeper, Peter F. Leadlay, Marcio V. B. Dias, Yuhui Sun
Summary: The study reveals the dideoxygenation process of intermediates JI-20A and JI-20B in gentamicin, starting with phosphorylation catalyzed by GenP and then modified by GenB3 and GenB4 to form gentamicin C complex. Insights into the catalytic mechanisms of GenB3 and GenB4 are provided through crystal structures and site-directed mutagenesis.
Article
Biochemistry & Molecular Biology
Lei Chen, Die Zhang, Ling-Feng Wei, Wei-Jia Zhu, Xiao-Qin Yan, Rui Zhou, Zia-ud Din, Wen-Ping Ding, Tie-Zheng Ma, Jie Cai
Summary: This study presents a self-assembly method for the fabrication of multilayer-starch-based microgels used for anthocyanin encapsulation. The molecular interactions between the starch and anthocyanins facilitated the encapsulation process. The increase in the number of layers resulted in a more compact microgel structure and improved encapsulation stability.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Weili Heng, Yutong Song, Minqian Luo, Enshi Hu, Yuanfeng Wei, Yuan Gao, Zunting Pang, Jianjun Zhang, Shuai Qian
Summary: In this study, the effect of the coformer on the crystallization kinetics of coamorphous systems was investigated. The addition of SAC to LH changed the crystallization mechanism and reduced the crystallization rates. Although the coamorphous system had higher molecular mobility and dynamic fragility, it also had higher configurational entropy which improved its stability. The study provides a better understanding of the crystallization behavior of coamorphous systems and highlights the importance of configurational entropy in stabilizing them.
JOURNAL OF CONTROLLED RELEASE
(2023)
Review
Biochemistry & Molecular Biology
Theresa M. Smith, Barry M. Willardson
Summary: The cytosolic chaperonin CCT is essential for eukaryotes as it folds a significant portion of the proteome, including actin and tubulin. It is also involved in human diseases and can be a potential therapeutic target. Recent studies have focused on understanding CCT's mechanisms in substrate recognition and folding, revealing new binding sites and mechanisms. These findings provide insights into CCT's function and its implications for human health.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Bai Li, Manoj Kumar, Chuan Zhou, Lei Li, Joseph S. Francisco
Summary: This study simulated the reaction between Criegee intermediates and hydroperoxyl radicals and found that the reaction is temperature-dependent. The results suggest that HO2 radicals may play a role in the formation of new particles in the troposphere, and water molecules may also be important in the reactions of Criegee intermediates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Ashwin Chaturvedi, Gavin A. McCarver, Soumalya Sinha, Elijah G. Hix, Konstantinos D. Vogiatzis, Jianbing Jiang
Summary: The study validates the effectiveness of a main-group-element-based tin porphyrin complex as a molecular electrocatalyst for proton reduction. The PEGylated Sn porphyrin complex exhibited high activity and high selectivity in acetonitrile. Spectroelectrochemical analysis and quantum chemical calculations provided insights into the mechanism of proton reduction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Inorganic & Nuclear
Jimin Yang, Qingde Zhuo, Zhenbo Mo, Zhaomin Hou, Yi Luo
Summary: The mechanism of dinitrogen cleavage by a PNP-coordinated dititanium polyhydride complex has been computationally investigated, revealing a multi-state reactivity scenario for the process. Prior to N-N cleavage, H-2 elimination is facilitated by coupling two terminal hydrides, with stabilization provided by a planar PNP-pincer ligand. Additionally, the THF solvent promotes H-2 elimination due to the similar polarity of intermediates or transition states.
DALTON TRANSACTIONS
(2022)
Article
Multidisciplinary Sciences
Shan Lu, Qiaozhen Ye, Digvijay Singh, Yong Cao, Jolene K. Diedrich, John R. Yates, Elizabeth Villa, Don W. Cleveland, Kevin D. Corbett
Summary: The SARS-CoV-2 nucleocapsid (N) protein binds viral RNA and undergoes liquid-liquid phase separation driven by its central intrinsically-disordered region, modulated by phosphorylation. Additionally, the N protein interacts with the membrane protein M to form mutually exclusive compartments in a three-component mixture with RNA.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Xiaojing Pan, Zhangqiang Li, Xueqin Jin, Yanyu Zhao, Gaoxingyu Huang, Xiaoshuang Huang, Zilin Shen, Yong Cao, Mengqiu Dong, Jianlin Lei, Nieng Yan
Summary: The high-resolution structures of human Na(v)1.1 and Na(v)1.5 channels associated with epilepsy and cardiac disorders were reported. Comparative structural analysis revealed common clusters of disease mutations in both channels. These mutations may affect the structural integrity and electromechanical coupling of the channels.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Si-Yao Lu, Chong-Lei Fu, Liang Liang, Bo Yang, Wei Shen, Qiu-Wen Wang, Yun Chen, Yan-Fen Chen, Yao-Nan Liu, Lin Zhu, Jieqing Zhao, Wei Shi, Shuangli Mi, Jun Yao
Summary: miR-218-2 plays a crucial role in the cognitive functions of mice by regulating C3 to affect presynaptic functions, and synaptic and learning deficits can be rescued by restoring C3 activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Yun Chen, Ying-Han Wang, Yi Zheng, Meijing Li, Bing Wang, Qiu-Wen Wang, Chong-Lei Fu, Yao-Nan Liu, Xueming Li, Jun Yao
Summary: Synaptic vesicle docking is a dynamic multi-stage process essential for efficient neurotransmitter release. In mouse hippocampal synapses, SV docking is initiated by Syt1 at approximately 12 nm to the active zone, with PI(4,5)P2 being the membrane partner of Syt1. The SNARE complex contributes only to tight SV docking within 0-2 nm.
Article
Biology
Heesun Kim, Yue-He Ding, Shan Lu, Mei-Qing Zuo, Wendy Tan, Darryl Conte, Meng-Qiu Dong, Craig C. Mello
Summary: Germlines play a crucial role in maintaining germline fate and surveillance in adult germlines. Research has found that PIE-1 plays a key role in integrating and regulating genetic information, engaging in SUMO pathway and capturing HDAC SUMOylation.
Article
Biochemistry & Molecular Biology
Qiu-Wen Wang, Ying-Han Wang, Bing Wang, Yun Chen, Si-Yao Lu, Jun Yao
Summary: Synaptotagmin-7 (Syt7) acts as a redundant Ca2+ sensor along with Syt1/Doc2 to drive spontaneous glutamate release, which activates GluN2B-NMDARs and contributes significantly to mental illness. Experimental results demonstrate that Syt7 triggers spontaneous release directly through its Ca2+ binding motif, and the localization of Syt7 in the active zone is crucial for its function. Identified Syt7 SNPs in bipolar disorder patients impair the function of Syt7 in spontaneous release, suggesting its potential involvement in neuropsychiatric disorders.
Article
Immunology
Qiaozhen Ye, Shan Lu, Kevin D. Corbett
Summary: The COVID-19 pandemic caused by SARS-CoV-2 is a severe public health event, requiring rapid and accurate diagnostic methods. Antigen tests, especially those detecting the SARS-CoV-2 Nucleocapsid protein, are effective in detecting active infections. Research has shown that three llama-derived single-domain antibodies have high affinity for the SARS-CoV-2 Nucleocapsid protein, offering potential for developing affordable diagnostic tests for all circulating variants of SARS-CoV-2.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Chenchen Mi, Li Zhang, Guoqiang Huang, Guangcan Shao, Fan Yang, Xin You, Meng-Qiu Dong, Shan Sun, Sen-Fang Sui
Summary: This study presents cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states, revealing a dimeric architecture assembled by two triangle-shaped monomers. The Ypt32-bound monomer captures the closed conformation and interacts with core TRAPP/TRAPPI, Trs120, and Trs31. These structures provide insights into the assembly of TRAPPII and the mechanism of Ypt31/Ypt32 activation by TRAPPII.
Article
Multidisciplinary Sciences
Jiayue Su, Desheng Liu, Fan Yang, Mei-Qing Zuo, Chang Li, Meng-Qiu Dong, Shan Sun, Sen-Fang Sui
Summary: The TOM complex, composed of Tom 20, Tom22, and Tom70, plays a crucial role in recognizing and transferring preproteins across the mitochondrial membrane. Cryo-EM structures of the complex have been reported, but the exact function and mechanism of Tom22 and Tom20 as TOM receptors remain unclear. This study provides structural and biochemical insights into their roles in presequence binding and protein translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Chao Zhai, Nan Zhang, Xi-Xia Li, Xi Chen, Fei Sun, Meng-Qiu Dong
Summary: This study investigated the changes in distribution of vitellogenins (Vtg) in C. elegans as it ages. The levels of Vtg increase significantly with age, and inhibiting their production extends lifespan. Additionally, the study found that mislocalized yolk organelles in post-reproductive worms also increase in size, potentially worsening aging pathologies.
Article
Multidisciplinary Sciences
Yan-Ping Zhang, Wen-Hong Zhang, Pan Zhang, Qi Li, Yue Sun, Jia-Wen Wang, Shaobing O. Zhang, Tao Cai, Cheng Zhan, Meng-Qiu Dong
Summary: This study explores the expression and regulation of the daf-2 gene, which is responsible for doubling the lifespan of Caenorhabditis elegans. The findings reveal that daf-2 and its downstream transcription factor daf-16 are expressed ubiquitously in the organism. Additionally, the study shows that intracellular signaling between DAF-2 and DAF-16 in the intestine plays a major role in lifespan regulation. Altering metabolism, particularly down-regulating insulin/IGF-1 signaling, is suggested as a possible mechanism for promoting longevity.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Atomic, Molecular & Chemical
Mei-Qing Zuo, Rui-Xiang Sun, Meng-Qiu Dong
Summary: Based on high-resolution and accurate-mass MS analysis, this study reveals that highly acidic D/E-rich peptides or proteins are difficult to identify by positive-ion-mode mass spectrometry (MS), and negative-ion-mode MS is a potential alternative. The study identifies abundant backbone or side-chain neutral losses (NL) induced by higher-energy collisional dissociation (HCD) of deprotonated peptides, and provides an updated ranking list of NLs by abundance. The findings suggest that under negative-ion HCD, D/E-rich peptides are challenging to identify, and choosing a protease that generates peptides with fewer D/E residues can improve the identification of highly acidic proteins.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Yong Cao, Xin-Tong Liu, Peng-Zhi Mao, Zhen-Lin Chen, Ching Tarn, Meng-Qiu Dong
Summary: In mass spectrometry data analysis, different search engines have different settings for cross-linkable sites. Some only include lysine and protein N-terminus, while others also include serine, threonine, and tyrosine by default. By using chemically inert amino acids as cross-linkable sites, we show that STY-cross-links identified by software are as reliable as GVL-cross-links.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Rui-Xiang Sun, Mei-Qing Zuo, Ji-Shuai Zhang, Meng-Qiu Dong
Summary: Mass spectrometry (MS) analysis is important in RNA therapeutics and epitranscriptomics research. In this study, we characterized the fragmentation behaviors of 26 synthetic RNA oligonucleotides using collision-induced dissociation (CID). We found that sequencing ions accounted for the majority of the peak intensity in the CID spectra, while precursor ions with loss of a nucleobase also contributed significantly. The precursor charge of the RNA oligonucleotides had a significant impact on their fragmentation behaviors.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Haiyang Yu, Shan Lu, Kelsey Gasior, Digvijay Singh, Sonia Vazquez-Sanchez, Olga Tapia, Divek Toprani, Melinda S. Beccari, John R. Yates, Sandrine Cruz, Jay M. Newby, Miguel Lafarga, Amy S. Gladfelter, Elizabeth Villa, Don W. Cleveland
Summary: This study found that the RNA binding protein TDP-43 forms intranuclear or cytoplasmic aggregates in age-related neurodegenerative diseases. Through mathematical modeling, the primary components of TDP-43 liquid core were identified to be HSP70 family chaperones, and these structures converted to aggregates when ATP levels were reduced.
