Article
Biochemistry & Molecular Biology
Ying-Ying Wang, Jianxiu Zhang, Xiao-Man Liu, Yulu Li, Jianhua Sui, Meng-Qiu Dong, Keqiong Ye, Li-Lin Du
Summary: This study uncovers the mechanism of how a receptor called Nbr1 in fission yeast recognizes specific protein cargos, revealing the mechanism of autophagy cargo recognition. The research shows that Nbr1-ZZ1 can not only recognize the N-termini of cargos via a conserved acidic pocket, but also engage other parts of the cargos in a cargo-specific manner.
Editorial Material
Cell Biology
Zhao-Qian Pan, Keqiong Ye, Li-Lin Du
Summary: In selective macroautophagy, autophagy receptors play a crucial role in determining cargo specificity. Most autophagy receptors are found only in certain eukaryotic lineages, except for Nbr1 proteins, which are conserved across eukaryotes. Our study discovered that the FW domain in the Nbr1 protein of Chaetomium thermophilum can bind to the autophagy cargo alpha-mannosidase Ams1, and this binding promotes the autophagic delivery of Ams1 into vacuoles. We also revealed the structural mechanism of Ams1 recognition by the FW domain through solving the structure of the FW-Ams1 complex.
Review
Biochemistry & Molecular Biology
Matthew P. Hardy, Mariam Mansour, Tony Rowe, Sandra Wymann
Summary: This review provides a detailed understanding of how the extracellular domain of human complement receptor 1 (CR1) mediates complement cascade regulation through decay acceleration activity and co-factor activity mechanisms. It also discusses the interaction of CR1 with multiple ligands and explains the differential complement pathway inhibition observed with CR1-based therapeutic compounds.
Article
Biochemistry & Molecular Biology
Mariona Torrens-Fontanals, Alejandro Peralta-Garcia, Carmine Talarico, Ramon Guixa-Gonzalez, Toni Giorgino, Jana Selent
Summary: SCoV2-MD is an online resource that organizes atomistic simulations of the SARS-CoV-2 proteome. It cross-references molecular data with pandemic evolution and allows interactive analysis through a web interface for studying the structure and function of viral proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biochemistry & Molecular Biology
Zhenbiao Yang
Summary: This study reveals that a rice wall-associated kinase, OsWAK11, can perceive pectin and regulate growth by binding to the receptor OsBRI1.
Article
Biochemistry & Molecular Biology
Shuwei Xie, Naava Naslavsky, Steve Caplan
Summary: Primary cilia are sensory organelles that coordinate diverse signaling pathways, controlling development and homeostasis. In this study, we found that EHD1 regulates the ubiquitination of CP110, a protein required for ciliogenesis, and identified HERC2 and MIB1 as E3 ubiquitin ligases that interact with and ubiquitinate CP110. We also discovered that HERC2 is necessary for ciliogenesis and localizes to centriolar satellites, which play a role in ciliogenesis regulation. Our findings highlight a mechanism in which EHD1 controls the movement of centriolar satellites and HERC2 to the mother centriole during ciliogenesis, promoting CP110 ubiquitination and degradation.
Article
Medicine, General & Internal
V. Shinde, S. Bhikha, Z. Hoosain, M. Archary, Q. Bhorat, L. Fairlie, U. Lalloo, M. S. L. Masilela, D. Moodley, S. Hanley, L. Fouche, C. Louw, M. Tameris, N. Singh, A. Goga, K. Dheda, C. Grobbelaar, G. Kruger, N. Carrim-Ganey, V. Baillie, T. de Oliveira, A. Lombard Koen, J. J. Lombaard, R. Mngqibisa, A. E. Bhorat, G. Benade, N. Lalloo, A. Pitsi, P. -L. Vollgraaff, A. Luabeya, A. Esmail, F. G. Petrick, A. Oommen-Jose, S. Foulkes, K. Ahmed, A. Thombrayil, L. Fries, S. Cloney-Clark, M. Zhu, C. Bennett, G. Albert, E. Faust, J. S. Plested, A. Robertson, S. Neal, I. Cho, G. M. Glenn, F. Dubovsky, S. A. Madhi
Summary: The NVX-CoV2373 vaccine showed efficacy in preventing Covid-19, with higher vaccine efficacy observed among HIV-negative participants. Most infections were caused by the B.1.351 variant.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Vadim R. Viviani, Jaqueline Rodrigues Silva, Paulo Lee Ho
Summary: A novel bioluminescent fusion protein was developed in this study, showing higher bioluminescence activity and sustained emission in immunoassays. It successfully detected various antigens and antibodies, with potential application in Western Blotting.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Matheus V. F. Ferraz, Emerson G. Moreira, Danilo F. Coelho, Gabriel L. Wallau, Roberto D. Lins
Summary: Immune evasion of SARS-CoV-2 variants is primarily attributed to decreased cross-reactivity of previously elicited antibodies, with increased affinity to hACE2 playing a smaller role. The affinity between antibodies and variants is influenced by the remodeling of electrostatic surface potential of the Spike RBDs. The P.3 variant is considered a putative VOC.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Darren P. Martin, Steven Weaver, Houriiyah Tegally, James Emmanuel San, Stephen D. Shank, Eduan Wilkinson, Alexander G. Lucaci, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J. Lessells, Ravindra K. Gupta, Joel O. Wertheim, Anton Nekturenko, Ben Murrell, Gordon W. Harkins, Philippe Lemey, Oscar A. MacLean, David L. Robertson, Tulio de Oliveira, Sergei L. Kosakovsky Pond
Summary: The emergence of the 501Y lineages of SARS-CoV-2 in 2020 coincided with a global shift in selective forces acting on various genes, leading to repeated convergent mutations at 35 genome sites known as the 501Y meta-signature. This meta-signature includes multiple mutation combinations that promote the persistence of diverse SARS-CoV-2 lineages in the face of increasing host immune recognition.
Article
Biochemical Research Methods
Gabriel Cia, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci
Summary: The article introduces a structure-based computational model called SpikePro, which can quickly and accurately predict the viral fitness of newly emerging SARS-CoV-2 variants. The model evaluates the virus's transmissibility, infectivity, immune escape, and reproduction rate, providing crucial information for decision-making in the formulation of COVID-19 plans before new waves occur.
Article
Multidisciplinary Sciences
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Nei-Yuan Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N. Bhiman, Carolyn Williamson, Tulio de Oliveira
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Multidisciplinary Sciences
Yunlong Cao, Jing Wang, Fanchong Jian, Tianhe Xiao, Weiliang Song, Ayijiang Yisimayi, Weijin Huang, Qianqian Li, Peng Wang, Ran An, Yao Wang, Xiao Niu, Sijie Yang, Hui Liang, Haiyan Sun, Tao Li, Yuanling Yu, Qianqian Cui, Shuo Liu, Xiaodong Yang, Shuo Du, Zhiying Zhang, Xiaohua Hao, Fei Shao, Ronghua Jin, Xiangxi Wang, Junyu Xiao, Youchun Wang, Xiaoliang Sunney Xie
Summary: The Omicron variant of SARS-CoV-2 contains 15 mutations in the receptor-binding domain, leading to evasion of over 85% of tested neutralizing antibodies. Different epitope groups of neutralizing antibodies are affected to varying degrees by single mutations of Omicron. Antibodies targeting the conserved region of sarbecovirus remain most effective against Omicron.
Article
Multidisciplinary Sciences
Sebastian Weigang, Jonas Fuchs, Gert Zimmer, Daniel Schnepf, Lisa Kern, Julius Beer, Hendrik Luxenburger, Jakob Ankerhold, Valeria Falcone, Janine Kemming, Maike Hofmann, Robert Thimme, Christoph Neumann-Haefelin, Svenja Ulferts, Robert Grosse, Daniel Hornuss, Yakup Tanriver, Siegbert Rieg, Dirk Wagner, Daniela Huzly, Martin Schwemmle, Marcus Panning, Georg Kochs
Summary: In a longitudinal case study, researchers demonstrate that SARS-CoV-2 variants with reduced sensitivity to neutralizing antibodies can evolve within persistently infected immunosuppressed patients. The study suggests that immunocompromised patients may serve as a potential source for the emergence of harmful variants, although immune control against these variants can still be achieved in some cases through the generation of neutralizing antibodies upon lowering immunosuppressive treatment.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
M. Cyrus Maher, Istvan Bartha, Steven Weaver, Julia di Iulio, Elena Ferri, Leah Soriaga, Florian A. Lempp, Brian L. Hie, Bryan Bryson, Bonnie Berger, David L. Robertson, Gyorgy Snell, Davide Corti, Herbert W. Virgin, Sergei L. Kosakovsky Pond, Amalio Telenti
Summary: This study predicts future variants of SARS-CoV-2 by analyzing various factors affecting its evolution, including ACE2-mediated transmissibility and host immunity. The researchers successfully identified mutations that will emerge in different phases of the pandemic and assessed their impact on therapeutic antibodies. This modeling approach has important implications for predicting emerging variants of SARS-CoV-2 and can be applied to other rapidly evolving pathogens.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Editorial Material
Cell Biology
Yi Zhang, Su Ran Mun, Juan F. Linares, Christina G. Towers, Andrew Thorburn, Maria T. Diaz-Meco, Yong Tae Kwon, Tatiana G. Kutateladze
Editorial Material
Biochemistry & Molecular Biology
Yi Zhang, Tatiana G. Kutateladze
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
News Item
Chemistry, Multidisciplinary
Yi Zhang, Tatiana G. Kutateladze
Article
Biochemistry & Molecular Biology
Jiuyang Liu, Zhaoyu Xue, Yi Zhang, Kendra R. Vann, Xiaobing Shi, Tatiana G. Kutateladze
Editorial Material
Multidisciplinary Sciences
Yi Zhang, Tatiana G. Kutateladze
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Yi Zhang, Yiran Guo, Sheryl M. Gough, Jinyong Zhang, Kendra R. Vann, Kuai Li, Ling Cai, Xiaobing Shi, Peter D. Aplan, Gang Greg Wang, Tatiana G. Kutateladze
NATURE COMMUNICATIONS
(2020)
Review
Biochemistry & Molecular Biology
Yi Zhang, Geeta J. Narlikar, Tatiana G. Kutateladze
Summary: Biological enzymes accelerate chemical reactions in living organisms, and the complex environment within cells is a major regulator of enzyme activity. Biological condensates, formed spontaneously through phase separation, offer new possibilities for modulating enzymatic reactions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yi Zhang, Kyle Brown, Yucong Yu, Ziad Ibrahim, Mohamad Zandian, Hongwen Xuan, Steven Ingersoll, Thomas Lee, Christopher C. Ebmeier, Jiuyang Liu, Daniel Panne, Xiaobing Shi, Xiaojun Ren, Tatiana G. Kutateladze
Summary: The transcriptional co-activator and acetyltransferase p300 forms phase separated condensates in the cell nucleus, which sequester chromatin components and show decreased catalytic activity due to occlusion of the active site. However, p300 condensates can act as a storage pool of the protein with reduced HAT activity, allowing p300 to be compartmentalized and concentrated at poised or repressed chromatin regions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Brianna J. Klein, Anagha Deshpande, Khan L. Cox, Fan Xuan, Mohamad Zandian, Karina Barbosa, Sujita Khanal, Qiong Tong, Yi Zhang, Pan Zhang, Amit Sinha, Stefan K. Bohlander, Xiaobing Shi, Hong Wen, Michael G. Poirier, Aniruddha J. Deshpande, Tatiana G. Kutateladze
Summary: Chromosomal translocations involving the AF10 gene, particularly with CALM, are linked to aggressive leukemias. The exclusion or impairment of the PZP domain of AF10 in AF10 fusions leads to cellular transformation, while the introduction of this domain downregulates Hoxa genes and blocks leukemogenesis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yi Zhang, Christina G. Towers, Upendra K. Singh, Jiuyang Liu, Maria Hakansson, Derek T. Logan, Oreola Donini, Tatiana G. Kutateladze
Summary: This study describes the structural basis and biological consequences of the interaction between p62 and the next generation of IDR dusquetide. The findings show that dusquetide forms a complex with p62, modulates the p62-RIP1 complex, enhances p38 phosphorylation, and increases CEBP/B expression without activating autophagy. These findings provide insights into the molecular details of IDR action and may have implications for the development of new strategies to target p62 pharmacologically.
Article
Multidisciplinary Sciences
Thilini Abeywansha, Wei Huang, Xuan Ye, Allison Nawrocki, Xin Lan, Eckhard Jankowsky, Derek J. J. Taylor, Yi Zhang
Summary: Arginyl-tRNA-protein transferase 1 (ATE1) is a key regulator involved in protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The mechanism of how ATE1 hijacks tRNA and catalyzes the arginylation reaction from the ribosomal protein synthesis pathways remains unknown.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Dustin C. Becht, Brianna J. Klein, Akinori Kanai, Suk Min Jang, Khan L. Cox, Bing-Rui Zhou, Sabrina K. Phanor, Yi Zhang, Ruo-Wen Chen, Christopher C. Ebmeier, Catherine Lachance, Maxime Galloy, Amelie Fradet-Turcotte, Martha L. Bulyk, Yawen Bai, Michael G. Poirier, Jacques Cote, Akihiko Yokoyama, Tatiana G. Kutateladze
Summary: In this study, the authors identified and characterized two structured winged helix (WH) domains, WH1 and WH2, in MOZ and MORF, which play important roles in DNA binding. WH1 specifically recognizes unmethylated CpG sequences and WH2 binds to the dyad of the nucleosome. The DNA binding functions of WHs target MORF/MOZ to gene promoters, stimulate transcription and H3K23 acetylation, and recruit oncogenic fusions to HOXA genes, leading to leukemogenesis. These findings provide mechanistic insight into the DNA-binding mechanism of MOZ/MORF and may have implications for the development of therapeutics for diseases associated with aberrant MOZ/MORF acetyltransferase activities.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Srinivasa Penumutchu, Jiuyang Liu, Upendra K. Singh, Tatiana G. Kutateladze, Yi Zhang
Summary: The protocol describes the determination of dusquetide-binding sites of p62 using solution NMR spectroscopy, which can be applied to characterize other small molecules targeting p62.
Article
Multidisciplinary Sciences
Adam H. Tencer, Khan L. Cox, Gregory M. Wright, Yi Zhang, Christopher J. Petell, Brianna J. Klein, Brian D. Strahl, Joshua C. Black, Michael G. Poirier, Tatiana G. Kutateladze
NATURE COMMUNICATIONS
(2020)
