Article
Biochemistry & Molecular Biology
Natalie Jay, Janie E. McGlohon, Fernando Estrada
Summary: This study investigated the interactions between human Adx and CYP enzymes as well as AdR using protein NMR spectroscopy. The results suggested that monomeric Adx forms a functional complex with CYP enzymes in a 1:1 ratio, while Adx dimers may regulate access to monomeric Adx. These findings are important for revising the model of the Adx electron shuttle mechanism.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Theresa S. Braun, Juliane Stehle, Sylwia Kacprzak, Patrick Carl, Peter Hoefer, Vinod Subramaniam, Malte Drescher
Summary: Protein-membrane interactions are crucial for cellular processes, and the study of these interactions presents a challenge in modern biophysical chemistry. By employing rapid-scan electron paramagnetic resonance spectroscopy, the interaction between αS and negatively charged vesicles in vitro was studied, with reflections observed in cells as well.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Yutaro Chikuma, Masayuki Miyata, Young-Ho Lee, Toshiharu Hase, Yoko Kimata-Ariga
Summary: This study investigated the molecular mechanism of negative cooperativity between FNR and Fd in plants, caused by the allosteric binding of NADP(H) on FNR. It identified a salt bridge between Asp60 of Fd and Lys33 of FNR as crucial for this negative cooperativity. Site-specific mutants of FdD60 and FNRK33 confirmed the involvement of this salt bridge in downregulating the interaction between FNR and Fd by NADPH.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Morgane Adelaide, Evgeniy Salnikov, Francisco Ramos-Martin, Christopher Aisenbrey, Catherine Sarazin, Burkhard Bechinger, Nicola D'Amelio
Summary: SAAP-148 is an antimicrobial peptide derived from LL-37 with excellent activity against drug-resistant bacteria and biofilms. Its mechanism of action at the molecular level has not been explored despite its optimal pharmacological properties.
Article
Biology
Jiemin Shen, Gang Wu, Ah-Lim Tsai, Ming Zhou
Summary: This study demonstrates the formation of stable binary and ternary complexes between mammalian cytochrome b(5), cytochrome b(5) reductase, and stearoyl-CoA desaturase-1, which enhance electron transfer rates.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biophysics
Stanislav D. Zakharov, Sergei Savikhin, Yuko Misumi, Genji Kurisu, William A. Cramer
Summary: This study confirms the absence of a significant interaction between FNR and the b(6)f complex through thermodynamic analysis. It also provides a precedent for considering protein-detergent interactions in ITC analyses.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Xun-Cheng Su, Bo Ma, Jia-Liang Chen, Chao-Yu Cui, Feng Yang, Yan-Jun Gong
Summary: This study demonstrates two rigid, reactive, and stable paramagnetic tags for protein modification, which exhibit high reactivity and rigidity for high-resolution NMR measurements of biological macromolecules and their complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Mindaugas Lesanavicius, Daisuke Seo, Narimantas Cenas
Summary: RpFNR is a novel thioredoxin reductase-type FNR with partly characterized redox properties. It can be oxidized by various nonphysiological electron acceptors, and the reactivity is influenced by the single-electron reduction midpoint potential of the compounds.
Article
Biochemistry & Molecular Biology
Jinjing Jia, Guangtao Xu, Dongsheng Zhu, Hongjun Liu, Xiansi Zeng, Li Li
Summary: This review highlights the significance of the thioredoxin system in CNS diseases and suggests that it may be a promising therapeutic target. The article also proposes future directions for research in developing effective inducers of Trx and specific inhibitors of TXNIP for the treatment of CNS diseases.
ANTIOXIDANTS & REDOX SIGNALING
(2023)
Article
Chemistry, Multidisciplinary
Jan H. Overbeck, Jennifer Vogele, Felix Nussbaumer, Elke Duchardt-Ferner, Christoph Kreutz, Jens Wohnert, Remco Sprangers
Summary: The synthetic neomycin-sensing riboswitch interacts with neomycin, ribostamycin, and paromomycin. However, only neomycin can efficiently repress translation initiation due to differences in ligand:riboswitch dynamics. Five complementary fluorine-based NMR methods were used to accurately quantify dynamics in the riboswitch complexes and identified four structurally different states. These findings highlight the potential of F-19 NMR methods in characterizing complex exchange processes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Chuanlong Cui, Ping Shu, Tanaz Sadeghian, Waqas Younis, Hong Li, Annie Beuve
Summary: Soluble guanylyl cyclase (GC1) and oxido-reductase thioredoxin (Trx1) form a complex that mediates two NO signaling pathways. Under physiological conditions, reduced Trx1 supports the canonical NO-GC1-cGMP pathway, while under oxidative stress, the NO-cGMP pathway is disrupted. An inhibitory peptide was designed to block the interaction between GC1 and Trx1, which resulted in the loss of their enhancing effects and identified GC1's novel reductase activity. Moreover, the peptide blocked the transfer of S-nitrosothiols, leading to increased caspase-3 activity and providing a promising therapy for some cancers.
Article
Biochemistry & Molecular Biology
Fernando Toshio Ogata, Alex Yuri Simoes Sato, Lucia Coppo, Roberto Jun Arai, Arnold Ira Stern, Hugo Pequeno Monteiro
Summary: The epithelial/mesenchymal transition (EMT) is associated with tumor metastasis. Cancer cells have high levels of antioxidants, such as the Trx/TrxR and GSH/Grx systems, to counteract oxidative and nitrosative stress. These systems play a significant role in EMT signaling and cancer cell progression.
ANTIOXIDANTS & REDOX SIGNALING
(2022)
Article
Chemistry, Physical
Jia-Liang Chen, Xiao Wang, Feng Yang, Bin Li, Gottfried Otting, Xun-Cheng Su
Summary: We report the solution structure of an authentic sortaseA thioester intermediate with the bound substrate. Through advanced techniques, we determined the 3D structure of this short-lived enzymatic reaction intermediate at atomic resolution. The formation and stability of the intermediate are influenced by calcium binding and its interaction with the substrate, highlighting the importance of calcium in the function of sortase A.
Article
Chemistry, Applied
Yuning Liu, Xiaohui Feng, Qingshi Meng, Jiawei Zhu, Xueting Jia, Qingyu Zhao, Chaohua Tang, Yanan Yu, Junmin Zhang
Summary: Nap-DNB, an off-on fluorescent probe based on naphthimide, was developed for the detection of biological selenols in vitro. It can rapidly and sensitively respond to selenocysteine, with a detection limit of 92 nM. By adopting a low-pH detection environment and robust reaction sites, Nap-DNB successfully detected selenols in selenium-enriched Tan sheep's serum, liver, and longissimus dorsi.
Review
Plant Sciences
Serena Schwenkert, Alisdair R. Fernie, Peter Geigenberger, Dario Leister, Torsten Moehlmann, Belen Naranjo, H. Ekkehard Neuhaus
Summary: Changes in chloroplast metabolism play a critical role in the comprehensive cellular response to challenging environments, starting with rapid modifications of processes in the thylakoid membrane, followed by changes in the stroma and transport activities across the chloroplast envelope. Understanding the characteristics of the 'modulators' involved is essential for enhancing plant stress tolerance and developing targeted breeding strategies.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Antonella Di Savino, Johannes M. Foerster, G. Matthias Ullmann, Marcellus Ubbink
Summary: Formation of protein complexes heavily relies on electrostatic interactions, which guide recognition and binding through optimized charge distributions on the surface of redox proteins. Investigating the interactions between cytochrome c peroxidase (CcP) and cytochrome c (Cc), it was found that additional charge patches can either enhance or disrupt productive complex formation depending on the presence of negative residues in the regular binding site.
Article
Biochemistry & Molecular Biology
Kim Marneth, Hans van den Elst, Anneloes Cramer-Blok, Jeroen Codee, Hermen S. Overkleeft, Johannes M. F. G. Aerts, Marcellus Ubbink, Fredj Ben Bdira
Summary: GHs are attractive tools for multiple biotechnological applications due to their ability to perform transglycosylation under specific conditions. The flexibility of the binding site architecture distinguishes them from glycosyltransferases (GTs), making them promising for improving transglycosylation efficiency.
Article
Chemistry, Physical
Rubin Dasgupta, Karthick B. S. S. Gupta, Huub J. M. de Groot, Marcellus Ubbink
Summary: The enzyme laccase catalyzes the reduction of dioxygen to water at the trinuclear copper center, comprising a type-3 and a type-2 copper site. The paramagnetic NMR spectrum of the small laccase from Streptomyces coelicolor shows a mixture of two catalytic states, with the resting oxidized state exhibiting hydrogen resonances only of the T3 copper ligands. A double mutant variant lacking the copper ion at the T1 site is exclusively in the resting oxidized state, revealing a subtle balance between the resting oxidized and native intermediate states.
Article
Chemistry, Physical
Rubin Dasgupta, Karthick B. S. S. Gupta, Derek Elam, Marcellus Ubbink, Huub J. M. de Groot
Summary: This study demonstrates the efficacy of REDOR-type sequences in determining dipolar coupling strength in a paramagnetic environment, providing reliable structural and dynamical information. The scaling factor of the dipolar coupling strength is influenced by rotational motion of the surrounding methyl group, with limited variation at different temperatures.
SOLID STATE NUCLEAR MAGNETIC RESONANCE
(2021)
Editorial Material
Biochemistry & Molecular Biology
Sung-Kun Kim, Ki Duk Park, Dong-Woo Lee
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Soumya Deep Chatterjee, Juan Zhou, Rubin Dasgupta, Anneloes Cramer-Blok, Monika Timmer, Mario van der Stelt, Marcellus Ubbink
Summary: PLAAT3 and PLAAT4 are enzymes involved in the synthesis of bioactive lipids, with structural similarities but differences in activity and specificity. Research shows that PLAAT3 has less protein dynamics and lower activity in specific loops, and swapping these loops can increase PLAAT3 activity. Despite structural similarity, substantially different protein dynamics between PLAAT variants can help explain their activity and specificity differences.
Correction
Chemistry, Multidisciplinary
Qing Miao, Enrico Zurlo, Donny de Bruin, Joeri A. J. Wondergem, Simon P. Skinner, Monika Timmer, Anneloes Blok, Doris Heinrich, Mark Overhand, Martina Huber, Marcellus Ubbink
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Antonella Di Savino, Johannes M. Foerster, G. Matthias Ullmann, Marcellus Ubbink
Summary: Optimal charge distribution is important for efficient formation of protein complexes, as electrostatic interactions guide encounter complex formation. However, introducing extra charged patches on a protein surface does not necessarily reduce productive encounters. A complex with a high population of encounter complex may be more affected by suboptimal charge distribution, as demonstrated in interactions between cytochrome c mutants and wild-type or variant cytochrome c peroxidases.
Article
Biochemistry & Molecular Biology
Fredj Ben Bdira, Amanda M. Erkelens, Liang Qin, Alexander N. Volkov, Andrew M. Lippa, Nicholas Bowring, Aimee L. Boyle, Marcellus Ubbink, Simon L. Dove, Remus T. Dame
Summary: H-NS family proteins play important roles in genome organization and regulation of foreign genes, with gene repression directly dependent on their DNA binding modes. The protein gp4 encoded by Pseudomonas lytic phage LUZ24 can specifically interfere with the formation and stability of the bridged MvaT-DNA complex, relieving gene silencing and adversely affecting P. aeruginosa growth. Controlling H-NS conformation may provide new ways to combat Pseudomonas multidrug resistance.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Chemistry, Multidisciplinary
Qing Miao, Christoph Nitsche, Henry Orton, Mark Overhand, Gottfried Otting, Marcellus Ubbink
Summary: Paramagnetic chemical probes have been widely used in EPR and NMR spectroscopy, especially in the study of biological macromolecules. Recent developments include an increase in the variety of paramagnetic probes, the development of lanthanoid probes for protein studies, and the development of isotropic paramagnetic probes for NMR and EPR measurements.
Article
Biochemistry & Molecular Biology
Aleksandra Chikunova, Marcellus Ubbink
Summary: Evolution minimizes the number of highly conserved amino acid residues in proteins to ensure evolutionary robustness and adaptability. This study analyzes the roles of all highly conserved, non-catalytic residues in class A beta-lactamase and reveals their importance in fine-tuning the active site structure, maintaining protein folding and stability.
Article
Biochemistry & Molecular Biology
Andrew E. Huckleby, Jhawn G. Saul, Hyunshun Shin, Staci Desmarais, Apparao Bokka, Junha Jeon, Sung-Kun Kim
Summary: This study demonstrated the inhibitory effect of two compounds with two hydroxamate functional groups on MBL from Bacillus anthracis. The inhibition was found to be competitive and the compounds showed potential as inhibitors to overcome bacterial resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ilona van Alen, Aleksandra Chikunova, Danny B. van Zanten, Amber A. de Block, Monika Timmer, Steffen Brunle, Marcellus Ubbink
Summary: Conserved residues are usually essential for protein function, but mutations in highly conserved residues of BlaC did not significantly affect the enzyme. One mutation, D179N, even increased ceftazidime resistance while maintaining good activity against penicillins. Crystal structures of BlaC D179N revealed minor structural changes compared to wild-type BlaC, and introducing this mutation in other beta-lactamases resulted in decreased antibiotic resistance. The importance of the interaction with Arg164 explains why Asp179 is not essential in BlaC.
Article
Chemistry, Inorganic & Nuclear
Qing Miao, Rene Dekkers, Karthick Babu Sai Sankar Gupta, Mark Overhand, Rubin Dasgupta, Marcellus Ubbink
Summary: A hydrophilic rigid macrocyclic ligand was designed and synthesized for investigating the conformational dynamics of its complex with europium using NMR spectroscopy. The results showed that the complex exists in two conformers, with the twisted square antiprismatic one being favored. This ligand is suitable for developing rigid probes for paramagnetic NMR of proteins and is less likely to cause protein precipitation due to its hydrophilic nature.
INORGANIC CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Qing Miao, Christoph Nitsche, Henry Orton, Mark Overhand, Gottfried Otting, Marcellus Ubbink
Summary: This review provides a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications in the study of biological macromolecules. Recent developments have seen a rapid expansion of lanthanoid probes with anisotropic magnetic susceptibilities and isotropic paramagnetic probes for protein studies and investigations of biological macromolecules.