Review
Biochemistry & Molecular Biology
Jean Chaudiere
Summary: Selenocysteine is a catalytic residue essential for the function of selenoenzymes in bacteria and mammals, being incorporated into polypeptides through a recoding process. Mammals possess 25 genes encoding selenoproteins, which primarily function as antioxidants and regulators of cell metabolism. Selenoprotein P serves as a reservoir for selenocysteine in mammals, while glutathione peroxidases, although extensively studied, still have unknown distribution and regulatory functions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anupama K. Puppala, Jennifer Castillo Suchkou, Rachel L. French, Kaitlyn A. Kiernan, Miljan Simonovic
Summary: Using high-resolution X-ray crystallography, the study visualized tRNA-dependent conformational changes in human SepSecS and showed that tRNA(Sec) binding organizes the active sites of the catalytic protomer. The study also demonstrated that productive SepSecS·tRNA(Sec) complex formation is driven by electrostatic interactions between tRNA(Sec) and SepSecS. This research provides a structural basis for understanding the terminal reaction of Sec formation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Applied
Ryohei Sato, Yutaka Amao
Summary: The study investigates the participation of protein motions in the biocatalytic reaction of formate oxidation catalyzed by CbFDH by means of isotope substitution of the substrate. It is found that isotope-labelled NAD+ and deuterium or 13C-labelled formate exhibit an isotope effect in the formate oxidation reaction, while 13C-labelled formate does not significantly affect the reaction rate. The results suggest that C-H bond cleavage of formate and nucleophilic attack of hydrogen on NAD+ dominate the reaction rate in CbFDH-catalyzed formate oxidation, and the hydrogen bonds formed between formate, NAD+, and water molecules also play an important role in the oxidation of formate to CO2.
Article
Biochemistry & Molecular Biology
Ana Rita Oliveira, Cristiano Mota, Kateryna Klymanska, Frederic Biaso, Maria Joao Romao, Bruno Guigliarelli, Ines Cardoso Pereira
Summary: The study investigated the structure and catalytic mechanism of metal-dependent formate dehydrogenases, revealing their high activity and structural stability. Spectroscopic and crystallographic analysis determined the redox characteristics and structural changes of the metal centers.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Wenjin Li, Yanxin Gao, Xuan Sun, Lei Wan, Haishuo Ji, Hang Luo, Yao Tian, Hao Song, Geng Wu, Liyun Zhang
Summary: In this study, the adsorption characteristics and catalytic properties of formate dehydrogenase from Clostridium ljungdahlii (ClFDH) on electrodes were investigated. The electrochemical signals observed on the electrodes were attributed to the reduction and oxidation potential of the [4Fe-4S](2+/+) cluster. Upon adding substrates, the signals transformed into a specific redox center that catalytically engages in electron transport and promotes the rapid and efficient reversible interconversion between CO2 and formate. The results provide valuable insights into the understanding of the catalytic mechanism of FDH and the design of synthetic catalysts.
Article
Biotechnology & Applied Microbiology
Mohd Farid Abdul Halim, Leslie A. Day, Kyle C. Costa
Summary: Hydrogenotrophic methanogens produce methane using H-2 as an electron donor, but can also utilize formate or alcohols as alternative electron donors. Methanogens from the order Methanomicrobiales lack genes encoding hydrogenases, but are capable of growth using formate as an electron donor. Studies on Methanoculleus thermophilus highlight the importance of formate as an electron donor for methanogenesis and suggest its close integration into the metabolic pathway of methanogens from the order Methanomicrobiales.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Agronomy
Yuanchuang Lu, Dongxiao Li, Changqing Li, Mengyu Sun, Zhijie Wu, Zhimei Sun
Summary: In this study, the inhibitory effect and regulatory mechanism of 3,5-dimethylpyrazole (DMP) on soil nitrogen (N) transformation were investigated. The results showed that DMP effectively inhibited soil nitrification, decreased nitrate reductase activity, and increased nitrite reductase and dehydrogenase activities. The inhibitory effect was dose-dependent, with a rate of 0.025 g kg(-1) dry soil showing the strongest effect. DMP application also led to changes in soil chemical and biological properties, providing new insights into the involvement of DMP in soil N transformation.
Article
Chemistry, Physical
MengYa Guo, TingTing Zhai, CaiHong Wang, ZiHui Meng, WenFang Liu
Summary: PEI is commonly used in CO2 adsorption but rarely in enzyme immobilization. In this study, FDH was immobilized on PEI modified surfaces, resulting in significantly improved catalytic performance, stability, and activity compared to free enzymes. Polydopamine/PEI-SiO2 attached FDH showed higher activity and stability than biocatalytic membrane.
CATALYSIS COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Hui Dai, Anhang Zhang, Siqi Xiong, Xin Xiao, Changjian Zhou, Yi Pan
Summary: The conversion of CO2 into other C1 raw materials is considered the best way to solve the greenhouse effect and energy crisis. By developing Ga2O3 CeO2 composite oxide catalysts, high selectivity in the reverse water gas shift reaction can be achieved.
Article
Biochemistry & Molecular Biology
Breeanna Mintmier, Jennifer M. McGarry, Daniel J. Bain, Partha Basu
Summary: The molybdopterin enzyme family, including the diverse dimethyl sulfoxide reductase (DMSOR) subfamily, catalyzes various reactions important in microbial processes. The molybdenum coordinating residue in these enzymes may tune substrate preference, with quantitative information and understanding still limited. Further studies on variants with different molybdenum coordinating cysteine residues provide insight into the function of these enzymes.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Ryohei Sato, Yutaka Amao
Summary: The effects of isotope-labelled NADH and CO2 on the CO2 reduction activity of CbFDH were investigated. It was found that using deuterium-labelled NADH decreased the rate of CO2 reduction to formate, while using (CO2)-C-13 as a substrate had no effect on the reduction rate. However, a curious phenomenon of decreased CO2 reduction activity was observed when a mixture of (CO2)-C-12 and (CO2)-C-13 was used as substrates.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2022)
Article
Biology
Yunus Emre Arvas, Ismail Kocacaliskan, Semiha Erisen, Emel Ordu
Summary: This study was conducted to investigate the physiological effects, antioxidant activities, and gene expressions of different rice varieties under salt stress. The results showed that the varieties exhibited different responses to salt concentrations in terms of root and stem length, enzyme activities, and gene expression.
Article
Microbiology
Helge M. Dietrich, Florian Kremp, Christian Oppinger, Luna Ribaric, Volker Mueller
Summary: Methanol, the simplest of all alcohols, is attracting attention for its potential as a substrate for anaerobes to produce value-added chemicals. However, the lack of information on the biochemistry and bioenergetics during methanol conversion in bacteria is hindering the development of environmentally friendly but economically attractive biotechnological processes. The study on Eubacterium callanderi KIST612 aims to analyze the genes and enzymes involved in methanol conversion to acetate, shedding light on the bioenergetics of the process.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
K. C. Khadanand, Jing Yang, Martin L. Kirk
Summary: Two new desoxo molybdenum(V) complexes have been synthesized as models for the paramagnetic high-g split intermediate in the catalytic cycle of dimethyl sulfoxide reductase (DMSOR). The geometric and electronic structures of high-g split and other EPR-active type II/III DMSOR family enzyme forms have been characterized using EXAFS and EPR data, supporting a specific 6-coordinate structure for the high-g split.
INORGANIC CHEMISTRY
(2021)
Article
Plant Sciences
Vedat Beyyavas, Emrah Ramazanoglu, Erdal Sakin, Cevher Ilhan Cevheri, Ali Seyrek
Summary: The application of ferrous sulfate is important for improving agricultural production, addressing micronutrient deficiencies, and promoting sustainable food and feed production. This study investigated the effects of foliar iron sulfate application on cotton yield, soil enzyme activity, and chlorophyll content. The results showed that the 0.4% FeSO4 application dose had the most significant impact, increasing cotton yield, SPAD value, and NDVI values. Soil enzymes also responded positively to FeSO4 application.
JOURNAL OF PLANT NUTRITION
(2023)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria J. Ramos, Pedro A. Fernandes
Summary: In this study, the catalytic mechanism of RVV-X was determined using a density functional theory/molecular mechanics approach. The results showed that the catalytic process occurs in two steps, involving nucleophilic attack and protonation of the substrate. Zn2+ was found to play a unique role in catalysis by lowering the pKa of the Zn2+-bound water molecule.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Joao Carneiro, Rita P. Magalhaes, Victor de la Oliva M. Roque, Manuel Simoes, Diogo Pratas, Sergio F. Sousa
Summary: This study developed a machine learning multitechnique consensus workflow to predict the protein targets of molecules with confirmed inhibitory activity against biofilm formation by Pseudomonas aeruginosa. The implemented algorithm is freely available and can be improved as more data become available.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2023)
Article
Chemistry, Medicinal
Juliana Castro-Amorim, Ana Novo de Oliveira, Saulo Luis Da Silva, Andreimar M. Soares, Ashis K. Mukherjee, Maria Joao Ramos, Pedro A. . Fernandes
Summary: Snake venom-secreted phospholipase A(2) (svPLA(2)) enzymes play a crucial role in envenoming by disrupting the cell membrane's integrity and inducing various pharmacological effects. However, the reaction mechanisms of svPLA(2) are still not fully understood. This review presents and analyzes the most plausible reaction mechanisms, including the single-water mechanism and the assisted-water mechanism. The importance of interfacial activation and a potential catalytic mechanism for noncatalytic PLA(2)-like proteins are also discussed.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Jovana B. Araskov, Natalia Maciejewska, Mateusz Olszewski, Aleksandar Visnjevac, Vladimir Blagojevic, Henrique S. Fernandes, Sergio F. Sousa, Adrian Puerta, Jose M. Padron, Berta Barta Hollo, Miguel Monge, Maria Rodriguez-Castillo, Jose M. Lopez-de-Luzuriaga, Ozlem Uguz, Atif Koca, Tamara R. Todorovic, Nenad R. Filipovic
Summary: In this study, three neutral Zn(II) complexes with pyridine-based TH ligands were synthesized and characterized. The influence of the ligands' charge on the structure, intermolecular interactions, and photophysical properties was investigated. The deprotonation of the ligands mainly affected the relative energies of electronic levels in the complexes, resulting in similar photoluminescence mechanisms and quantum yields. The substituents at the ligands' periphery had localized effects on the selected quantum molecular descriptors of the complexes.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Review
Biochemistry & Molecular Biology
Maria F. Araujo, Elisabete M. S. Castanheira, Sergio F. Sousa
Summary: Insecticides are crucial in controlling the spread of insect-borne diseases and protecting crop health. They are formulated to kill or manage insect populations, but their use can have potential consequences on non-target species, the environment, and human health. It is important to follow recommended instructions and employ integrated pest management practices for responsible and sustainable utilization. This review article provides a comprehensive examination of insecticides, including their modes of action, physiological targets, impacts on the environment and human health, and alternatives.
Article
Biochemistry & Molecular Biology
Joao P. M. De Sousa, Nuno C. S. A. Oliveira, Pedro A. Fernandes
Summary: (S)-Norcoclaurine is a crucial compound for the biosynthesis of benzylisoquinoline alkaloids, including various drugs. The genetic modification of (S)-norcoclaurine synthase has been proven to be an effective strategy for large-scale bioproduction of (S)-norcoclaurine in heterologous hosts such as bacteria or yeast.
Article
Chemistry, Physical
Rui P. P. Neves, Bruno Araujo, Maria J. Ramos, Pedro A. Fernandes
Summary: The bacterium Rhodococcus erythropolis (strain IGTS8) has a significant potential in the industry for its ability to remove sulfur from crude oil through the 4S metabolic pathway. The rate-limiting enzyme DszC is prone to feedback inhibition. Molecular docking and dynamics simulations were used to identify binding sites wherein two products of the pathway induce feedback inhibition. The study revealed four potential binding sites, and the proposed mechanism of feedback inhibition involves disturbance of oligomerization and weakening of key interactions within DszC.
Article
Chemistry, Medicinal
Mariana Novo Belchor, Caroline Ramos da Cruz Costa, Airam Roggero, Laila L. F. Moraes, Ricardo Samelo, Isabelly Annunciato, Marcos Antonio de Oliveira, Sergio F. Sousa, Marcos Hikari Toyama
Summary: In this study, in silico tools were used to evaluate the potential of quercetin methylated derivatives in inhibiting snake venom toxins and phospholipase A2. The results showed that certain residues, including Leu2, Phe5, Tyr28, glycine in the calcium-binding loop, His48, and Asp49, were the main targets for inhibition. These findings are important for further research on the anti-inflammatory effects of quercetin derivatives.
Article
Chemistry, Medicinal
Joas T. S. Coimbra, Pedro A. Fernandes, Maria J. Ramos
Summary: Due to antibiotic resistance, it is crucial to explore new antibiotics and/or strategies to counter resistance. This study used molecular dynamics simulations and quantum mechanics/molecular mechanics methods to investigate the degradation of a streptogramin B antibiotic by Vgb lyase and assess the impact of point mutations on the reaction. The findings provide valuable insights into the linearization reactions of cyclic antibiotics and aid in the development of novel strategies against antibiotic resistance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Microbiology
E. Mauro, D. Lapaillerie, C. Tumiotto, C. Charlier, F. Martins, S. F. Sousa, M. Metifiot, P. Weigel, K. Yamatsugu, M. Kanai, H. Munier-Lehmann, C. Richetta, M. Maisch, J. Dutrieux, J. Batisse, M. Ruff, O. Delelis, P. Lesbats, V. Parissi
Summary: Researchers used AlphaLISA technology to monitor the interaction between retroviral intasomes and nucleosomes, and identified drugs that disrupt or prevent their association, inhibiting HIV-1 integration.
Article
Materials Science, Multidisciplinary
Fabio G. Martins, Chanchal Kiran Thakur, Chandrabose Karthikeyan, N. S. Hari Narayana Moorthy, Sergio F. Sousa
Summary: This study used computational models to investigate the pH dependent loading of doxorubicin onto multiwalled carbon nanotubes (MWCNTs). The results showed that systems under acidic conditions had lower adsorption compared to their neutral counterparts, and carbohydrate-modified lysinated MWCNTs had higher adsorption compared to pristine or carboxylated nanotubes. These findings are consistent with previous experimental work and suggest that sugar-tethered multiwalled carbon nanotubes hold promise for doxorubicin delivery to cancer cells.
Article
Chemistry, Multidisciplinary
How Chee Ong, Joao T. S. Coimbra, Maria J. Ramos, Bengang Xing, Pedro A. Fernandes, Felipe Garcia
Summary: Mitochondrial targeting is a promising strategy for treating various diseases, and Triphenylphosphonium (TPP+) moieties have been widely used for this purpose. However, the core structure of TPP+ remains largely unchanged, so this study explored the use of novel phosphorus-nitrogen based frameworks as mitochondrial delivery vectors. The phosphazenylphosphonium (PPN+) moiety was found to be highly effective in delivering cargo to mitochondria, with unique electronic properties and high lipophilicity.
Article
Chemistry, Multidisciplinary
Carola Jerves, Rui P. P. Neves, Saulo L. da Silva, Maria J. Ramos, Pedro A. Fernandes
Summary: The PETase enzyme from Ideonella sakaiensis can degrade PET at room temperature. Computational enzyme optimization can accelerate enzyme engineering. Mutations can stabilize transition states and decrease activation barriers. Rational enzyme engineering on PETase and other enzymes is encouraged.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Tatiana F. Vieira, Nuno M. F. S. A. Cerqueira, Manuel Simoes, Sergio F. Sousa
Summary: PqsD is an enzyme involved in the synthesis of essential secondary metabolites for Pseudomonas quinolone signal (PQS) inducer molecules. Inhibition of PqsD activity can inhibit biofilm formation and can be combined with PqsR inhibition. This study used computational methods to screen and select eight compounds as potential quorum sensing inhibitors.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2024)