Review
Biochemistry & Molecular Biology
Lisa R. Knoke, Lars I. Leichert
Summary: Due to its nucleophilicity, the thiol group of cysteine plays an important role in protein chemistry. The nucleophilicity of the thiol group makes cysteine susceptible to oxidative modifications, which can alter protein function and are reversible in vivo. Therefore, studying oxidative posttranslational modifications of cysteine is crucial for understanding redox biology.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Nicholas J. Day, Matthew J. Gaffrey, Wei-Jun Qian
Summary: The review highlights how mass spectrometry-based redox proteomics has enabled accurate quantification of reversible oxidative modifications on specific cysteine residues of proteins, emphasizing the significance and application of such measurements in the field of redox biology.
Review
Biochemistry & Molecular Biology
Patrick Willems, Jingjing Huang, Joris Messens, Frank Van Breusegem
Summary: Deep learning algorithms, such as AlphaFold2, accurately predict the three-dimensional structure of proteins, providing an unparalleled resource for annotating protein function. This study analyzed the function and evolution of cysteine residues in plants using AlphaFold2 predicted structures. The analysis identified metal ligands coordinated by cysteine residues and systematically analyzed cysteine disulfides. The results showed that most of the predicted disulfides were reliable, with high agreement with known protein structures and characteristic features.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Meytal Radzinski, Tal Oppenheim, Norman Metanis, Dana Reichmann
Summary: Protein homeostasis and redox regulation are closely connected, with redox-regulated proteins or thiol-based switches at the core. Research discusses the redox code of the proteostasis network and evolving strategies of antioxidant proteins under oxidative stress conditions. The importance of cysteine in protein degradation is also highlighted.
Review
Biochemical Research Methods
Xiaolu Li, Austin Gluth, Tong Zhang, Wei-Jun Qian
Summary: Redox post-translational modifications greatly impact protein structure and function, allowing for the regulation of biological processes. Redox proteomics approaches use mass spectrometry to study these modifications and have contributed to our understanding of redox signaling and regulation. Various strategies, including blocking free thiols and using selective reduction and enrichment techniques, are employed to analyze redox PTMs. This review discusses the principles and recent advances in redox proteomics and highlights its applications in generating novel biological insights.
Article
Plant Sciences
Lara Vogelsang, Karl-Josef Dietz
Summary: This study investigates the regeneration specificity of thiol-dependent peroxiredoxins and glutathione peroxidase-like enzymes in the cytosol of Arabidopsis thaliana cells. The results demonstrate redundancy and specificity in the redox regulatory network of the cytosol, providing insights into the role of thioredoxins in this process.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Biochemistry & Molecular Biology
Agnieszka Mostek-Majewska, Anna Janta, Anna Majewska, Andrzej Ciereszko
Summary: The study found that under control conditions, 2-Cys PRDX oxidizes a group of sperm mitochondrial and actin cytoskeleton proteins. However, under oxidative stress conditions, 2-Cys PRDX primarily protects glycolytic, TCA pathway, and respiratory chain enzymes as well as sperm axonemal tubulins from oxidative damage. The inhibition of PRDX resulted in oxidation of a group of rate-limiting glycolytic proteins, triggering the switching of glucose metabolism from glycolysis to pentose phosphate pathway (PPP).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Electrochemistry
Daria A. Burmistrova, Andrey Galustyan, Ivan Smolyaninov, Nadezhda T. Berberova
Summary: Two approaches to synthesis of unsymmetrical disulfides, namely electrochemical method and microwave irradiation, were discussed. The oxidative coupling of sulfur-centered radicals and a redox-mediator promoted thiol-disulfide exchange were found to be the main mechanisms of the electrochemical method. Microwave-assisted synthesis showed variable yields depending on irradiation parameters.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2022)
Article
Chemistry, Medicinal
Inga S. Shchelik, Karl Gademann
Summary: Novel vancomycin derivatives containing thiol-and disulfide-containing moieties exhibit enhanced antibacterial activity against a broad range of bacterial strains, including vancomycin-resistant microbes and Gram-negative bacteria. These derivatives also demonstrate improved antibiofilm formation activity against VanB-resistant Enterococcus compared to vancomycin, providing a promising strategy for combating drug-resistant bacterial infections or disrupting biofilm formation.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Microbiology
Xinrong Zhang, Zhenhua Zhang, Xiao-Lin Chen
Summary: Redox modification plays significant roles in plant pathogenic fungi, impacting various biological and cellular functions, such as fungal growth and pathogenicity. The global thiol proteome survey in Magnaporthe oryzae provides valuable insights for future studies on redox modification in fungi.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaolu Li, Nicholas J. Day, Song Feng, Matthew J. Gaffrey, Tai-Du Lin, Vanessa L. Paurus, Matthew E. Monroe, Ronald J. Moore, Bin Yang, Ming Xian, Wei-Jun Qian
Summary: Thiol-based post-translational modifications play a crucial role in redox-dependent regulation and signaling, with functional cysteine sites serving as redox switches regulated through various types of PTMs. A direct detection workflow using LC-MS/MS was established to characterize the complexity of thiol PTMs at the proteome level, showing simultaneous quantification of protein abundances and different thiol PTMs. The study demonstrated the utility of this workflow by identifying over 9000 proteins and multiple types of thiol PTMs in mouse pancreatic beta-cells under ER stress, indicating independent translational and post-translational regulation of enzyme activity.
Review
Biochemistry & Molecular Biology
Kathrin Ulrich, Blanche Schwappach, Ursula Jakob
Summary: Thiol-based redox switches have evolved as efficient post-translational regulatory mechanisms that enable proteins to rapidly respond to environmental changes. This review focuses on the thiol-based activation mechanisms of stress-sensing chaperones, which convert into high affinity binding platforms for unfolding proteins under stress conditions. Cells have evolved different strategies to rapidly increase the pool of ATP-independent chaperones upon oxidative stress, providing mechanistic insights into how stress conditions are utilized to convert cellular proteins into ATP-independent holding chaperones.
BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Organic
Olga Firstova, Oleg Melnyk, Vincent Diemer
Summary: The arylthiol 4-mercaptophenylacetic acid is a powerful catalyst for the reduction of selenosulfide bonds by the water-soluble trisodium salt. It is particularly suitable for working with unprotected peptidic substrates and does not induce deselenization reactions.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Anna Noble, Matthew Guille, James N. Cobley
Summary: Measuring protein thiol redox state is crucial for understanding redox signaling in health and disease. Developing a microplate assay, like the Antibody-Linked Oxi-State Assay (ALISA), enables greater accessibility and advancement in the field of protein thiol redox biology. ALISA is a high throughput, time- and cost-efficient method that can help researchers study specific redox states of proteins in various biological processes.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Tamara Tomin, Matthias Schittmayer, Simon Sedej, Heiko Bugger, Johannes Gollmer, Sophie Honeder, Barbara Darnhofer, Laura Liesinger, Andreas Zuckermann, Peter P. Rainer, Ruth Birner-Gruenberger
Summary: Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of antioxidative defense, dysregulation of redox signaling, and protein damage. The study found that failing hearts have lower glutathione to glutathione disulfide ratios and increased oxidation of various proteins, impacting heart function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Cecilia Picazo, Brian McDonagh, Jose Peinado, Jose A. Barcena, Emilia Matallana, Agustin Aranda
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
C. A. Padilla, J. A. Barcena, M. J. Lopez-Grueso, R. Requejo-Aguilar
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2019)
Article
Biochemistry & Molecular Biology
M. J. Lopez-Grueso, R. Gonzalez-Ojeda, R. Requejo-Aguilar, B. McDonagh, C. A. Fuentes-Almagro, J. Muntane, J. A. Barcena, C. A. Padilla
Article
Biochemistry & Molecular Biology
Maria Jose Lopez-Grueso, Raul Gonzalez, Jordi Muntane, Jose Antonio Barcena, C. Alicia Padilla
Article
Biochemistry & Molecular Biology
Maria Jose Lopez Grueso, Rosa Maria Tarradas Valero, Beatriz Carmona-Hidalgo, Daniel Jose Lagal Ruiz, Jose Peinado, Brian McDonagh, Raquel Requejo Aguilar, Jose Antonio Barcena Ruiz, Carmen Alicia Padilla Pena
Article
Biochemical Research Methods
Elena Bonzon-Kulichenko, Emilio Camafeita, Juan Antonio Lopez, Maria Gomez-Serrano, Inmaculada Jorge, Enrique Calvo, Estefania Nunez, Marco Trevisan-Herraz, Navratan Bagwan, Jose Antonio Barcena, Belen Peral, Jesus Vazquez
JOURNAL OF PROTEOMICS
(2020)
Article
Cell Biology
Katarzyna Goljanek-Whysall, Ana Soriano-Arroquia, Rachel McCormick, Caroline Chinda, Brian McDonagh
Review
Geriatrics & Gerontology
Alice Shally, Brian McDonagh
Review
Biochemistry & Molecular Biology
Maria A. Rodriguez-Hernandez, P. de la Cruz-Ojeda, Ma Jose Lopez-Grueso, Elena Navarro-Villaran, Raquel Requejo-Aguilar, Beatriz Castejon-Vega, Maria Negrete, Paloma Gallego, Alvaro Vega-Ochoa, M. Victor Victor, Mario D. Cordero, Jose A. Del Campo, J. Antonio Barcena, C. Alicia Padilla, Jordi Muntane
Article
Biochemistry & Molecular Biology
Raul Gonzalez, Maria A. Rodriguez-Hernandez, Maria Negrete, Kalina Ranguelova, Aurelie Rossin, Carmen Choya-Foces, Patricia de la Cruz-Ojeda, Antonio Miranda-Vizuete, Antonio Martinez-Ruiz, Sergio Rius-Perez, Juan Sastre, Jose A. Barcena, Anne-Odile Hueber, C. Alicia Padilla, Jordi Muntane
Article
Biochemistry & Molecular Biology
Maria Jose Lopez-Grueso, Daniel Jose Lagal, Alvaro Fernando Garcia-Jimenez, Rosa Maria Tarradas, Beatriz Carmona-Hidalgo, Jose Peinado, Raquel Requejo-Aguilar, Jose Antonio Barcena, Carmen Alicia Padilla
Article
Biochemistry & Molecular Biology
Jose A. Martina, David Guerrero-Gomez, Eva Gomez-Orte, Jose Antonio Barcena, Juan Cabello, Antonio Miranda-Vizuete, Rosa Puertollano
Summary: Mammalian TFEB and TFE3, as well as their ortholog in Caenorhabditis elegans HLH-30, are regulated by a novel mechanism involving cysteine-mediated redox switch under stress conditions, leading to oligomer formation and increased stability to stress. Cysteine oxidation acts as a molecular switch linking redox balance changes with expression of target genes.
Article
Cell Biology
Ana Soriano-Arroquia, John Gostage, Qin Xia, David Bardell, Rachel McCormick, Eugene McCloskey, Ilaria Bellantuono, Peter Clegg, Brian McDonagh, Katarzyna Goljanek-Whysall
Summary: The decline in satellite cell-dependent skeletal muscle regeneration with aging is associated with alterations in miR-24 expression and its target gene Prdx6. Changes in miR-24 levels impact mitochondrial ROS generation, DNA damage pathways, and the viability and myogenic potential of myogenic progenitors, with more pronounced effects observed in old mice. The downregulation of miR-24 and subsequent upregulation of Prdx6 in response to aging may represent an adaptive mechanism to maintain satellite cell function in muscle.
Article
Biochemistry & Molecular Biology
Qin Xia, Jose C. Casas-Martinez, Eduardo Zarzuela, Javier Munoz, Antonio Miranda-Vizuete, Katarzyna Goljanek-Whysall, Brian McDonagh
Summary: Exercise increases Reactive Oxygen Species (ROS) in muscle, promoting changes in gene transcription and mitochondrial biogenesis. Peroxiredoxin 2 (Prdx2) is necessary for the adaptive response to physiological levels of H2O2 and exercise. H2O2 improves mitochondrial capacity and myogenesis in myoblasts, which is suppressed when Prdxs expression is decreased. Swimming exercise in C. elegans enhances mitochondrial content, fitness, survival, and longevity, but these benefits are diminished in prdx-2 mutant worms. Prdx-2 plays a key regulatory role in the redox signalling cascade following endogenous ROS generation.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
