Article
Biochemistry & Molecular Biology
Sebastian F. Villar, Joaquin Dalla-Rizza, Matias N. Moller, Gerardo Ferrer-Sueta, Leonel Malacrida, David M. Jameson, Ana Denicola
Summary: Protein self-assembly is a common feature in biology, and a new method utilizing intrinsic fluorescence lifetime with phasors is presented to study protein associations. The method was successfully applied to determine the equilibrium dissociation constant (K-D) of hPrx1 and identify its oligomeric states. The phasor approach is highly sensitive and quantitative, offering a valuable tool for assessing protein oligomerization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tan Qin, Yu Wang, Jing Nie, Lushan Yu, Su Zeng
Summary: This study showed that NTCP formed oligomers in Sf9 cells, and the FRET analysis of NTCP variants provided further insight into the molecular mechanism of NTCP oligomerization.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Chemistry, Multidisciplinary
Jacob R. Pope, Rachel L. Johnson, W. David Jamieson, Harley L. Worthy, Senthilkumar Kailasam, Rochelle D. Ahmed, Ismail Taban, Husam Sabah Auhim, Daniel W. Watkins, Pierre J. Rizkallah, Oliver K. Castell, D. Dafydd Jones
Summary: Fluorescent proteins (FPs) are often used in pairs to monitor biomolecular events. GFP homodimers are brighter than monomers, while heterodimers typically have lower FRET efficiency than predicted.
Article
Biochemistry & Molecular Biology
Clara Diaz-Garcia, Maria Lourdes Renart, Jose Antonio Poveda, Ana Marcela Giudici, Jose M. Gonzalez-Ros, Manuel Prieto, Ana Coutinho
Summary: The study investigated the allosteric coupling between activation and inactivation processes in K+ channels, specifically in the prokaryotic KcsA channel. By labeling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background, the conformational changes of both the inner gate and selectivity filter (SF) were simultaneously monitored using time-resolved homo-Forster Resonance Energy Transfer (homo-FRET) measurements. The results confirmed the allosteric communication between the two gates of KcsA and proposed a simple TMR homo-FRET based ratiometric assay for studying the conformational dynamics associated with the gating of other ion channels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Lianmin Cui, Ling Zhang, Heping Zeng
Summary: The study systematically investigates fluorescence resonance energy transfers (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) on nanoporous gold (NPG) by controlling the distance between NPG and fluorescent proteins with polyelectrolyte multilayers. It is found that NPG significantly enhances FRET between CFP and YFP, with the maximum enhancement related to both ligament size of NPG and the distance between NPG and proteins. After optimizing the distance, an 18-fold FRET enhancement was obtained on NPG compared to glass, with a conversion efficiency of about 90%.
Article
Biology
William N. Zagotta, Brandon S. Sim, Anthony K. Nhim, Marium M. Raza, Eric G. B. Evans, Yarra Venkatesh, Chloe M. Jones, Ryan A. Mehl, E. James Petersson, Sharona E. Gordon
Summary: With the recent explosion in high-resolution protein structures, there is a new frontier in biology to elucidate the mechanisms of conformational rearrangements in proteins to meet the changing needs of cells. By rigorously measuring protein energetics and dynamics through new methods like tmFRET, differences in conformational states and accurate quantification of distributions can be revealed. This new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
Article
Biochemistry & Molecular Biology
M. Victoria Cappellari, Luis F. Marcano-Garcia, Sabrina Simoncelli, Pedro F. Aramendia
Summary: Single molecule fluorescence localization microscopy allows for high-precision molecular localization and correlation analysis. This study presents a method to calculate thermodynamic equilibrium constants and tests it using two different fluorescently labeled chains. The results show that the values obtained from STORM experiments are consistent with those from bulk experiments.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Nina Gloeckner, Sven zur Oven-Krockhaus, Leander Rohr, Frank Wackenhut, Moritz Burmeister, Friederike Wanke, Eleonore Holzwart, Alfred J. Meixner, Sebastian Wolf, Klaus Harter
Summary: Protein-protein interaction studies are crucial for understanding cellular signaling. This study used three-fluorophore FRET and FRET-fluorescence lifetime imaging microscopy techniques to demonstrate the formation of a ternary complex involving Receptor-Like Protein 44, Brassinosteroid Insensitive 1, and Brassinosteroid Insensitive 1 Associated Kinase 1 in living plant cells. The researchers also found that this complex is localized in a distinct plasma membrane nanodomain.
Article
Chemistry, Medicinal
Dhulfiqar Ali Abed, Ahmed R. Ali, Sumi Lee, Mai-Uyen Nguyen, Michael P. Verzi, Longqin Hu
Summary: Direct inhibition of the PPI between Keap1 and Nrf2 leads to Nrf2 accumulation and nuclear translocation, activating antioxidant response genes. A series of 1,4-bis(arylsulfonamido)naphthalene-N,N'-diacetic acid analogs were tested for Keap1-binding activity, with compound 24a showing the strongest binding affinity. In addition, compounds 12b, 15, and 24a were found to activate the Nrf2 pathway in NCM460D cells, increasing mRNA levels of GSTM3, HMOX1, and NQO1.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Francisco Fueyo-Gonzalez, Rosario Herranz, Simona Plesselova, Maria D. Giron, Rafael Salto, Jose Manuel Paredes, Angel Orte, May C. Morris, Juan A. Gonzalez-Vera
Summary: CDK5 kinase is activated through interactions with different partners, playing a key role in neuronal functions and contributing to neurodegenerative diseases and human cancers. The design of fluorescently labeled peptides allowed for the detection of CDK5 partners, demonstrating the potential of the biosensor to report on the relative abundance of p25.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biophysics
Taylor A. Phillips, Garrett T. Hauck, Marsha P. Pribadi, Ellen E. Cho, Sean R. Cleary, Seth L. Robia
Summary: The sarco(endo)plasmic reticulum calcium ATPase (SERCA) is an ion transporter that regulates intracellular calcium levels. It can be influenced by various membrane micropeptides, such as another-regulin, dwarf open reading frame, endoregulin, phospholamban (PLB), and sarcolipin. These micropeptides can interact with each other and form homo-oligomers or hetero-oligomers. The affinity of hetero-oligomerization between different micropeptides depends on their relative abundance. The complexity of micropeptide interactions exponentially increases with the number of coexpressed micropeptides in a tissue.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Renuka Ranjan, Nidhi Tiwari, Arvind M. Kayastha, Neeraj Sinha
Summary: The study utilizes mutant polypeptide as a model to gain insights into the mechanism of domain-swapped aggregation through real-time monitoring, showing the transition of dimer into monomeric intermediates and the presence of other species during aggregation via UV monitoring, DLS profiles, and NMR spectra. Diffusion NMR reveals changes in mobility of dimeric species, indicating the formation of lower molecular weight species during aggregation. This preliminary study explores the possibility of using biophysical methods to understand different stages of aggregation at an atomistic level.
Article
Chemistry, Multidisciplinary
Huntley H. Chang, Alex M. Bennett, William D. Cameron, Eric Floro, Aaron Au, Christopher M. McFaul, Christopher M. Yip, Jonathan V. Rocheleau
Summary: This study utilized multiple organelle-targeted Apollo-NADP+ sensors to reveal the prominent role of beta-cell mitochondria in determining NADPH production in the cytoplasm, nucleus, and peroxisome.
Article
Biochemistry & Molecular Biology
Nina Komaniecka, Marta Porras, Louis Cairn, Jon Ander Santas, Nerea Ferreiro, Juan Carlos Penedo, Sonia Banuelos
Summary: APE1 is a key enzyme in the BER pathway, involved in repairing oxidative DNA damage. Its structure includes a catalytic domain and a flexible N-terminal extension. Conformational rearrangements occur internally and between molecules when APE1 binds DNA and interacts with NPM1. These findings suggest that the N-terminal region approaches the DNA near the abasic site, and its spatial configuration is sensitive to NPM1, potentially impacting APE1's regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Rocio Corfield, Gabriel Lalou, Santiago Di Lella, Karina D. Martinez, Carolina Schebor, Mariana C. Allievi, Oscar E. Perez
Summary: Complexes of β-lactoglobulin or whey protein isolate with folic acid were developed as potential food ingredients. The binding sites of the vitamin on the protein were elucidated using dilute concentrations. The zeta potential, aggregation kinetics, and particle size distributions were studied, and in silico studies were carried out. The bioaccessibility of the vitamin was also assessed.
FOOD HYDROCOLLOIDS
(2023)
Review
Biochemistry & Molecular Biology
David Young, Brandan Pedre, Daria Ezerina, Barbara De Smet, Aleksandra Lewandowska, Maria-Armineh Tossounian, Nandita Bodra, Jingjing Huang, Leonardo Astolfi Rosado, Frank Van Breusegem, Joris Messens
ANTIOXIDANTS & REDOX SIGNALING
(2019)
Article
Cell Biology
Valeriy V. Pak, Daria Ezerina, Olga G. Lyublinskaya, Brandan Pedre, Pyotr A. Tyurin-Kuzmin, Natalie M. Mishina, Marion Thauvin, David Young, Khadija Wahni, Santiago Agustin Martinez Gache, Alexandra D. Demidovich, Yulia G. Ermakova, Yulia D. Maslova, Arina G. Shokhina, Emrah Eroglu, Dmitry S. Bilan, Ivan Bogeski, Thomas Michel, Sophie Vriz, Joris Messens, Vsevolod V. Belousov
Review
Biochemistry & Molecular Biology
Brandan Pedre, Tobias P. Dick
Summary: 3-Mercaptopyruvate sulfurtransferase (MPST) is involved in hydrogen sulfide generation, protein modification, and cyanide detoxification, while also playing a crucial role in oxidative stress resistance, mitochondrial function, and fatty acid metabolism. However, the overall role and regulation of MPST in the broader physiological context remain to be fully understood.
BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Deepti Talwar, Joris Messens, Tobias P. Dick
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Laure-Anne Ligeon, Maria Pena-Francesch, Liliana Danusia Vanoaica, Nicolas Gonzalo Nunez, Deepti Talwar, Tobias P. Dick, Christian Munz
Summary: LC3-associated phagocytosis (LAP) is an important contributor to cellular processes and immunity. NOX2-generated ROS stabilize LAPosomes by inhibiting deconjugation of LC3, supporting sustained MHC class II antigen presentation.
NATURE COMMUNICATIONS
(2021)
Article
Food Science & Technology
Bogdan Jovanovic, Nina Eiermann, Deepti Talwar, Maria Boulougouri, Tobias P. Dick, Georg Stoecklin
Summary: Arsenic exerts its toxicity on cells through the inhibition of Trx1-induced SGs, which is crucial for cell survival in response to ASN exposure. The assembly of SGs plays a significant role in the toxic properties of ASN, highlighting the importance of Trx1 in cellular response to ASN exposure.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Review
Pharmacology & Pharmacy
Brandan Pedre, Uladzimir Barayeu, Daria Ezerina, Tobias P. Dick
Summary: Originally used as a mucolytic, N-acetylcysteine (NAC) is now a standard treatment for paracetamol poisoning and a widely used antioxidant. In addition to its traditional mechanisms, a newly discovered mechanism involves the conversion of NAC into hydrogen sulfide and sulfane sulfur species, which may explain many of its effects.
PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Chemistry, Multidisciplinary
Danny Schilling, Uladzimir Barayeu, Raphael R. Steimbach, Deepti Talwar, Aubry K. Miller, Tobias P. Dick
Summary: Protein persulfides can be conserved by certain alkylating agents for subsequent mass spectrometry detection, while others rapidly convert into thioethers. N-ethylmaleimide and iodoacetamide are unsuitable for conserving persulfides, but monobromobimane and N-t-butyl-iodoacetamide are able to generate stable alkylated persulfides.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Microbiology
Roger D. Castillo Arteaga, Leandro M. Garrido, Brandan Pedre, Irina Helmle, Harald Gross, Bertolt Gust, Gabriel Padilla
Summary: Streptomyces olindensis strain DAUFPE 5622 has developed multiple self-resistance mechanisms to protect against the toxicity of the antibiotics it produces. One novel self-resistance mechanism encoded by cosP responds to peroxides by the enzyme MPx to protect the strain from the effects of toxic substances.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Brandan Pedre, Deepti Talwar, Uladzimir Barayeu, Danny Schilling, Marcin Luzarowski, Mikolaj Sokolowski, Sebastian Glatt, Tobias P. Dick
Summary: Protein S-persulfidation (P-SSH) is a common posttranslational modification that occurs under basal conditions and is often elevated under stress conditions. The mechanism by which proteins are persulfidated inside cells has remained unclear. This study identifies 3-mercaptopyruvate sulfur transferase (MPST) as a protein that directly engages in protein-to-protein transpersulfidation reactions, promoting cytoprotective functions through protein persulfidation.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Endocrinology & Metabolism
Deepti Talwar, Colin G. G. Miller, Justus Grossmann, Lukasz Szyrwiel, Torsten Schwecke, Vadim Demichev, Ana-Matea Mikecin Drazic, Anand Mayakonda, Pavlo Lutsik, Carmen Veith, Michael D. D. Milsom, Karin Mueller-Decker, Michael Muelleder, Markus Ralser, Tobias P. P. Dick
Summary: This study reveals that human and mouse cells expressing a redox-insensitive GAPDH mutant are unable to upregulate the oxidative pentose phosphate pathway in response to oxidative stress. The redox switch of GAPDH plays a crucial role in anchorage-independent growth of cells and spheroids as well as tumor growth, and disabling this switch can suppress tumor growth. The findings demonstrate the physiological and pathophysiological relevance of oxidative GAPDH inactivation in mammals.
Meeting Abstract
Biochemistry & Molecular Biology
Bogdan Jovanovic, Nina Eiermann, Deepti Talwar, Maria Boulougouri, Tobias P. Dick, Georg Stoecklin
FREE RADICAL BIOLOGY AND MEDICINE
(2021)