Article
Biochemistry & Molecular Biology
Azahara Casatejada, Leonor Puerto-Galan, Juan M. Perez-Ruiz, Francisco J. Cejudo
Summary: Oxidizing signals mediated by thiol-dependent peroxidase activity play a crucial role in chloroplast redox balance, with both 2-Cys peroxiredoxins (PRXs) and glutathione peroxidases (GPXs) being involved. However, the specific contribution of GPXs in this process is not well understood. This study generated mutant plants devoid of GPXs to investigate their functional relationship with the NADPH-dependent thioredoxin reductase C (NTRC)-2-Cys PRXs redox system. The results indicate that GPXs contribute to chloroplast redox homeostasis independently of NTRC.
Article
Biochemistry & Molecular Biology
Victor Delgado-Requerey, Francisco Javier Cejudo, Maria-Cruz Gonzalez
Summary: The NTRC-2-Cys-Prx system plays a central role in the coordinated regulation of chloroplast biosynthetic pathways and NADPH extrusion via malate valve. The functional relationship between NTRC, 2-Cys Prxs, and m-type Trxs is established. The impairment of NTRC-2-Cys-Prx system leads to severe phenotypic defects in Arabidopsis, which can be suppressed by decreasing the content of 2-Cys Prx.
Article
Biochemical Research Methods
Florent Velay, Melanie Soula, Marwa Mehrez, Clement Belbachir, Stefano D'Alessandro, Christophe Laloi, Patrice Crete, Ben Field
Summary: This study describes the development of a flexible modular cloning-based toolkit for bimolecular fluorescence complementation (BiFC) and proximity labelling in the chloroplast and other cellular compartments. The toolkit simplifies the construction of chloroplast fusion proteins, enables robust ratiometric quantification, and provides model positive and negative controls. The study highlights potential pitfalls in designing BiFC experiments, such as the choice of FP split, negative controls, cell type, and reference FP.
Article
Biochemistry & Molecular Biology
Maria Ancin, Joaquin Fernandez-Irigoyen, Enrique Santamaria, Luis Larraya, Alicia Fernandez-San Millan, Jon Veramendi, Inmaculada Farran
Summary: Post-translational redox modifications, particularly mediated by thioredoxins (Trxs), play a crucial role in controlling cellular processes. In this study, a new in vivo approach was developed to identify potential targets of Trx f, Trx m, and NTRC. The results revealed new insights into the specificity and function of these proteins in various cellular processes.
Article
Plant Sciences
Yonghong Li, Lin Zhang, Yurou Shen, Lianwei Peng, Fudan Gao
Summary: Thiol/disulfide-based redox regulation is essential for controlling the activity of target proteins in plant chloroplasts in response to light signals. In this study, the role of CBSX2 in the oxidation of redox-regulated enzymes in chloroplasts was investigated. The results suggest that CBSX2 participates in the oxidation of these enzymes in darkness, probably through regulation of the activity of chloroplast redox systems in vivo.
Article
Biotechnology & Applied Microbiology
Shams T. A. Islam, Jie Zhang, Fabio Tonin, Renske Hinderks, Yanthi N. Deurloo, Vlada B. Urlacher, Peter-Leon Hagedoorn
Summary: Lignin valorization through laccase catalysis can release aromatic products, but different enzymes exhibit significant variations in conversion efficiency and rate. Trametes versicolor laccase follows Michaelis-Menten kinetics in converting Kraft lignin, with specific thermodynamic and kinetic parameters, making it a promising tool for guiding enzymatic lignin valorization strategies.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Physical
Pablo F. Garrido, Margarida Bastos, Adrian Velazquez-Campoy, Alfredo Amigo, Philippe Dumas, Angel Pineiro
Summary: The injection of air into an isothermal titration calorimeter's sample cell allows for accurate determination of the surface tension of the target liquid, despite the periodic contribution from bubbles. The new algorithm successfully identifies and analyzes these contributions, improving the analysis of calorimetric signals.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Review
Pharmacology & Pharmacy
Iago Dillion Lima Cavalcanti, Francisco Humberto Xavier Junior, Nereide Stela Santos Magalhaes, Mariane Cajuba de Britto Lira Nogueira
Summary: Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. In the field of pharmaceutical nanotechnology, ITC has been increasingly used to understand the interaction mechanisms in the formation of nanoparticles and the behavior of nanocarriers in in vivo studies. This technique provides quick and easy results to optimize the formulation process of nano-systems.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Tzu-Yi Tai, Fanrui Sha, Xiaoliang Wang, Xingjie Wang, Kaikai Ma, Kent O. Kirlikovali, Shengyi Su, Timur Islamoglu, Satoshi Kato, Omar K. Farha
Summary: This study presents the first systematic investigation on the thermodynamics of protein immobilization in metal-organic frameworks (MOFs). It demonstrates that MOFs provide a hydrophobic stabilizing microenvironment for proteins, leading to an entropically driven encapsulation process. Among a series of Zr-MOFs, pyrene-based NU-1000 exhibits the most favorable encapsulation process for insulin.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Thermodynamics
Ziga Medos, Isidora Cobanov, Marija Bester-Rogac, Bojan Sarac
Summary: This research paper examines the issues associated with power compensation isothermal titration calorimetry, highlighting the possibility of obtaining different enthalpy values with different instruments and setting parameters. It emphasizes that modern calorimeters' dynamic power compensation mode may lead to overcompensation of heat effects, resulting in experimental results heavily reliant on chosen parameters. To avoid these problems, the paper suggests checking raw signals and conducting experiments with low or disabled power compensation when observing switching effects.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2021)
Article
Biochemistry & Molecular Biology
Adam Jugl, Miloslav Pekar
Summary: The interactions between hyaluronan and cecropin B were investigated using high-resolution ultrasonic spectroscopy and isothermal titration calorimetry. The study found that the molecular weight of hyaluronan played a significant role in the interactions, particularly the transition between different conformations. In water, interactions were saturated at a molar charge ratio of 1.5, possibly due to steric hinderance or functional group interactions. However, in PBS, no interactions were observed, regardless of the molecular weight of hyaluronan, indicating that the interactions were suppressed at higher ionic strength.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Cell Biology
Daniel Wittmann, Peter Geigenberger, Bernhard Grimm
Summary: Redox regulation plays a crucial role in the expression of plastid genes and different metabolic pathways. In this study, the authors investigated how the redox state of plastids and the contributing reducing enzymes control the enzymes involved in tetrapyrrole biosynthesis (TBS), which is essential for chlorophyll and heme production in higher plants. The researchers found that the content of certain TBS enzymes was light intensity-dependent and decreased under oxidizing conditions. They also demonstrated that a deficiency of thiol-redox transmitters in plastids led to enhanced degradation of TBS enzymes. Additionally, the study showed that the Clp protease plays a role in the degradation of TBS proteins. The findings contribute to a better understanding of the regulation of TBS and its importance in plant metabolism.
Article
Chemistry, Multidisciplinary
Fanrui Sha, Tzu-Yi Tai, Madeleine A. Gaidimas, Florencia A. Son, Omar K. Farha
Summary: Isothermal titration calorimetry (ITC) is a technique for measuring the thermodynamic parameters of binding events, which has applications not only in biological macromolecules but also in synthetic systems like metal-organic frameworks (MOFs). Utilizing ITC in MOFs can provide insights into small molecule adsorption mechanisms and the formation of MOF-based composite materials through non-covalent interactions, with specific experimental considerations discussed. Furthermore, underexplored research directions related to MOFs that could benefit from ITC are highlighted.
Article
Polymer Science
Jacek J. Walkowiak, Rohit Nikam, Matthias Ballauff
Summary: The effective charge of highly charged polyelectrolytes is significantly lowered by a condensation of counterions. This effect is more pronounced for divalent ions. Our study on dendritic polyglycerol sulfate (dPGS) demonstrates that the interactions between dPGS and divalent ions (Mg2+ and Ca2+) show no ion specificity but clear competition between monovalent and divalent ions. These findings support the latest theoretical studies and indicate the sequential replacement of monovalent ions with divalent ions.
Review
Biochemistry & Molecular Biology
Daniel Wittmann, Neha Sinha, Bernhard Grimm
Summary: Plastids, particularly chloroplasts, are specialized organelles in plants that play a crucial role in photosynthesis. A redox-based regulatory network involving thioredoxins and TRX-like proteins is important for coordinating the metabolic activities of chloroplasts in response to environmental changes.
BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jose L. Neira, Bruno Rizzuti, Salome Araujo-Abad, Olga Abian, Maria Esther Farez-Vidal, Adrian Velazquez-Campoy, Camino de Juan Romero
Summary: This study describes the interaction between PKP1 and PADI4 and provides insights into their binding mode and binding hot-spot. This is of importance for understanding tumor development and the formation of neutrophil extracellular traps.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Chemistry, Medicinal
Francisca Pinheiro, Irantzu Pallares, Francesca Peccati, Adria Sanchez-Morales, Nathalia Varejao, Filipa Bezerra, David Ortega-Alarcon, Danilo Gonzalez, Marcelo Osorio, Susanna Navarro, Adrian Velazquez-Campoy, Maria Rosario Almeida, David Reverter, Felix Busque, Ramon Alibes, Mariona Sodupe, Salvador Ventura
Summary: This study discovered a series of novel halogenated kinetic stabilizers for transthyretin (TTR) through rational design and molecular dynamics (MD) simulations. Among them, M-23 displayed high affinity for TTR and demonstrated enhanced tetramer stability. The crystal structure confirmed the unprecedented protein-ligand contacts predicted by MD simulations.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
David Ortega-Alarcon, Rafael Claveria-Gimeno, Sonia Vega, Olga C. Jorge-Torres, Manel Esteller, Olga Abian, Adrian Velazquez-Campoy
Summary: Hydroxymethylated cytosine (5hmC) is a stable DNA epigenetic mark that interacts with MeCP2 in a distinct mode with a specific thermodynamic signature. Mutations associated with Rett syndrome alter the interaction between MeCP2 and dsDNA in a cytosine modification-specific manner, which may be correlated with disease onset time and clinical severity score.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Antonia M. Gallardo-Martinez, Julia Jimenez-Lopez, Maria Luisa Hernandez, Juan Manuel Perez-Ruiz, Francisco Javier Cejudo
Summary: The absence of 2-Cys Prxs leads to inhibition of seed development in Arabidopsis, highlighting the significance of plastid redox systems in embryogenesis.
Article
Multidisciplinary Sciences
Jorge Lozano-Juste, Lourdes Infantes, Irene Garcia-Maquilon, Rafael Ruiz-Partida, Ebe Merilo, Juan Luis Benavente, Adrian Velazquez-Campoy, Alberto Coego, Mar Bono, Javier Forment, Begona Pampin, Paolo Destito, Adrian Monteiro, Ramon Rodriguez, Jacobo Cruces, Pedro L. Rodriguez, Armando Albert
Summary: Through structure-based targeted design, a chemical-genetic orthogonal approach was used to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL1(5m), which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and significant improvement in drought tolerance.
Article
Oncology
Sonia Hermoso-Duran, Maria Jose Domper-Arnal, Pilar Roncales, Sonia Vega, Oscar Sanchez-Gracia, Jorge L. L. Ojeda, Angel Lanas, Adrian Velazquez-Campoy, Olga Abian
Summary: The aim of this study was to investigate the interference of colonoscopy bowel preparation on the results of thermal liquid biopsy (TLB). The results showed that bowel preparation altered serum protein levels, affected TLB parameters, and may compromise the diagnostic capability of other liquid-biopsy-based methods. Therefore, blood extraction after bowel preparation for colonoscopy should be avoided.
Article
Biochemistry & Molecular Biology
Victor Delgado-Requerey, Francisco Javier Cejudo, Maria-Cruz Gonzalez
Summary: The NTRC-2-Cys-Prx system plays a central role in the coordinated regulation of chloroplast biosynthetic pathways and NADPH extrusion via malate valve. The functional relationship between NTRC, 2-Cys Prxs, and m-type Trxs is established. The impairment of NTRC-2-Cys-Prx system leads to severe phenotypic defects in Arabidopsis, which can be suppressed by decreasing the content of 2-Cys Prx.
Article
Chemistry, Medicinal
Maria Nuria Peralta-Moreno, Vanessa Anton-Munoz, David Ortega-Alarcon, Ana Jimenez-Alesanco, Sonia Vega, Olga Abian, Adrian Velazquez-Campoy, Timothy M. Thomson, Jose Manuel Granadino-Roldan, Claudia Machicado, Jaime Rubio-Martinez
Summary: Since the outbreak of the COVID-19 pandemic, there have been over 750 million reported cases of COVID-19 caused by SARS-CoV-2. In order to find effective treatments, intensive research has been conducted on therapeutic agents derived from pharmaceutical repositioning or natural products. This study focuses on identifying inhibitors for the SARS-CoV-2 M-pro main protease dimer using virtual screening of natural compounds derived from Peruvian flora. The compound Hyperoside displayed inhibitory activity against M-pro in vitro, with a K-i value lower than 20 μM, possibly through allosteric modulation.
Article
Biochemistry & Molecular Biology
Salome Araujo-Abad, Bruno Rizzuti, Adrian Villamarin-Ortiz, David Pantoja-Uceda, Celia M. Moreno-Gonzalez, Olga Abian, Adrian Velazquez-Campoy, Jose L. Neira, Camino de Juan Romero
Summary: PADI4 and MDM2 were found to interact in the nucleus and cytosol of various cancer cell lines, and this binding was inhibited by GSK484. Further experiments revealed that the N-terminal region of MDM2 interacted with PADI4, and certain amino acid residues were affected by the enzyme. This finding suggests potential therapeutic value in utilizing MDM2 citrullination to improve cancer treatment.
Article
Multidisciplinary Sciences
Margarida Bastos, Olga Abian, Christopher M. Johnson, Frederico Ferreira-da-Silva, Sonia Vega, Ana Jimenez-Alesanco, David Ortega-Alarcon, Adrian Velazquez-Campoy
Summary: Isothermal titration calorimetry (ITC) has become the gold standard for studying molecular interactions in solution. It is widely used for characterizing molecular interactions between ligands and macromolecules. This Primer provides an overview of ITC's foundations, instrumentation, common applications, extensions and modifications, advantages and caveats, as well as recent and future developments.
NATURE REVIEWS METHODS PRIMERS
(2023)
Article
Biochemistry & Molecular Biology
Bruno Rizzuti, Olga Abian, Adrian Velazquez-Campoy, Jose L. Neira
Summary: This study investigates the stability and conformational features of the N-terminal region of MDM2, revealing the low stability and unfolding intermediates of this region. The low stability of this protein may be related to its inherent flexibility and ability to interact with multiple molecular partners.
Article
Multidisciplinary Sciences
Nerea Novo, Silvia Romero-Tamayo, Carlos Marcuello, Sergio Boneta, Irene Blasco-Machin, Adrian Velazquez-Campoy, Raquel Villanueva, Raquel Moreno-Loshuertos, Anabel Lostao, Milagros Medina, Patricia Ferreira
Summary: AIF is a moonlighting flavoenzyme that is involved in the assembly of mitochondrial respiratory complexes in healthy cells but can also trigger DNA cleavage and cell death. This study demonstrates the molecular assembly of a DNA-degradosome complex involving AIF, CypA, and histone H2AX, and the cooperative effects of these components in degrading genomic DNA. Additionally, the study reveals that AIF possesses nuclease activity that is stimulated by the presence of Mg2+ or Ca2+, which allows it to efficiently degrade genomic DNA alone or in cooperation with CypA. It is also found that the TopIB and DEK motifs in AIF are responsible for its nuclease activity. These findings enhance our understanding of AIF's role in promoting apoptosis and provide potential avenues for the development of new therapeutic strategies.
Article
Biochemistry & Molecular Biology
Cristina Sarasa-Buisan, Etienne Emonot, Marta Martinez-Julvez, Emma Sevilla, Adrian Velazquez-Campoy, Serge Crouzy, M. Teresa Bes, Isabelle Michaud-Soret, Maria F. Fillat
Summary: Metal and redox homeostasis in cyanobacteria is tightly controlled by the FUR proteins. This study focuses on the characterization of the FurC protein in Anabaena sp. PCC7120 and reveals its involvement in metal and redox regulation. The study provides insights into the mechanisms of FurC and the reversible inactivation of the protein through disulfide bonds and metal catalyzed oxidation.
Article
Biochemistry & Molecular Biology
Miguel A. Casado-Combreras, Francisco Rivero-Rodriguez, Carlos A. Elena-Real, Dmitry Molodenskiy, Antonio Diaz-Quintana, Marlene Martinho, Guillaume Gerbaud, Katiuska Gonzalez-Arzola, Adrian Velazquez-Campoy, Dmitri Svergun, Valerie Belle, Miguel A. De la Rosa, Irene Diaz-Moreno
Summary: Intrinsic protein flexibility is crucial for the adaptability and recognition of complexes. This study reveals that the flexible region of the protein SET/TAF-I beta can activate PP2A by interacting with cytochrome c in a dynamic manner.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
