Article
Biochemistry & Molecular Biology
Corey J. Herbst-Gervasoni, David W. Christianson
Summary: Histone deacetylase 10 (HDAC10) is a zinc-dependent polyamine deacetylase with potential as a target for cancer chemotherapy. Detailed structural information on the enzyme's active site is crucial for the design of selective inhibitors.
Article
Chemistry, Multidisciplinary
Jun Zhu, Yibin Xue, Rui Zhang, Benjamin L. Ratchford, Guangbin Dong
Summary: This article describes a catalytic method for activating unstrained and nonpolar C-C bonds, using removable directing groups to aid in the hydrogenolysis of unstrained C(aryl)-C(alkyl) bonds in 2,2'-methylenediphenols. The method yields high amounts of monophenol products and is tolerant of a wide range of functional groups. Additionally, the reaction is scalable and the catalyst loading can be reduced to as low as 0.5 mol %. The method also proves effective in cleaving C(aryl)-C(alkyl) linkages in both phenolic resins and commercial novolacs resins. Experimental and computational mechanistic studies show that the transformation occurs through a directed C(aryl)-C(alkyl) oxidative addition pathway, with C-H activation being a competitive but reversible off-cycle reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Xing Liu, Xiao Han, Yuan Peng, Chunlin Tan, Jing Wang, Hongsong Xue, Ping Xu, Fei Tao
Summary: In this study, a highly efficient whole-cell catalyst for l-DOPA production using Vibrio natriegens as the chassis was developed. Vibrio natriegens exhibited rapid protein expression and catalytic rate, leading to higher productivity in the early stage of biocatalysis. These findings highlight the remarkable potential of Vibrio natriegens as a whole-cell catalysis chassis for the production of valuable chemicals.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Keke Zhang, Yan Yang, Weidong Wang, Weizhi Liu, Qianqian Lyu
Summary: The study demonstrated that protein engineering of alginate lyase AlyF can alter product distribution, and redesigning sugar-binding affinity can achieve this goal.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Review
Multidisciplinary Sciences
Hidehiko Kumagai, Takane Katayama, Takashi Koyanagi, Hideyuki Suzuki
Summary: This article discusses a simple enzymatic synthesis method using bacterial L-tyrosine phenol-lyase (Tpl) for the production of L-DOPA, a treatment for Parkinson's disease. The research covers screening of bacterial strains, culture conditions, properties and reaction mechanism of the enzyme, as well as the reaction conditions for L-DOPA production. Additionally, the article explores molecular breeding of Tpl-over-producing strains through mutations in the DNA binding protein TyrR.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2023)
Article
Chemistry, Physical
Nangagoundan Vinoth, Chinnasamy Kalaiarasi, Poomani Kumaradhas, Appaswami Lalitha
Summary: The study presents a novel synthetic method for the efficient generation of benzo[4,5]imidazo[1,2-c]quinazolin-6(5H)-one derivatives with high yields and short reaction time. The synthesized compounds were confirmed through various analytical techniques.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Review
Chemistry, Multidisciplinary
Wang Ziwei, Shu Hao, Chen Yizhen, Liu Ben, Xu Yaowei, Wang Wanxia, Wang Kaiyue, Lei Mengheng, Guo Li, Wang Lei
Summary: This paper discusses the importance of utilizing catalytic conversion techniques to achieve high-value utilization of lignin, with a specific emphasis on selective depolymerization. It provides a comprehensive discussion on the reaction pathways and mechanisms among different catalysts. Furthermore, the prospects of rational catalyst design in biomass valorization are analyzed.
Article
Chemistry, Multidisciplinary
Yunbeom Lee, Hosung Ki, Donghwan Im, Seunghwan Eom, Jain Gu, Seonggon Lee, Jungmin Kim, Yongjun Cha, Kyung Won Lee, Serhane Zerdane, Matteo Levantino, Hyotcherl Ihee
Summary: This study utilized time-resolved X-ray liquidography (TRXL) to directly observe the structure and reaction intermediates of [Ce(III)Cl-6](3-) photocatalyst. The results showed that the excited state of [Ce(III)Cl-6](3-) has shorter Ce-Cl bonds compared to the ground state, and these bonds further contract upon oxidation. Additionally, the study revealed the influence of substrate on the reaction dynamics of the photocatalyst.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Hang-Qin Zhu, Wen-Ye Hu, Xiao-Ling Tang, Ren-Chao Zheng, Yu-Guo Zheng
Summary: A novel assay format for detecting TPL activity based on C23O-catalyzed reaction was presented in this study. The assay achieved a unique balance between ease of operation and analytical performance, and enabled real-time monitoring of TPL activity. It was applicable to both crude cell extracts and the whole-cell system.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Xiao-Ling Tang, Wen-Ye Hu, Zhi-Chao Wang, Ren-Chao Zheng, Yu-Guo Zheng
Summary: By promoting the strategies for plasmid stability in recombinant E. coli, the instability issue during microbial fermentation was successfully solved, leading to a significant increase in the specific activity of tyrosine phenol lyase and volumetric activity for l-DOPA biosynthesis. These results not only contribute to the application of l-DOPA production, but also provide important guidance for industrial fermentation with enhanced microbial productivity.
BIOTECHNOLOGY LETTERS
(2021)
Article
Chemistry, Organic
Shenghai Guo, Ziyi Zhang, Yuanqing Zhu, Zhaotong Wei, Xinying Zhang, Xuesen Fan
Summary: A practical and selective method for the synthesis of novel isoquinolone-containing spirocyclic and oxepine-fused polycyclic skeletons through rhodium-catalyzed oxidative [4 + 1] spiroannulation or formal [4 + 3] annulation reactions has been reported. The protocol exhibits wide substrate scope, simple operation procedures, and excellent regioselectivity. The obtained products also hold potential applications in further transformations.
ORGANIC CHEMISTRY FRONTIERS
(2022)
Article
Biochemistry & Molecular Biology
Luam E. Araya, Ishankumar Soni, Jeanne A. Hardy, Olivier Julien
Summary: Caspases are a family of enzymes that regulate biological processes such as inflammation and programmed cell death through proteolysis. A deep analysis revealed hundreds of potential protein substrates associated with Caspase-3 and Caspase-9 in native cell lysates, suggesting their functions may be broader and more complex than previously thought. Additionally, there is a significant overlap in substrate cleavage between the two caspases, indicating a potential evolved functional redundancy.
ACS CHEMICAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Francesca Ruffolo, Tamara Dinhof, Leanne Murray, Erika Zangelmi, Jason P. Chin, Katharina Pallitsch, Alessio Peracchi
Summary: Phosphonates are compounds with a C-P bond that is resistant to degradation. Man-made phosphonates cause pollution, while microorganisms have evolved systems to degrade them. This review summarizes the molecular systems, pathways, and regulatory mechanisms involved in phosphonate degradation.
Article
Chemistry, Physical
Georgios Toupalas, Bill Morandi
Summary: This study presents a strategy to eliminate the need for an exogenous base in catalytic reactions by using non-innocent electrophiles (NIE) equipped with a masked base that is released during the reaction. The universal applicability of this strategy was demonstrated by converting multiple base-dependent reactions into base-free homogeneous processes, and the advantageous features of NIEs were showcased in various applications.
Article
Biochemistry & Molecular Biology
Zainab K. Sanusi, Monsurat M. Lawal, Pancham Lal. Gupta, Thavendran Govender, Sooraj Baijnath, Tricia Naicker, Glenn E. M. Maguire, Bahareh Honarparvar, Adrian E. Roitberg, Hendrik G. Kruger
Summary: The present study explores the mechanism of proteolysis catalyzed by HIV-1 PR and validates the proposed model through theoretical calculations and experimental evidence. The findings suggest that the proposed mechanism is consistent with experimental data. Therefore, we suggest that the QM/MM MD method can be a reliable computational technique for designing potential drugs targeting specific proteins such as HIV-1 PR.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Virology
Emelie Nilsson, Oliver W. Bayfield, Daniel Lundin, Alfred A. Antson, Karin Holmfeldt
Article
Biochemistry & Molecular Biology
Kristina V. Tugaeva, James Titterington, Dmitriy V. Sotnikov, Eugene G. Maksimov, Alfred A. Antson, Nikolai N. Sluchanko
Article
Immunology
Yanchun Peng, Alexander J. Mentzer, Guihai Liu, Xuan Yao, Zixi Yin, Danning Dong, Wanwisa Dejnirattisai, Timothy Rostron, Piyada Supasa, Chang Liu, Cesar Lopez-Camacho, Jose Slon-Campos, Yuguang Zhao, David Stuart, Guido C. Paesen, Jonathan M. Grimes, Alfred A. Antson, Oliver W. Bayfield, Dorothy E. D. P. Hawkins, De-Sheng Ker, Beibei Wang, Lance Turtle, Krishanthi Subramaniam, Paul Thomson, Ping Zhang, Christina Dold, Jeremy Ratcliff, Peter Simmonds, Thushan de Silva, Paul Sopp, Dannielle Wellington, Ushani Rajapaksa, Yi-Ling Chen, Mariolina Salio, Giorgio Napolitani, Wayne Paes, Persephone Borrow, Benedikt M. Kessler, Jeremy W. Fry, Nikolai F. Schwabe, Malcolm G. Semple, J. Kenneth Baillie, Shona C. Moore, Peter J. M. Openshaw, M. Azim Ansari, Susanna Dunachie, Eleanor Barnes, John Frater, Georgina Kerr, Philip Goulder, Teresa Lockett, Robert Levin, Yonghong Zhang, Ronghua Jing, Ling-Pei Ho, Richard J. Cornall, Christopher P. Conlon, Paul Klenerman, Gavin R. Screaton, Juthathip Mongkolsapaya, Andrew McMichael, Julian C. Knight, Graham Ogg, Tao Dong
Article
Chemistry, Physical
Mengyu Ge, Robert W. Molt, Huw T. Jenkins, G. Michael Blackburn, Yi Jin, Alfred A. Antson
Summary: The octahedral TSA complex MgF3(H2O)(-) observed in a 1.5 A resolution crystal structure of Zika virus NS3 helicase, along with independent validation by F-19 NMR, highlights the significance of this complex in studies of biological motors.
Article
Biochemistry & Molecular Biology
Kristina Tugaeva, Dorothy E. D. P. Hawkins, Jake L. R. Smith, Oliver W. Bayfield, De-Sheng Ker, Andrey A. Sysoev, Oleg Klychnikov, Alfred A. Antson, Nikolai N. Sluchanko
Summary: Phosphorylated SARS-CoV-2 N protein binds to 14-3-3 protein, potentially playing a crucial role in nucleocytoplasmic shuttling and other functions. A critical phosphorylation site located within the SR-rich region of N, which is conserved among related coronaviruses, interacts with all seven human 14-3-3 isoforms.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Microbiology
De-Sheng Ker, Huw T. Jenkins, Sandra J. Greive, Alfred A. Antson
Summary: The study reports the first cryoEM structure of a Henipavirus RNA-bound nucleocapsid assembly, revealing the composition of its helical assembly and the wrapping of RNA. The structure shows similarities and differences with other members of the Paramyxoviridae family and the evolutionarily distant Filoviridae Ebola virus.
Article
Pharmacology & Pharmacy
Franziska Marie Heydenreich, Bianca Plouffe, Aurelien Rizk, Dalibor Milic, Joris Zhou, Billy Breton, Christian Le Gouill, Asuka Inoue, Michel Bouvier, Dmitry B. Veprintsev
Summary: By modeling G protein activation as a Michaelis-Menten reaction, we have developed a novel method for quantifying signaling bias. V2R activates, or at least engages, G proteins from all G protein subfamilies, including Gi2, Gz, Gq, G12, and G13. Their relative activation may explain its Gs-independent signaling.
MOLECULAR PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Herman K. H. Fung, Shelley Grimes, Alexis Huet, Robert L. Duda, Maria Chechik, Joseph Gault, Carol Robinson, Roger W. Hendrix, Paul J. Jardine, James F. Conway, Christoph G. Baumann, Alfred A. Antson
Summary: Many cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. Researchers have reconstituted a cos packaging system and provided a detailed description of its biochemical and structural properties, revealing similarities and differences in its mechanism and regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Kristina Tugaeva, Andrey A. Sysoev, Anna A. Kapitonova, Jake L. R. Smith, Phillip Zhu, Richard B. Cooley, Alfred A. Antson, Nikolai N. Sluchanko
Summary: Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins that play a role in virus replication. Using genetic code expansion, it is shown that 14-3-3 binding is triggered by phosphorylation at specific sites on the nucleoprotein. Crystal structures and biochemical data reveal that 14-3-3 binding obstructs a region of the nucleoprotein and inhibits its dephosphorylation. The strength of the 14-3-3/nucleoprotein interaction may be linked to the replicative fitness of the virus.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mehrnaz Mojtabavi, Sandra J. Greive, Alfred A. Antson, Meni Wanunu
Summary: The application of nanopores as label-free, single-molecule biosensors for structural features in biomolecules has been widely researched. While biological and solid-state nanopores have been extensively used, the study of hybrid nanopores, where an artificial membrane replaces the organic support membrane of proteins, is limited. In this study, a lipid-free hybrid nanopore was developed by connecting a solid-state pore and the G20c portal protein. The chemical functionalization of the synthetic nanopore improved the stability, lifetime, and voltage resilience of the hybrid pore. Additionally, electric-field-driven and motor protein-mediated transport of DNA molecules through the hybrid nanopore was demonstrated. This protein/solid-state device offers potential advantages in sensing and sequencing with higher resolution, signal-to-noise ratio, and throughput compared to conventional membrane-embedded protein platforms.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Oliver W. Bayfield, Andrey N. Shkoporov, Natalya Yutin, Ekaterina V. Khokhlova, Jake L. R. Smith, Dorothy E. D. P. Hawkins, Eugene V. Koonin, Colin Hill, Alfred A. Antson
Summary: CrAssphage and related crassviruses are the most abundant viruses in the human gut, with some individuals having up to 95% of viral sequences from these viruses. By reconstructing Bacteroides intestinalis virus fcrAss001 using cryo-electron microscopy, we gained insights into the structure and function of its proteins. The muzzle protein forms a new fold called the 'crass fold' and acts as a gatekeeper for controlling cargo release. Additionally, the fcrAss001 virus provides ample storage space for cargo proteins in both the capsid and the tail, with a mechanism for protein ejection involving partial unfolding during extrusion through the tail.
Article
Biochemistry & Molecular Biology
Dorothy E. D. P. Hawkins, Oliver W. Bayfield, Herman K. H. Fung, Daniel N. Grba, Alexis Huet, James F. Conway, Alfred A. Antson
Summary: Double-stranded DNA viruses utilize terminase proteins to package viral DNA into the capsid. In this study, the first structural data for a cos virus DNA packaging motor was presented, showing the assembly of terminase proteins, procapsids with the portal protein, and DNA with a cos site. The cryo-EM structure revealed the termination state of packaging and the asymmetry induced by the binding of large terminase/DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
K. Tugaeva, D. E. D. P. Hawkins, J. L. R. Smith, O. W. Bayfield, D. Ker, A. A. Sysoev, O. I. Klychnikov, R. B. Cooley, A. A. Antson, N. N. Sluchanko
Article
Biology
Franziska M. Heydenreich, Tamara Miljus, Dalibor Milic, Dmitry B. Veprintsev
Meeting Abstract
Biophysics
Mehrnaz Mojtabavi, Sandra Greive, Alfred Antson, Meni Wanunu
BIOPHYSICAL JOURNAL
(2020)