Review
Oncology
Simone Pellegrino, Salvatore Terrosu, Gulnara Yusupova, Marat Yusupov
Summary: Understanding the molecular basis of ribosomal inhibition by small molecules is essential for developing potential anticancer drugs. Recent advancements in structural studies have shed light on the binding modes of ribosome inhibitors, providing valuable insights for the development of more potent and specific treatments for cancer cells.
Article
Multidisciplinary Sciences
Long Zhou, Maria Maldonado, Abhilash Padavannil, Fei Guo, James A. Letts
Summary: This study reveals the functional and structural diversity of eukaryotic respiration through investigating the respiratory chain of the ciliate Tetrahymena thermophila. It expands our understanding of core metabolism by identifying divergence in key components of eukaryotic respiration.
Article
Biochemistry & Molecular Biology
Disha-Gajanan Hiregange, Andre Rivalta, Tanaya Bose, Elinor Breiner-Goldstein, Sarit Samiya, Giuseppe Cimicata, Liudmila Kulakova, Ella Zimmerman, Anat Bashan, Osnat Herzberg, Ada Yonath
Summary: Giardiasis is a disease caused by the protist Giardia lamblia. Developing new strategies to combat giardiasis is necessary due to the lack of approved vaccines and the spreading resistance to current drugs. The ribosome of G. lamblia, with its distinct sequence differences, could be a potential therapeutic target.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Hao-Yuan Wang, Haojun Yang, Mikael Holm, Keely Oltion, Harrison Tom, Amjad Ayad Qatran Al-Khdhairawi, Jean-Frederic F. Weber, Scott C. Blanchard, Davide Ruggero, Jack Taunton
Summary: Ternatin-family cyclic peptides inhibit protein synthesis by targeting eukaryotic elongation factor-1 alpha. The synthetic SR-A3 showed enhanced residence time and rebinding kinetics compared to SS-A3, both in vitro and in cells. Thrice-weekly dosing with SR-A3 reduced tumor burden and increased survival in a mouse lymphoma model. These findings demonstrate the potential of SR-A3 as a cancer therapeutic and suggest an evolutionary mechanism for enhancing cyclic peptide binding kinetics via stereospecific side-chain hydroxylation.
Review
Biochemistry & Molecular Biology
Gulnara Yusupova, Marat Yusupov
Summary: The first crystal structures of prokaryotic and eukaryotic ribosomes were resolved by the research group based on decades of accumulated knowledge, revealing the conserved nature of ribosomal structure and specific elements in eukaryotes. Through X-ray structural analysis, the group investigated the principles of protein biosynthesis inhibition and antibiotic resistance mechanisms in eukaryotic ribosomes, as well as established the structural differences between bacterial and eukaryotic ribosomes that determine their inhibition. These atomic-resolution structures provided detailed insights into the binding of messenger and transport RNAs, shedding light on how the ribosome structure determines its functions.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biochemistry & Molecular Biology
Su Wu, Gerhard Wagner
Summary: eIF4F plays diverse roles in human cancers, with overexpression of EIF4G1 being more selective than EIF4E, serving as a prognostic indicator in cancer patients. This expression imbalance affects housekeeping pathways and cancer-related pathways, leading to cap-independent initiation due to eIF4G1 hyperphosphorylation. These findings provide a novel model of dysregulated eIF4F function and highlight the clinical relevance of cap-(in)dependent initiation in cancer.
Article
Biochemistry & Molecular Biology
Matthew Thomas Doyle, John R. Jimah, Tyrone Dowdy, Shannon Ohlemacher, Mioara Larion, Jenny E. Hinshaw, Harris D. Bernstein
Summary: Using single-particle cryo-EM, we visualized the folding dynamics of a transmembrane beta barrel protein (EspP) by beta barrel assembly machinery (BAM) in the outer membrane of Gram-negative bacteria. Our findings suggest that BAM binds to the beta signal motif of EspP to correctly orient beta strands in the outer membrane during folding. We also discovered that the folding of EspP involves hybrid-barrel intermediates attached to the essential BAM subunit, BamA, and the beta sheets progressively fold towards BamA to form a beta barrel.
Article
Chemistry, Analytical
Qiongzheng Hu, Haina Jia, Yuhong Wang, Shoujun Xu
Summary: This paper reports a method for determining the functional positions of nucleic acids using mechanical force with single-nucleotide resolution. The method overcomes the variations in analyte concentration and buffer conditions commonly encountered in biological settings. Two examples are provided to validate the effectiveness of the method.
Article
Biochemical Research Methods
Kristyna Adamkova, Tomas Koval, Lars H. Ostergaard, Jarmila Duskova, Martin Maly, Leona Svecova, Tereza Skalova, Petr Kolenko, Jan Dohnalek
Summary: The handheld bio-detection device being developed by Manitech Technologies can detect and diagnose a variety of diseases. This mini device provides real-time data through simple blood sample analysis, helping doctors and patients better understand their physical condition.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Cell Biology
Gaoxingyu Huang, Dongliang Liu, Weipeng Wang, Qiurong Wu, Jiaofeng Chen, Xiaojing Pan, Huaizong Shen, Nieng Yan
Summary: This study reports the cryo-EM structure of Na(v)1.7 channel complexed with different subunits, revealing conformational differences and ligand-induced structural changes.
Article
Biochemistry & Molecular Biology
Soneya Majumdar, Andrew Emmerich, Sascha Krakovka, Chandra Sekhar Mandava, Staffan G. Svard, Suparna Sanyal
Summary: Using cryo-electron microscopy, we have determined high-resolution structures of six translocation intermediates from Giardia ribosomes. These ribosomes possess eukaryotic rRNAs and proteins, but also retain some bacterial features. The study elucidates the mechanism of translocation in protists and sheds light on the evolution of translation machinery.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Geochemistry & Geophysics
Yikang Zheng, Yibo Wang
Summary: Detailed imaging of subsurface structure, particularly fault systems, is essential for geothermal reservoir development. Reflection seismic imaging provides high-resolution depth information for evaluating drilling locations. Specialized seismic processing techniques are necessary for geothermal cases in hard-rock basements.
Article
Biochemistry & Molecular Biology
Nergis Imprachim, Yuliana Yosaatmadja, Joseph A. Newman
Summary: NSP14 is a dual function enzyme, consisting of an N-terminal exonuclease domain (ExoN) and a C-terminal guanine-N7-methyltransferase (N7-MTase) domain. The interaction between NSP14 and NSP10 enhances the nuclease activity. Structural analysis reveals conformational changes in the NSP14 ExoN domain upon binding of NSP10, which explains the stimulation of nuclease activity. Additionally, structural insights into the viral mRNA capping process are gained through the structure of NSP14 in complex with cap analogue (7Me)GpppG.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Bradley P. Klemm, Andrew P. Sikkema, Allen L. Hsu, James C. Horng, Traci M. Tanaka Hall, Mario J. Borgnia, Roel M. Schaaper
Summary: This study reveals the allosteric activation of a dGTPase by dATP, providing new insights into the regulatory function of dNTPases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Editorial Material
Cell Biology
Michael X. Zhu
Summary: This study reported the cryo-EM structures of TRPC5 in complex with Ga-i3, revealing that the G protein alpha subunit directly binds to an ankyrin-like repeat domain in the periphery of TRPC5's cytosolic portion some 50 angstrom away from the membrane. This confirms that TRPC4/C5 ion channels are true effectors of Ga subunits, with channel gating dependent on the coexistence of Ca2+ and phosphatidylinositol 4,5-bisphosphate.
Article
Biochemistry & Molecular Biology
Keven D. Juaire, Karine Lapouge, Matthias M. M. Becker, Irina Kotova, Michelle Michelhans, Raphael Carapito, Klemens Wild, Seiamak Bahram, Irmgard Sinning
Summary: Mutations in SRP54 have been found to cause a severe congenital neutropenia with symptoms overlapping with Shwachman-Diamond syndrome. These mutations result in critical protein destabilization, affecting the entire SRP pathway's function.
Article
Hematology
Christoph Schurch, Thorsten Schaefer, Joelle S. Muller, Pauline Hanns, Marlon Arnone, Alain Dumlin, Jonas Scharer, Irmgard Sinning, Klemens Wild, Julia Skokowa, Karl Welte, Raphael Carapito, Seiamak Bahram, Martina Konantz, Claudia Lengerke
Summary: Variants of SRP54 gene play a critical role in the development of congenital neutropenia, with knockout zebrafish serving as an in vivo model for the disease. The study reveals that SRP54 is crucial for tissue development, with neutrophils being particularly sensitive to its loss, suggesting potential therapeutic targets in patients with different phenotypes ranging from mild CN to SDS-like disease.
Article
Biochemistry & Molecular Biology
Jonas Weidenhausen, Juergen Kopp, Laura Armbruster, Markus Wirtz, Karine Lapouge, Irmgard Sinning
Summary: The majority of eukaryotic proteins undergo N-terminal acetylation, with Naa50 playing a crucial role in plant development and stress response regulation. The high-resolution crystal structures of AtNaa50 provide insights into its substrate specificity and enzymatic parameters, highlighting differences between species and serving as a basis for further studies.
Article
Biology
Dominik Layer, Juergen Kopp, Miriam Fontanillo, Maja Koehn, Karine Lapouge, Irmgard Sinning
Summary: Layer et al. present a crystal structure of Naa20, the catalytic subunit of an N-terminal acetyltransferase NatB, in complex with its competitive inhibitor CoA-Ac-MDEL. They find that Naa20 alone can acetylate NatB in vitro while Naa25, the auxiliary subunit of Naa20, increases the substrate affinity of Naa20. This study provides insights into the development of NAT inhibitors.
COMMUNICATIONS BIOLOGY
(2021)
Article
Cell Biology
Lyudmila Dimitrova-Paternoga, Pravin Kumar Ankush Jagtap, Anna Cyrklaff, Vaishali, Karine Lapouge, Peter Sehr, Kathryn Perez, Simone Heber, Christian Low, Janosch Hennig, Anne Ephrussi
Summary: Kinesin-1 transports cargos within cells by forming a complex with atypical tropomyosin, aTm1, and a study on the Khch-aTm1 complex reveals the mechanism of this interaction. Additionally, aTm1 plays a stabilizing role in the interaction of Khc with RNA, distinguishing it from classical motor adaptors.
GENES & DEVELOPMENT
(2021)
Article
Multidisciplinary Sciences
Pavlina Miklankova, Eric Linster, Jean-Baptiste Boyer, Jonas Weidenhausen, Johannes Mueller, Laura Armbruster, Karine Lapouge, Carolina De La Torre, Willy Bienvenut, Carsten Sticht, Matthias Mann, Thierry Meinnel, Irmgard Sinning, Carmela Giglione, Rudiger Hell, Markus Wirtz
Summary: This study identifies AtHYPK protein as the first in vivo regulator of NatA activity in plants, which interacts with the ribosome-anchoring subunit of NatA and promotes N-terminal acetylation of various substrates. Loss-of-AtHYPK mutants exhibit remarkable resistance to drought stress and resemble the phenotype of NatA-depleted plants. HYPK regulates plant metabolism and development by modulating NatA activity, and plays a critical role in global proteostasis.
Article
Biochemistry & Molecular Biology
Jonas Weidenhausen, Juergen Kopp, Carmen Ruger-Herreros, Frank Stein, Per Haberkant, Karine Lapouge, Irmgard Sinning
Summary: Most eukaryotic proteins are N-terminally acetylated by NATs, and this modification is important for protein homeostasis and can be linked to human diseases. In this study, Naa50 homologs from the filamentous fungi Chaetomium thermophilum and Neurospora crassa were analyzed. The CtNaa50 protein shares structural and substrate specificity with other homologs but does not form the NatE complex.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Migle Kisonaite, Klemens Wild, Karine Lapouge, Genis Valentin Gese, Nikola Kellner, Ed Hurt, Irmgard Sinning
Summary: The authors used cryo-EM to investigate how the RAC complex, a conserved ribosome-associated chaperone triad, assists in cotranslational protein folding. They determined cryo-EM structures of RAC bound to 80S ribosomes, revealing two distinct conformations and a tight interaction between the RAC components. They also discovered a non-canonical interaction that masks the HPD motif in the J domain protein Zuo1, allowing proper positioning of Ssb for activation. These findings provide insights into the dynamic interaction and protein folding process involving RAC and Ssb.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
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
Microbiology
Milka Marjut Hammaren, Hanna Luukinen, Alina Sillanpaeae, Kim Remans, Karine Lapouge, Tania Custodio, Christian Loew, Henna Myllymaeki, Toni Montonen, Markus Seeger, Joseph Robertson, Tuula A. Nyman, Kirsi Savijoki, Mataleena Parikka
Summary: Combining in vitro and ex vivo proteomics, researchers identified surface-exposed proteins on mycobacterial biofilms and developed nanobodies that bind to these proteins, offering a new approach for treating tuberculosis.