Article
Chemistry, Multidisciplinary
Nikola Kenjic, Kathleen M. Meneely, Daniel J. Wherritt, Melissa C. Denler, Timothy A. Jackson, Graham R. Moran, Audrey L. Lamb
Summary: RibB is a magnesium-dependent enzyme that catalyzes the removal of C4 from D-Ru5P to generate formate. Our study characterizes the chemistry catalyzed by RibB from Vibrio cholera and reveals crucial transient chemical states in its mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Yuda Chen, Axel Loredo, Anna Chung, Mengxi Zhang, Rui Liu, Han Xiao
Summary: The creation of cells that can use noncanonical amino acids as protein building blocks holds great promise for novel medicines and biological studies. This study reports the development of a bacterium that can utilize 3,4-dihydroxy-L-phenylalanine as an additional amino acid building block, with high protein production yields. The unique properties of this noncanonical amino acid enable site-specific protein functionalization.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Zeyaul Islam, Pankaj Kumar
Summary: Multiple drug resistance is a major challenge in treating bacterial diseases, necessitating the exploration of new antimicrobial drug targets. Enzymes involved in the riboflavin biosynthetic pathway have been identified as crucial for bacterial survival and thus offer potential targets for resistant strains. Understanding the structure, mechanism, and interaction of these enzymes can aid in the development of inhibitors. This review highlights the research on these enzymes' structures, active sites, catalytic mechanisms, and the inhibitors developed against them.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biology
Daniel A. O. Rotter, Christoph Heger, Luis M. Oviedo-Bocanegra, Peter L. Graumann
Summary: The localization and diffusion of Rib enzymes in the cytoplasm of B. subtilis were investigated, revealing that RibH shows confined diffusion at cell poles while RibE is mostly diffusive. The results suggest locally different motion of active enzymes within the bacterial cytoplasm, setting up metabolic compartmentalization mostly at the poles of cells.
Article
Biotechnology & Applied Microbiology
Osakina Aron, Min Wang, Anjago Wilfred Mabeche, Batool Wajjiha, Meiqin Li, Shuai Yang, Haixia You, Yan Cai, Tian Zhang, Yunxi Li, Baohua Wang, Dongmei Zhang, Zonghua Wang, Wei Tang
Summary: MoCpa1-mediated arginine biosynthesis is crucial for fungal development, sporulation, appressorium formation, and infection-related morphogenesis in M. oryzae, making it an attractive target for mitigating obstinate fungal plant pathogens.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Jiancai Li, Rayko Halitschke, Dapeng Li, Christian Paetz, Haichao Su, Sven Heiling, Shuqing Xu, Ian T. Baldwin
Summary: Many plant specialized metabolites play a role in herbivore defense, but interrupting their biosynthetic pathways can lead to autotoxicity. Research has shown that tobacco plants avoid autotoxicity by regulating metabolic modifications, while achieving herbivore defense through inhibition of herbivore sphingolipid biosynthesis.
Article
Multidisciplinary Sciences
Linxia Liu, Jinlong Li, Yuanming Gai, Zhizhong Tian, Yanyan Wang, Tenghe Wang, Pi Liu, Qianqian Yuan, Hongwu Ma, Sang Yup Lee, Dawei Zhang
Summary: Vitamin B6 is a vital nutrient widely used in medicine, food, animal feed, and cosmetics industries. Researchers have developed an engineered strain of Escherichia coli to produce vitamin B6 more efficiently and affordably. By optimizing the metabolic pathway and enzyme efficiency, the final strain achieved a high productivity of 1.4 g/L of vitamin B6 through fed-batch fermentation. These strategies are valuable for developing microbial strains for producing vitamins and other bioproducts with low metabolic fluxes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Madison M. Smith, Brett A. Beaupre, Dariush C. Fourozesh, Kathleen M. Meneely, Audrey L. Lamb, Graham R. Moran
Summary: RibA is an important enzyme in riboflavin biosynthesis, regulated by zinc and magnesium metal ions. Studies have found that PPi is cleaved by RibA into two phosphate ions, redefining the reaction stoichiometry. Additionally, both PPi and GTP stimulate conformational changes in RibA before hydrolytic chemistry occurs.
Article
Multidisciplinary Sciences
Hui Tao, Lukas Lauterbach, Guangkai Bian, Rong Chen, Anwei Hou, Takahiro Mori, Shu Cheng, Ben Hu, Li Lu, Xin Mu, Min Li, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Toshiya Senda, Xinghuan Wang, Zixin Deng, Ikuro Abe, Jeroen S. Dickschat, Tiangang Liu
Summary: In this study, two fungal chimeric class I triterpene synthases (TrTSs) were characterized, which represent the first examples of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms and catalytic mechanisms of these enzymes were investigated, providing detailed insights into triterpene biosynthesis. Additionally, a screening platform was developed to discover a new TrTS. These findings reveal a new enzymatic mechanism for triterpene biosynthesis and enhance our understanding of terpene biosynthesis in nature.
Article
Multidisciplinary Sciences
Nathalie Ollivier, Magalie Senechal, Remi Desmet, Benoit Snella, Vangelis Agouridas, Oleg Melnyk
Summary: Phosphorylation is a mechanism used by cells to promote protein-biomolecule association. In this study, the authors demonstrate the effects of interactions between proteins equipped with positively charged arginines and peptides harboring negatively charged phosphoserines, enabling rate acceleration and chemical processes under dilute conditions.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Laura Villanueva, F. A. Bastiaan von Meijenfeldt, Alexander B. Westbye, Subhash Yadav, Ellen C. Hopmans, Bas E. Dutilh, Jaap S. Sinninghe Damste
Summary: The study has shown the existence of a putative archaeal pathway for membrane lipid synthesis in bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes group, indicating the possibility of "mixed membranes" in natural environments and potentially bridging the once-thought fundamental divide in biology.
Article
Chemistry, Multidisciplinary
Mario Prejano, Jana Skerlova, Pal Stenmark, Fahmi Himo
Summary: In this study, density functional theory calculations were used to investigate the reaction mechanism of Human PAICS. The results demonstrate a two-step mechanism for the carboxylation reaction and show that the phosphorylation-condensation reaction occurs after the carboxylation reaction. The three active site magnesium ions were found to play a role in binding substrates and stabilizing transition states and intermediates. The calculated barriers are in agreement with experimental data.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Chemistry, Multidisciplinary
Xiang Sheng, Fahmi Himo
Summary: The quantum chemical cluster approach has been used for over two decades to model enzyme active sites and reaction mechanisms. This methodology involves selecting a small part of the enzyme as a model and using quantum chemical methods to calculate energies and properties. Over the years, this approach has been used to solve various enzyme mechanisms and has been expanded to address new questions.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Plant Sciences
Xuan Feng, Qingzhi Zhang, David J. Clarke, Hai Deng, David O'Hagan
Summary: 3'-O-ss-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is a natural product of Streptomyces calvus and Streptomyces virens, and can also be generated in vitro by the enzyme NucGT. Experimental results using oxygen-18 and deuterium isotopes confirm that 13 is not a biosynthetic precursor to nucleocidin 1.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Jeonghun Lee, Eun-Taex Oh, Eunkyung Lee, Heon Joo Park, Chulhee Kim
Summary: The intracellular native chemical ligation (NCL) reaction can induce cytotoxicity in cancer cells, making it a potential method for preparing peptide therapeutic agents. This study demonstrates that by combining in situ reduction and spontaneous thioester formation, the NCL reaction can occur naturally in cancer cells. The resulting elongated cyclic peptides, such as NCL-Pep-1, induce cancer cell death through the enhanced helicity after elongation.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Madison M. Smith, Dariush C. Forouzesh, Nicholas E. Kaley, Dali Liu, Graham R. Moran
Summary: Dihydropyrimidine dehydrogenase (DPD) is a flavin dependent enzyme that catalyzes the reduction of pyrimidines uracil and thymine. The enzyme undergoes reductive activation prior to reducing the pyrimidine. DPD can be activated by NADPH and dihydropyrimidines, and the activation can stimulate the reinstatement of the active state.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Madison M. Smith, Tyler B. Alt, Graham R. Moran, David L. Williams
Summary: Thioredoxin/glutathione reductase (SmTGR) from Schistosoma mansoni has been identified as a drug target for the treatment of Schistosomiasis. It plays a crucial role in the detoxification of reactive oxygen species by utilizing reduced thioredoxin and glutathione.
Article
Biochemistry & Molecular Biology
Sebastian Flieger, Mao Takagaki, Natsuko Kondo, Marlon R. Lutz, Yash Gupta, Hiroki Ueda, Yoshinori Sakurai, Graham Moran, Prakasha Kempaiah, Narayan Hosmane, Minoru Suzuki, Daniel P. Becker
Summary: New carborane-bearing hydroxamate matrix metalloproteinase (MMP) ligands with nanomolar potency against MMP-2, -9 and -13 have been synthesized for boron neutron capture therapy (BNCT). In vitro studies showed that these new MMP ligands had high tumoricidal effects in the BNCT assay. This study highlights the importance of targeting MMP enzymes overexpressed on the surface of tumor cells for BNCT efficacy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Correction
Chemistry, Multidisciplinary
Wei Zhu, Arseniy Butrin, Rafael D. Melani, Peter F. Doubleday, Glaucio Monteiro Ferreira, Mauricio T. Tavares, Thahani S. Habeeb Mohammad, Brett A. Beaupre, Neil L. Kelleher, Graham R. Moran, Dali Liu, Richard B. Silverman
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Luca De Angelis, Chao Pei, Ana L. Narro, Daniel Wherritt, Rene M. Koenigs, Michael P. Doyle
Summary: The synthesis and characterization of organic compounds with unique atom or functional group connectivity is a significant interest for chemists. Polycarbonyl compounds, in which multiple carbonyl groups are directly adjacent and influence each other's reactivity, have been extensively studied. However, little is known about 1,2,3,4-tetracarbonyl compounds. In this study, a synthesis strategy involving C-nitrosation of enoldiazoacetates is reported, which allows for the synthesis of 1,2,3,4-tetracarbonyl compounds where each carbonyl group is orthogonally masked.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tyler B. Alt, Matthew R. Hoag, Graham R. Moran
Summary: This article presents the first comprehensive kinetic investigation of a bacterial form of DPD, revealing its similarity to the mammalian form in terms of mechanism but with distinct aspects in substrate roles.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Kathleen M. Meneely, Jeffrey S. McFarlane, Collette L. Wright, Kathryn Vela, Liskin Swint-Kruse, Aron W. Fenton, Audrey L. Lamb
Summary: Human liver pyruvate kinase (hlPYK) catalyzes the formation of pyruvate and ATP from phosphoenolpyruvate (PEP) and ADP. Fructose 1,6-bisphosphate (FBP) serves as an allosteric activator of hlPYK. Zymomonas mobilis pyruvate kinase (ZmPYK) performs a similar function in the Entner-Doudoroff pathway, but does not have FBP as an allosteric activator.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Kayla Glockzin, Kathleen M. Meneely, Ryan Hughes, Sean W. Maatouk, Grace E. Pina, Kajitha Suthagar, Keith Clinch, Joshua N. Buckler, Audrey L. Lamb, Peter C. Tyler, Thomas D. Meek, Ardala Katzfuss
Summary: More than 8 million people worldwide are infected with Trypanosoma cruzi, the etiological agent of Chagas Disease (CD), and over 70 million people are at risk of infection. Innovative therapies are needed as current treatments are limited. Hypoxanthine-guanine-xanthine phosphoribosyltransferases (HGXPRTs) are promising targets for CD treatment, and a set of transition-state analogue inhibitors (TSAIs) have been identified as potential lead compounds.
Correction
Chemistry, Multidisciplinary
Wei Zhu, Arseniy Butrin, Rafael D. Melani, Peter F. Doubleday, Glaucio Monteiro Ferreira, Mauricio T. Tavares, Thahani S. Habeeb Mohammad, Brett A. Beaupre, Neil L. Kelleher, Graham R. Moran, Dali Liu, Richard B. Silverman
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Nikola Kenjic, Kathleen M. Meneely, Daniel J. Wherritt, Melissa C. Denler, Timothy A. Jackson, Graham R. Moran, Audrey L. Lamb
Summary: RibB is a magnesium-dependent enzyme that catalyzes the removal of C4 from D-Ru5P to generate formate. Our study characterizes the chemistry catalyzed by RibB from Vibrio cholera and reveals crucial transient chemical states in its mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Melissa Cadena, Roberto Silva Villatoro, Jyoti Shah Gupta, Cody Phillips, Jonathan B. Allen, Hadi D. Arman, Daniel J. Wherritt, Nicholas A. Clanton, Alexander L. Ruchelman, Eric M. Simmons, Albert J. DelMonte, John R. Coombs, Doug E. Frantz
Summary: We have developed a highly selective Pd-catalyzed O-benzylation reaction and identified the formation of a key intermediate through detailed reaction analysis. This method enables the selective O-alkylation of substituted 2-quinolinones with high efficiency using a minimal amount of Pd catalyst.
Article
Biochemistry & Molecular Biology
Catherine L. Shelton, Kathleen M. Meneely, Trey A. Ronnebaum, Annemarie S. Chilton, Andrew P. Riley, Thomas E. Prisinzano, Audrey L. Lamb
Summary: Pseudomonas aeruginosa is a pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. The crystal structure of the pyochelin adenylation domain PchD, which is involved in the biosynthesis of the siderophore pyochelin, is reported in this study. Understanding the structure of PchD can aid in the development of new antibiotics against antibiotic-resistant organisms.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2022)