Article
Chemistry, Inorganic & Nuclear
Rajeh Alotaibi, Amy Booth, Edmund Little, Adam Brookfield, Amritroop Achari, Selena J. Lockyer, Grigore A. Timco, George F. S. Whitehead, Inigo J. Vitorica-Yrezabal, Nicholas F. Chilton, Rahul R. Nair, David Collison, Richard E. P. Winpenny
Summary: We synthesized and characterized a series of heterometallic rings using alkylammonium or imidazolium cations as templates. The structure of these rings can be controlled by the template and the coordination geometry preference of each metal, resulting in rings with eight, nine, ten, twelve, and fourteen metals. The compounds were analyzed using various techniques, including X-ray diffraction, elemental analysis, magnetometry, and EPR measurements. The magnetic measurements showed antiferromagnetic exchange coupling between the metal centers, while the EPR spectroscopy revealed different ground and excited states for different ring structures. These findings provide insights into the transferability of magnetic parameters among related compounds.
DALTON TRANSACTIONS
(2023)
Article
Multidisciplinary Sciences
GeunYoung Sim, Audrey C. Kehling, Mi Seul Park, Jackson Secor, Cameron Divoky, Huaqun Zhang, Nipun Malhotra, Divyaa Bhagdikar, Ekram W. Abd El-Wahab, Kotaro Nakanishi
Summary: MicroRNAs (miRNAs), a type of noncoding RNA with about 22 nucleotides, can form complexes with Argonaute (AGO) proteins to repress gene expression. This study discovered that certain exonucleases, including ISG20, TREX1, and ERI1, are capable of trimming AGO-associated full-length miRNAs to shorter tyRNAs in a manganese-dependent manner. The study also showed that ISG20-mediated trimming converts AGO3 into a slicer. These findings shed light on the roles of manganese-dependent exonucleases in gene silencing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Mengting Niu, Quan Zou, Chen Lin
Summary: In this study, a novel calculation model CRBPDL is proposed to accurately identify the binding sites of circular RNA-RBP. By integrating deep learning model, the prediction performance and reliability of the model are improved. Experimental results on multiple datasets demonstrate the universality, reliability, and robustness of CRBPDL.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cell Biology
Qi Xiao, Ruihua Yin, Yuan Wang, Shaonan Yang, Aijun Ma, Xudong Pan, Xiaoyan Zhu
Summary: Exosomal circRNAs in large artery atherosclerotic (LAA) stroke were comprehensively analyzed using RNA sequencing and qRT-PCR techniques. The study identified differentially expressed circRNAs and confirmed their potential roles in LAA progression. Two circRNAs were suggested as novel biomarkers, and combining multiple circRNAs improved diagnostic accuracy.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Physical
Milan Kumar Jena, Diptendu Roy, Biswarup Pathak
Summary: Solid-state nanopore-based electrical detection of DNA nucleotides using quantum tunneling technique shows promise as the next-generation sequencing technology. However, the complexity of experiments has hindered the achievement of accurate and scalable high-throughput analysis. In this study, we have developed a machine-learning-assisted method to predict the transmission function of nucleotides, achieving low root-mean-square error scores and providing interpretable explanations for the relationship between nucleotide properties and transmission functions. Experimental integration of this method could lead to cheap, accurate, and ultrafast DNA sequencing.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Review
Cell Biology
Andrea Putnam, Laura Thomas, Geraldine Seydoux
Summary: This review discusses the current understanding of RNA granules, which are intracellular phase-separated sites of RNA metabolism containing factors for RNA biogenesis and turnover. The authors introduce the concept of incidental condensates, which are tolerated by cells but do not provide additional functionality beyond that of soluble RNP complexes. The article also explores best practices for distinguishing functional RNA granules from incidental condensates.
GENES & DEVELOPMENT
(2023)
Article
Biochemical Research Methods
Corinna J. Ulshoefer, Christina Pfafenrot, Albrecht Bindereif, Tim Schneider
Summary: CircRNAs have been extensively studied in recent years, revealing functional roles in various cell types and organisms. However, the specific interaction partners for most circRNAs remain unknown due to technical difficulties, presenting challenges in systematically studying circRNA-protein complexes.
Article
Chemistry, Multidisciplinary
Marcus J. Giansiracusa, Michele Vonci, Yasmin L. Whyatt, Carys Williams, Kevin Mason, David Parker, Eric J. L. McInnes, Nicholas F. Chilton
Summary: EPR spectroscopy is used to show that a t-butyl-pyridyl-functionalised Er-III DOTA derivative coordinates water, while its methylphosphinate analogue does not.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Marco Marcia, Jacopo Manigrasso, Marco De Vivo
Summary: This viewpoint discusses the importance of computational analyses and simulations in gaining mechanistic insights into complex biological systems. Two newly resolved cryoEM structures have confirmed previous predictions of key catalytic ions, highlighting the synergy of computational and experimental methods in exploring large multicomponent biosystems.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biology
Haibo Xu, Xiaowen Hu, Xiaoguang Yan, Wei Zhong, Dongsheng Yin, Yunfeng Gai
Summary: This study presents TCGCN, a linear residual graph convolution network, for predicting ncRNA-thyroid cancer associations. By collecting a large amount of ncRNA-disease association data and constructing a bipartite graph, TCGCN combines linear embedding propagation and graph convolutional layers to achieve significantly better performance in prediction.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Quentin Duez, Paul Tinnemans, Johannes A. A. W. Elemans, Jana Roithova
Summary: We present a new approach to determine ligand exchange parameters based on electrospray ionization mass spectrometry (ESI-MS). This method allows for the quantitative investigation of the solution-phase equilibria by introducing isotopically labelled ligands to a solution of metal host and unlabelled ligands. Our ESI-MS approach provides rate constants and activation parameters for ligand dissociation in the solution, providing mechanistic insights that are not easily obtained from traditional solution-phase techniques.
Article
Chemistry, Inorganic & Nuclear
Md. Ashraful Islam, Matthieu Autillo, Clovis Poulin-Ponnelle, Christelle Tamain, Helene Bolvin, Claude Berthon
Summary: We investigated An(V) and An(VI) complexes with a neutral and slightly flexible TEDGA ligand using NMR spectroscopy, CAS-based method calculations, and X-ray diffraction. By analyzing pNMR shifts considering the axial and rhombic anisotropy of the actinyl magnetic susceptibilities, we found that 5f(2) cations (Pu-VI and Np-V) are ideal for determining the structure of actinyl complexes in solution by H-1 NMR spectroscopy. In contrast, Np-VI complexes with a 5f(1) configuration showed different magnetic properties.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Tong Cao, Francisco Javier Valverde-Munoz, Xiaoyi Duan, Mingjian Zhang, Ping Wang, Lingbao Xing, Fenggang Sun, Zhen Zhou, Hui Liu, Jianzhuang Jiang, M. Carmen Munoz, Jose Antonio Real, Daopeng Zhang
Summary: The self-assembly of tetrahedral building blocks and iron(II) ions resulted in a series of heterobimetallic Hg-II-Fe-II coordination polymers with diverse structural and magnetic properties. The nature of the bridging organic ligands plays a crucial role in determining the structural features of the products.
INORGANIC CHEMISTRY
(2021)
Article
Virology
Igor Zaiets, Sumedha Gunewardena, Stephan Menne, Steven A. Weinman, Severin O. Gudima
Summary: This study characterized the presence of different types of HBV RNAs in the serum of chronically infected individuals. The majority of serum HBV RNAs were replication-derived and associated with HBV virions. The study also identified a potential target area on the HBV genome for the detection of serum HBV RNAs and highlighted the importance of simultaneous quantification of rd-RNAs and rcDNA for evaluating HBV replication status and the efficacy of anti-HBV therapy.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Laurence Decourty, Christophe Malabat, Emmanuel Frachon, Alain Jacquier, Cosmin Saveanu
Summary: In this study, genetic interactions related to RNA metabolism were analyzed using 154 genetic interaction mapping screens in Saccharomyces cerevisiae, revealing links between 1471 genes and 117 biological processes. The results provide a valuable resource for discovering gene function in yeast by validating enhancement and suppression of growth rates in specific RNA-related pathways.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Inorganic & Nuclear
Daniel Ossadnik, Sergei Kuzin, Mian Qi, Maxim Yulikov, Adelheid Godt
Summary: The narrow central line and weak zero-field splitting (ZFS) of [GdIII(NO3Pic)] make it an attractive starting point for the development of spin labels. A substituent of alkyl with a remote functional group at the picolinate moiety can retain the narrow line and weak ZFS even with broken axial symmetry. By chemoselective labeling reaction, a spin label targeting cysteines in peptides (NDSE-{GdIII(NO3Pic)}) has been successfully designed for distance determination in peptides.
INORGANIC CHEMISTRY
(2023)
Article
Nutrition & Dietetics
Pornpimol Scheuchzer, Victoria N. Syryamina, Michael Bruce Zimmermann, Christophe Zeder, Laura Nystroem, Maxim Yulikov, Diego Moretti
Summary: The addition of citric acid/trisodium citrate (CA/TSC) can enhance iron absorption from rice, but phytic acid (PA) inhibits this effect. Sodium pyrophosphate (NaPP) may also enhance iron absorption from rice. Therefore, this study is important for the methods of iron fortification in rice.
JOURNAL OF NUTRITION
(2023)
Article
Chemistry, Multidisciplinary
Dario Faust Akl, Georgios Giannakakis, Andrea Ruiz-Ferrando, Mikhail Agrachev, Juan D. Medrano-Garcia, Gonzalo Guillen-Gosalbez, Gunnar Jeschke, Adam H. Clark, Olga V. Safonova, Sharon Mitchell, Nuria Lopez, Javier Perez-Ramirez
Summary: Copper catalysts are promising for Hg-free VCM production, but the optimal architecture at the nanoscale is not well understood. This study modifies the metal precursor and annealing temperature to prepare copper nanoparticles or single atoms on an unmodified carbon support. The performance of all materials converges to the stable VCM productivity of the single-atom catalyst. Advanced characterization techniques uncover a reaction-induced formation of low-valent, single atom Cu(I)Cl site motif, regardless of the initial nanostructure. The study highlights the sustainability of Cu-based catalysts for VCM production.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Joerg Wolfram Anselm Fischer, Andreas Brenig, Daniel Klose, Jeroen Anton van Bokhoven, Vitaly L. Sushkevich, Gunnar Jeschke
Summary: This study determined the Cu speciation in Cu-MOR materials with different Cu loadings using operando electron paramagnetic resonance (EPR), operando ultraviolet-visible (UV/Vis) spectroscopy, as well as in situ photoluminescence (PL) and Fourier-transform infrared (FTIR) spectroscopy. A novel pathway for CH4 oxidation involving paired [CuOH](+) and bare Cu2+ species was identified. The reduction of bare Cu2+ ions facilitated by adjacent [CuOH](+) demonstrates that the commonly assumed redox-inert Cu2+ centers do not generally apply. Site-specific reaction kinetics showed that dimeric Cu species exhibit a faster reaction rate and a higher apparent activation energy than monomeric Cu2+ active sites, highlighting their difference in the CH4 oxidation potential.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Applied
Xiaowen Wu, Samy Boulos, Victoria Syryamina, Laura Nystrom, Maxim Yulikov
Summary: The interactions between dietary fibers (DFs) and small molecules are of great interest in the fields of food chemistry and nutrition science. This study presents a methodology combining stochastic spin-labelling of DFs with pulse electron paramagnetic resonance techniques to determine the interactions between DFs and small molecules. The proposed methodology allows for the observation of subtle conformational changes and variations in binding propensities of DFs and small molecules.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Physical
Thaylan Pinheiro Araujo, Jordi Morales-Vidal, Tangsheng Zou, Mikhail Agrachev, Simon Verstraeten, Patrik O. O. Willi, Robert N. N. Grass, Gunnar Jeschke, Sharon Mitchell, Nuria Lopez, Javier Perez-Ramirez
Summary: Mixed zinc-zirconium oxides, ZnZrOx, synthesized using flame spray pyrolysis (FSP) exhibit higher methanol productivity and enhanced performance compared to coprecipitated (CP) catalysts. In-depth characterization and theoretical simulations reveal that FSP maximizes surface area and atomically dispersed Zn2+ sites, leading to improved catalytic activity. The study also demonstrates the working mechanism of the flame-made catalyst and provides valuable insights for the development of cost-effective and earth-abundant catalysts for methanol synthesis.
ADVANCED ENERGY MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Kavan Gor, Olivier Duss
Summary: Ribosome assembly is a crucial process in gene expression, and studying its molecular mechanisms has led to the development of novel approaches for investigating the assembly of other RNA-protein complexes. This review discusses biochemical, structural, and biophysical methods that have been used to understand the complex process of bacterial ribosome assembly. It also explores emerging approaches for studying how transcription, RNA processing, cellular factors, and the cellular environment influence ribosome and RNA-protein complex assembly.
Editorial Material
Biochemistry & Molecular Biology
Nusrat S. Qureshi, Olivier Duss
Summary: This review provides a mechanistic overview of the co-transcriptional protein-RNA complex assembly, including processes such as co-transcriptional RNA folding, processing, modification, and assembly within biomolecular condensates. These tightly coupled processes cooperate to achieve efficient and spatial-temporally regulated assembly.
Article
Chemistry, Inorganic & Nuclear
Patrick Mueller, Patrick Finkelstein, Nils Trapp, Alessandro Bismuto, Gunnar Jeschke, Bill Morandi
Summary: This paper presents a broad applicability of a specific method for preparing monovalent nickel complexes, and demonstrates the diversity and versatility of these complexes.
INORGANIC CHEMISTRY
(2023)
Editorial Material
Genetics & Heredity
Olivier Duss, Rainer Nikolay, Matthew L. Kraushar
Summary: The ribosome is an ancient macromolecular complex responsible for decoding mRNA and synthesizing proteins. A recent study by Holm et al. reveals evolutionary distinctions in the structure and kinetics of mRNA decoding by the human ribosome.
TRENDS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Vera Giulimondi, Andrea Ruiz-Ferrando, Georgios Giannakakis, Ivan Surin, Mikhail Agrachev, Gunnar Jeschke, Frank Krumeich, Nuria Lopez, Adam H. Clark, Javier Perez-Ramirez
Summary: This study demonstrates the bifunctionality of carbon supports and metal sites in the acetylene hydrochlorination catalytic cycle, and proposes potential binding sites for acetylene and a viable reaction profile. The results highlight the importance of optimizing both metal and support components for catalyst design.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Devi Prasad Adiyeri Saseendran, Jorg W. A. Fischer, Lea Muller, Daniel F. Abbott, Victor Mougel, Gunnar Jeschke, Carlos A. Triana, Greta R. Patzke
Summary: This report presents the synthesis and spectroscopic evidence of a new defect-cubane type copper complex that acts as a pre-catalyst for water oxidation. In situ and post-catalytic studies reveal that the tetrameric complex undergoes structural transformations into dimeric and monomeric species induced by water molecules and carbonate anions, respectively. Moreover, the observed electrocatalytic water oxidation activity is confirmed to arise from in situ-generated Cu(ii) oxidic nanostructures at the electrode interface.
CHEMICAL COMMUNICATIONS
(2023)
Meeting Abstract
Biophysics
Nusrat Qureshi, Olivier Duss
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Andrea Eggeling, Janne Soetbeer, Luis Fabregas-Ibanez, Daniel Klose, Gunnar Jeschke
Summary: This study introduces the methyl quantum rotor (MQR) model to describe the tunneling ESEEM originating from multiple methyl rotors coupled to the same electron spin. By formulating the MQR model based on a rotation barrier distribution P(V-3), the different local environments in a glassy matrix can be accounted for. The rotation barrier distribution of the methyl groups is determined from experimental data and shows good agreement with density functional theory (DFT) calculations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Biology
Simone Hoefler, Olivier Duss
Summary: Protein-RNA complexes play important roles in cellular functions, and the folding and modifications of RNA can greatly impact their formation and interactions. This review focuses on the mechanisms of m6A modification and its effects on RNA folding and protein-RNA interactions.
LIFE SCIENCE ALLIANCE
(2023)