Article
Chemistry, Physical
Angus J. Robertson, F. Aaron Cruz-Navarrete, Henry P. Wood, Nikita Vekaria, Andrea M. Hounslow, Claudine Bisson, Matthew J. Cliff, Nicola J. Baxter, Jonathan P. Waltho
Summary: Understanding the factors contributing to the high catalytic efficiencies of enzymes is crucial for catalysis and enzyme design. This study investigates the relationship between binding a phosphodianion group in a distal site, adopting a closed enzyme form, and catalytic proficiency. The results suggest that binding of a phosphodianion group in the distal site stimulates domain closure and stabilizes the closed active form, leading to high catalytic efficiencies.
Article
Biochemistry & Molecular Biology
Elena Ostertag, Liujuan Zheng, Karina Broger, Thilo Stehle, Shu-Ming Li, Georg Zocher
Summary: Prenylation plays a crucial role in primary and secondary metabolism, contributing to chemical diversity in natural systems. Recent structural studies on prenyltransferases shed light on their catalytic mechanisms and key residues, but the control of regioselectivity and chemoselectivity remains a challenge. Site-directed mutagenesis has been successfully utilized to modify prenyl donor specificity and switch the regioselectivity of prenyltransferases, showing potential for production of novel prenylated compounds.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Rylee Wander, Andrea M. Kaminski, Zhangjie Wang, Eduardo Stancanelli, Yongmei Xu, Vijayakanth Pagadala, Jine Li, Juno M. Krahn, Truong Quang Pham, Jian Liu, Lars C. Pedersen
Summary: The study presents the crystal structures of 3-OST-5 with substrates and PAP, revealing its substrate specificity and anti-factor Xa activity. The enzyme prefers to sulfate a 6-O-sulfo glucosamine saccharide that is surrounded by glucuronic acid. Additionally, it was found that substrate specificity is not only determined by the side chains of amino acid residues in the active site, but also by the conformational flexibility of 2-O-sulfated iduronic acid in the saccharide substrates.
Article
Biochemistry & Molecular Biology
Hao Cui, Xiaowen Cheng, Tahira Batool, Xiao Zhang, Jin-Ping Li
Summary: The study suggests that a defect in the key enzyme glucuronyl C5-epimerase (Hsepi) involved in heparan sulfate biosynthesis may lead to lung developmental failure in mice. Despite no significant morphological differences before E16.5, mutant animals show abnormal lung structure at E17.5-18.5, with impaired AT1 cell differentiation possibly associated with reduced lung vascularization.
Article
Cell Biology
Rana El Masri, Amal Seffouh, Caroline Roelants, Ilham Seffouh, Evelyne Gout, Julien Perard, Fabien Dalonneau, Kazuchika Nishitsuji, Fredrik Noborn, Mahnaz Nikpour, Goran Larson, Yoann Cretinon, Melanie Friedel-Arboleas, Kenji Uchimura, Regis Daniel, Hugues Lortat-Jacob, Odile Filhol, Romain R. Vives
Summary: This study found that human HSulf-2 enzyme carries a chondroitin/dermatan sulfate glycosaminoglycan (GAG) chain, which regulates the enzyme's activity and is promoted by mammalian hyaluronidase.
Article
Biochemistry & Molecular Biology
Seiji Negoro, Naoki Shibata, Dai-ichiro Kato, Yusuke Tanaka, Kengo Yasuhira, Keisuke Nagai, Shohei Oshima, Yoko Furuno, Risa Yokoyama, Kaito Miyazaki, Masahiro Takeo, Kowit Hengphasatporn, Yasuteru Shigeta, Young-Ho Lee, Yoshiki Higuchi
Summary: NylC is an enzyme responsible for the degradation of nylon. It undergoes autocleavage for activation and has a quaternary structure. The catalytic residues are initially covered, but become exposed through the movement of loop regions. Hydrogen-bonding networks are crucial for the reaction and substrate hydrolysis.
Article
Biochemistry & Molecular Biology
Qian Yu, Wei Lu, Daixi Li, Ting Shi
Summary: This study investigated the catalytic mechanism of thioesterase NocTE and proposed a substrate-assisted mechanism for the epimerization. The study revealed the roles of key water molecules and provided insights into the molecular basis for stereochemical selectivity. These findings pave the way for directed biosynthesis of novel peptide drugs with various stereostructural characteristics.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Jiandong Wu, Pradeep Chopra, Geert-Jan Boons, Joseph Zaia
Summary: A library of synthetic heparan sulfate oligosaccharides was used to analyze the substrate specificities of heparin lyase III enzymes from two different sources. The study found that specific modifications influenced the digestion of the oligosaccharides, and there were differences in substrate specificities between the two lyase III enzymes for highly sulfated oligosaccharides. These findings provide insights into the structure/function relationships of sulfated domains in biological processes.
Article
Multidisciplinary Sciences
Chongyang Wang, Changshui Liu, Xiaochuan Zhu, Quancai Peng, Qingjun Ma
Summary: This study reveals the structural flexibility of Vibrio dual lipases/transferases and proposes a mechanism for tuning the catalytic site to explain enzyme promiscuity. Enzyme promiscuity, the ability to catalyze multiple substrates and reactions, is widely observed but poorly understood. The researchers discovered a flexible catalytic triad machinery in Vibrio dual lipase/transferase that can undergo conformational changes to facilitate substrate and catalytic promiscuity.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Shun Maruyama, Kota Sawano, Satoko Amaki, Takehiro Suzuki, Satoru Narita, Kenta Kimura, Takatoshi Arakawa, Chihaya Yamada, Yukishige Ito, Naoshi Dohmae, Kiyotaka Fujita, Akihiro Ishiwata, Shinya Fushinobu
Summary: This study investigated the catalytic mechanism and substrate binding structure of the beta-l-arabinofuranosidase HypBA1 from Bifidobacterium longum. Zn2+ ion and cysteine were found to play key roles in catalysis, and the mode of substrate binding affected the catalytic activity.
Article
Biochemistry & Molecular Biology
Hao Cui, Zhaoguang Wang, Tianji Zhang, Jin-ping Li, Jianping Fang
Summary: The translation explores the role of Heparan sulfate (HS) in protein recognition and interaction, highlighting the importance of specific sulfation and epimerization patterns modulated by Golgi-localized enzymes. The study investigates the effects of restoring Hsepi in mutant MEF cells, showing increased IdoA residues and rescued cell signaling, although Hsepi knockout did not influence cellular transport or enzymatic activity of 2OST. These findings suggest potential differences in regulatory mechanisms for 2OST and Hsepi.
Article
Cell Biology
Killian O'Brien, Stefano Ughetto, Shadi Mahjoum, V. Anil Nair, Xandra O. Breakefield
Summary: Extracellular vesicles (EVs) are membrane-encapsulated particles carrying genetically active and protein/lipid cargo that can impact recipient cell function. This study demonstrates the functional delivery of EV-encapsulated RNA and protein cargo using luminescence and fluorescence reporters. The research highlights the retention of internalized cargo in the endosomal compartment and the re-release of intact EVs by recipient cells. These findings shed light on critical factors in cargo delivery and enhance the therapeutic potential of EVs.
Article
Chemistry, Inorganic & Nuclear
Matthieu Regnacq, Denis Lesage, Marte S. M. Holmsen, Karinne Miqueu, Didier Bourissou, Yves Gimbert
Summary: The study demonstrates the remarkable catalytic ability of (P,C)-cyclometalated Au(iii) complexes in the intermolecular hydroarylation of alkynes. The previous evidence of an outer-sphere mechanism is confirmed through the analysis of experimental data and DFT calculations. The evaluation of critical energies of dissociation of Au(iii) complexes with different substrates using energy-resolved mass spectrometry experiments and kinetic modeling supports the collisional model and its application to particularly fragile adducts.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Inorganic & Nuclear
Matthieu Regnacq, Denis Lesage, Marte S. M. Holmsen, Karinne Miqueu, Didier Bourissou, Yves Gimbert
Summary: In this study, the mechanism of (P,C)-cyclometalated Au(iii) complexes catalyzing the intermolecular hydroarylation of alkynes is confirmed through experimental data and theoretical calculations, as well as energy-resolved mass spectrometry experiments and kinetic modeling. The results support the previously proposed collisional model and provide insights into the application of this model on fragile adducts.
DALTON TRANSACTIONS
(2023)
Article
Materials Science, Multidisciplinary
Zahra Baradaran, Nasrin Oroujzadeh, Alireza Sedrpoushan
Summary: A new Ag(I) complex with a phosphoric triamide ligand was successfully synthesized and immobilized on SBA-15 support. The complex and its immobilized form were characterized and used as catalysts in the oxidation reaction of aldehydes and sulfides. Results showed that the immobilized complex had slightly lower catalytic efficiency but improved recoverability, within acceptable limits compared to other reports.
MATERIALS CHEMISTRY AND PHYSICS
(2022)
Review
Virology
Adeline Goulet, Silvia Spinelli, Jennifer Mahony, Christian Cambillau
Article
Virology
Silvia Spinelli, Denise Tremblay, Sylvain Moineau, Christian Cambillau, Adeline Goulet
Article
Biotechnology & Applied Microbiology
Katherine Lavelle, Adeline Goulet, Brian McDonnell, Silvia Spinelli, Douwe van Sinderen, Jennifer Mahony, Christian Cambillau
MICROBIAL BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Semeli Platsaki, Xin Zhou, Berangere Pinan-Lucarre, Vincent Delauzun, Haijun Tu, Pascal Mansuelle, Patrick Fourquet, Yves Bourne, Jean-Louis Bessereau, Pascale Marchot
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Review
Neurosciences
Davide Comoletti, Laura Trobiani, Arnaud Chatonnet, Yves Bourne, Pascale Marchot
Summary: Cell adhesion involves the formation of protein complexes between two cells, with neural cell-adhesion proteins using cholinesterase-like domains to bind cognate partners. These proteins, including neuroligins, have unique structural features but share the ability to recognize and bind protein partners.
Article
Biotechnology & Applied Microbiology
Sebastian Cerminati, Melanie Leroux, Pablo Anselmi, Salvador Peiru, Juan C. Alonso, Bernard Priem, Hugo G. Menzella
Summary: Hyaluronic acid, a valuable glycosaminoglycan, is widely used in health and cosmetic fields. Research shows that Bacillus subtilis could be a cost-effective host for HA production with potential economic benefits.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Correction
Biotechnology & Applied Microbiology
Sebastian Cerminati, Melanie Leroux, Pablo Anselmi, Salvador Peiru, Juan C. Alonso, Bernard Priem, Hugo G. Menzella
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Adeline Goulet, Christian Cambillau
Summary: This study utilized the AlphaFold2 algorithm to predict the structure and topology of adhesion devices of two lytic siphophages infecting wine bacteria, revealing their distinct composition, morphology, and potential different infection mechanisms. The results highlight the ability of AlphaFold2 to accurately predict protein structures and its potential in the study of phage structures and host-binding mechanisms.
Review
Biochemistry & Molecular Biology
Emeline Grellet, India L'Hote, Adeline Goulet, Isabelle Imbert
Summary: This article reviews the history of coronavirus replication and provides detailed information on the core replicative machinery of these viruses.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Veronique Roig-Zamboni, Sarah Barelier, Robert Dixon, Nicola F. Galley, Amani Ghanem, Heloize Cahuzac, Quoc Phong Nguyen, Bartlomiej Salamaga, Peter J. Davis, Yves Bourne, Stephane Mesnage, Florence Vincent
Summary: The cleavage of septal peptidoglycan during cell division helps in separating the daughter cells. The N-acetylglucosaminidase AtlA in Enterococcus faecalis plays a crucial role in cell separation and its mutants show decreased virulence. AtlA has structural homologs in other pathogens, making it a potential target for developing inhibitors of bacterial pathogenesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Firas Fadel, Violla Bassim, Vanessa Francis, Steven L. Porter, Thomas Botzanowski, Pierre Legrand, Maria Mate Perez, Yves Bourne, Sarah Cianferani, Florence Vincent
Summary: This study provides structural and functional insights into the interaction between GacS and RetS in Pseudomonas aeruginosa, including the signaling pathway and autokinase mechanism of GacS. The findings are of great significance for a better understanding of these regulatory networks and their roles in bacterial physiological activities.
Article
Virology
Adeline Goulet, Christian Cambillau, Alain Roussel, Isabelle Imbert
Summary: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in humans globally, and it is now a global public health concern. The recent advancement in protein structure prediction software allows accurate prediction of the composition and structure of HEV replicases, which is important for producing stable and active proteins and conducting studies on structure, function, and inhibition.
Article
Biochemistry & Molecular Biology
Sarah Barelier, Romain Avellan, Giri Raj Gnawali, Patrick Fourquet, Veronique Roig-Zamboni, Isabelle Poncin, Vanessa Point, Yves Bourne, Stephane Audebert, Luc Camoin, Christopher D. Spilling, Stephane Canaan, Jean-Francois Cavalier, Gerlind Sulzenbacher
Summary: We report the synthesis of new CyC alkyne-containing inhibitors (CyCyne) and their use for the direct fishing of target proteins in M. tb culture via bio-orthogonal click-chemistry activity-based protein profiling (CC-ABPP). This approach led to the capture and identification of a variety of enzymes, including HsaD, which is required for the survival of M. tb within macrophages and is a potential therapeutic target. The specificity of HsaD inhibition by the CyC analogues was confirmed through biochemical and structural approaches.
Article
Chemistry, Physical
Yoan Monneau, Cyrielle Arrault, Coraline Duroux, Marie Martin, Fabien Chirot, Luke Mac Aleese, Marion Girod, Clothilde Comby-Zerbino, Agnes Hagege, Olivier Walker, Maggy Hologne
Summary: Silver has been used as an antimicrobial agent, but some Gram-negative bacteria have developed resistance, leading to deaths in burn units. The protein SilE plays a crucial role in bacterial silver resistance. Through various techniques, it has been found that SilE consists of four helical segments and has four strong silver binding sites. These findings enhance our understanding of the mechanism of SilE in the silver efflux pump complex and aid in the development of inhibitors to combat bacterial silver resistance.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
P. Marchot, Y. Bourne