Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Crystallography
Jason C. Grigg, Ian R. Price, Ailong Ke
Summary: This study demonstrates that tRNA fusion can simplify the crystallization and structure determination of RNA molecules. The approach was applied to the T-box riboswitch system, capturing the dynamic interaction between tRNA and the T-box antiterminator.
Article
Chemistry, Multidisciplinary
Tom Pan, Shikai Jin, Mitchell D. Miller, Anastasios Kyrillidis, George N. Phillips
Summary: This paper develops an initial pathway to a deep learning neural network approach for solving the phase problem in protein crystallography. It uses a synthetic dataset of small fragments derived from a well curated subset of solved structures in the Protein Data Bank (PDB), and produces electron density estimates of simple artificial systems directly from corresponding Patterson maps using a convolutional neural network architecture as a proof of concept.
Review
Biochemistry & Molecular Biology
Ryland W. Jackson, Claire M. Smathers, Aaron R. Robart
Summary: Only a small fraction of the X-ray crystal structures in the Protein Data Bank are RNA or RNA-protein complexes, mainly due to obstacles such as low yields of pure, properly folded RNA, difficulty creating crystal contacts due to low sequence diversity, and limited methods for phasing. To overcome these obstacles, various approaches including native RNA purification, engineered crystallization modules, and incorporation of proteins have been developed. This review discusses these strategies and provides examples of their practical applications.
Review
Chemistry, Inorganic & Nuclear
Roberta Cargnelutti, Ricardo F. Schumacher, Andrei L. Belladona, Jean C. Kazmierczak
Summary: This review provides an overview of pyridyl-selenium compounds and their metal complexes in the fields of pharmacology, material science, and technology, covering coordination chemistry, synthetic methodologies, and structural characterization. Relevant direct applications in nanomaterial preparation, organic synthesis catalysis, photocatalytic hydrogen production, and oxygen activation are also discussed.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Agnieszka Ruszkowska, Ya Ying Zheng, Song Mao, Milosz Ruszkowski, Jia Sheng
Summary: The G·U wobble base pair is frequently found in RNA structures and has unique chemical, thermodynamic, and structural properties that are widely used in RNA biology. It plays important roles in folding, ribozyme catalysis, and protein interactions. The metal binding affinity of G·U pairs in tandem motifs differs due to variations in electrostatic potentials, which is essential for RNA folding, catalysis, and other interactions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Stavros Azinas, Marta Carroni
Summary: Cryo-EM is a major tool for determining protein structures, while AlphaFold2 enables high-confidence atomic models for polypeptide chains. Cryo-EM retains unique characteristics for determining structures of macromolecular complexes, allowing for near-atomic structures and exploring conformational panoramas. It also has the potential to develop a structural proteomic approach using ex vivo specimens.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Rachel A. Jones, Anna-Lena Steckelberg, Quentin Vicens, Matthew J. Szucs, Benjamin M. Akiyama, Jeffrey S. Kieft
Summary: During flavivirus infection, cells generate sfRNAs that interfere with antiviral pathways, with conserved nucleotides supporting a unique fold through specific tertiary interactions. By studying xrRNA from Tamana bat virus (TABV), researchers discovered that different sequences and interactions can achieve the same overall architecture, providing insight into the diversity of this type of RNA and informing searches for undiscovered xrRNAs in viruses and beyond.
Article
Multidisciplinary Sciences
Jie Deng, Xianyang Fang, Lin Huang, Shanshan Li, Lilei Xu, Keqiong Ye, Jinsong Zhang, Kaiming Zhang, Qiangfeng Cliff Zhang
Summary: RNA molecules have diverse functions that are closely related to their structures. Various techniques such as structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering have been used to analyze the structures of RNA. Recent advances in these techniques have led to the determination of important RNA structures.
FUNDAMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Shruti Chatterjee, Shankar V. Kundapura, Aditya J. Basak, Debangshu Mukherjee, Sagarika Dash, Namrata Ganguli, Amit K. Das, Gayatri Mukherjee, Dibyendu Samanta, Udupi A. Ramagopal
Summary: Tuberculosis is a disease caused by Mycobacterium tuberculosis, primarily transmitted through inhaling droplets from infected individuals. Mycobacteria use pathogen-associated molecular patterns (PAMPs) on their surface to enter alveolar macrophages by recognizing pattern recognition receptors on host cells. One important PAMP is the 19 kDa surface antigen LpqH, which plays a critical role in host-pathogen interactions and immune regulation. This study presents the crystal structure of non-acylated LpqH and demonstrates its functionality in inducing apoptosis in human monocytic cell line THP-1. Conservation analysis reveals a patch of conserved residues on the protein surface, potentially involved in binding partner recognition during host-pathogen interaction.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Chemistry, Multidisciplinary
Ha L. Nguyen
Summary: Reticular chemistry of covalent organic frameworks (COFs) focuses on linking discrete organic building units into extended structures through strong covalent bonds. Over the past decade, there has been rapid development in COF chemistry in terms of structural diversity and applications. Understanding the concept of reticular chemistry is essential for researching COFs and correlating their geometric structures and practical applications.
Review
Crystallography
Narsimha Pujari, Stephanie L. Saundh, Francis A. Acquah, Blaine H. M. Mooers, Adrian R. Ferre-D'Amare, Adelaine Kwun-Wai Leung
Summary: X-ray crystallography is a powerful method for studying the functional aspects of RNA molecules, but success is limited due to resource and time constraints. Various techniques, such as construct engineering and the use of chaperones and crystallization-friendly molecules, have been developed to aid in the formation of well-ordered RNA crystals and improve success rates in RNA crystallization.
Article
Chemistry, Multidisciplinary
Constantin Giurgiu, Ziyuan Fang, Harry R. M. Aitken, Seohyun Chris Kim, Lydia Pazienza, Shriyaa Mittal, Jack W. Szostak
Summary: The research on the mechanism of RNA copying chemistry has revealed that deprotonation of the primer 3'-hydroxyl occurs before the rate-limiting step in RNA synthesis. Additionally, analogs with E-3 ribose conformation show the fastest formation of 3'-5' phosphodiester bonds, with the reaction rate strongly correlated with the electronegativity of the 2'-substituent.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Martins Balodis, Manuel Cordova, Albert Hofstetter, Graeme M. Day, Lyndon Emsley
Summary: The determination of the three-dimensional atomic-level structure of powdered solids is an important goal in current chemistry. This study successfully determined the crystal structures of ampicillin, piroxicam, cocaine, and two polymorphs of the drug molecule AZD8329 using machine-learned isotropic chemical shifts generated on-the-fly to guide a Monte Carlo-based structure determination process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Yonatan G. Mideksa, Maximilian Fottner, Sebastian Braus, Caroline A. M. Weiss, Tuan-Anh Nguyen, Susanne Meier, Kathrin Lang, Matthias J. Feige
Article
Multidisciplinary Sciences
Alexandra Rehn, Jannis Lawatscheck, Marie-Lena Jokisch, Sophie L. Mader, Qi Luo, Franziska Tippel, Birgit Blank, Klaus Richter, Kathrin Lang, Ville R. I. Kaila, Johannes Buchner
NATURE COMMUNICATIONS
(2020)
Article
Optics
Marco Cinquino, Laura Polimeno, Giovanni Lerario, Milena De Giorgi, Anna Moliterni, Vincent Olieric, Antonio Fieramosca, Sonia Carallo, Rosanna Mastria, Vincenzo Ardizzone, Lorenzo Dominici, Dario Ballarini, Cinzia Giannini, Daniele Sanvitto, Aurora Rizzo, Luisa De Marco
JOURNAL OF LUMINESCENCE
(2020)
Article
Biochemistry & Molecular Biology
Aghil Soman, Chong Wai Liew, Hsiang Ling Teo, Nikolay Berezhnoy, Vincent Olieric, Nikolay Korolev, Daniela Rhodes, Lars Nordenskiold
NUCLEIC ACIDS RESEARCH
(2020)
Article
Instruments & Instrumentation
Isabelle Martiel, Dominik Buntschu, Nathalie Meier, Alexandre Gobbo, Ezequiel Panepucci, Roman Schneider, Peter Heimgartner, David Mueller, Kevin Buehlmann, Mario Birri, Jakub W. Kaminski, James Leuenberger, Vincent Olieric, Wayne Glettig, Meitian Wang
JOURNAL OF SYNCHROTRON RADIATION
(2020)
Article
Multidisciplinary Sciences
Jiqing Du, Marie-Kristin von Wrisberg, Burak Gulen, Matthias Stahl, Christian Pett, Christian Hedberg, Kathrin Lang, Sabine Schneider, Aymelt Itzen
Summary: Legionella pneumophila infects eukaryotic cells by modifying the activity of Rab1 protein through DrrA/SidM protein secretion. A chemical approach was used to study the interaction between Rab1 and DrrA, revealing a non-conventional Rab-binding site. This interaction allosterically activates DrrA, providing insights into Legionella infection mechanism.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Michael D. Bartoschek, Enes Ugur, Tuan-Anh Nguyen, Geraldine Rodschinka, Michael Wierer, Kathrin Lang, Sebastian Bultmann
Summary: The genetic code of mammalian cells can be expanded by incorporating non-canonical amino acids through the suppression of in-frame amber stop codons. A linear regression model called iPASS was developed to predict the efficiency of non-canonical amino acid incorporation based on the surrounding sequence context. Nucleotides up- and downstream of the stop codon were found to synergistically influence the incorporation efficiency, and iPASS can guide the optimization of insertion rates.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Shirley Tremel, Yohei Ohashi, Dustin R. Morado, Jessie Bertram, Olga Perisic, Laura T. L. Brandt, Marie-Kristin von Wrisberg, Zhuo A. Chen, Sarah L. Maslen, Oleksiy Kovtun, Mark Skehel, Juri Rappsilber, Kathrin Lang, Sean Munro, John A. G. Briggs, Roger L. Williams
Summary: The lipid phosphatidylinositol-3-phosphate (PI3P) acts as a regulator of endocytosis and autophagy, generated by two complexes containing the lipid kinase VPS34. Rab5 and Rab1a GTPases recruit and activate specific VPS34 complexes on membranes through unique binding interfaces, guiding them to distinct cellular locations. Insights into the recruitment and activation mechanisms of VPS34 complexes by specific Rab GTPases are provided through biochemical and structural analyses.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Konstantin Shatalin, Ashok Nuthanakanti, Abhishek Kaushik, Dmitry Shishov, Alla Peselis, Ilya Shamovsky, Bibhusita Pani, Mirna Lechpammer, Nikita Vasilyev, Elena Shatalina, Dmitri Rebatchouk, Alexander Mironov, Peter Fedichev, Alexander Serganov, Evgeny Nudler
Summary: The emergence of resistance to clinical antibiotics has prompted the development of a new antimicrobial strategy targeting the bacterial hydrogen sulfide (H2S) defense system. Inhibitors of the bacterial cystathionine g-lyase (CSE) have been found to enhance the effectiveness of bactericidal antibiotics against major human pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa. These inhibitors also disrupt bacterial tolerance, reduce biofilm formation, and decrease the number of persister bacteria surviving antibiotic treatment.
Article
Chemistry, Multidisciplinary
Tuan-Anh Nguyen, Thomas F. Gronauer, Timon Nast-Kolb, Stephan A. Sieber, Kathrin Lang
Summary: We used genetic code expansion, photocrosslinking, and proteomics to identify substrates of mitochondrial human caseinolytic protease P (hClpP). Our approach allowed us to trap substrate proteins of hClpP and reveal its involvement in maintaining mitochondrial homeostasis. We also discovered new proteins in the hClpP interactome and found that hClpP counteracts oxidative stress by processing proteins related to respiratory chain complex synthesis and maturation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Maximilian Fottner, Maria Weyh, Stefan Gaussmann, Dominic Schwarz, Michael Sattler, Kathrin Lang
Summary: The study develops chemoenzymatic tools for customizing Ub/Ubl chains and investigates the involvement of specific Ub/SUMO chains in DNA repair.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Maximilian Fottner, Johannes Heimgartner, Maximilian Gantz, Rahel Muehlhofer, Timon Nast-Kolb, Kathrin Lang
Summary: Asparaginyl endopeptidases (AEPs) are important tools for peptide and protein modification, with wide applications in therapeutic and diagnostic fields. Using genetic code expansion, we achieved site-specific modification of target proteins, providing a simple and flexible labeling approach for creating diverse conjugates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Yonatan G. Mideksa, Isabel Aschenbrenner, Anja Fux, Dinah Kaylani, Caroline A. M. Weiss, Tuan-Anh Nguyen, Nina C. Bach, Kathrin Lang, Stephan A. Sieber, Matthias J. Feige
Summary: This study investigates the molecular chaperones involved in the biogenesis of cytokines in the interleukin 12 (IL-12) family. The authors found that multiple endoplasmic reticulum chaperones interact with IL-12 alpha and IL-23 alpha subunits, and members of the protein disulfide isomerase family play a role in regulating the assembly of IL-12 family subunits. Furthermore, they discovered that specific endoplasmic reticulum chaperones can modulate cytokine secretion.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Athanasios Markos, Maurice Biedermann, Johannes Heimgartner, Adeline Schmitt, Kathrin Lang, Helma Wennemers
Summary: In this study, C,N-cyclic-N'-acyl azomethine imines (AMIs) were introduced to bioorthogonal reactions in an aqueous environment, showing stability under physiological conditions and selective reactivity with isonitriles. The AMI-isonitrile ligation demonstrated biocompatibility and orthogonality to commonly used bioorthogonal reactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Samuel L. Scinto, Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu, Christopher W. Am Ende, M. G. Finn, Kathrin Lang, Qing Lin, John Paul Pezacki, Jennifer A. Prescher, Marc S. Robillard, Joseph M. Fox
Summary: Bioorthogonal chemistry involves high-yielding chemical reactions in biological environments that are rapid and selective, playing essential roles in various fields such as biomedical imaging and drug delivery. Its applications are diverse and include genetic code expansion, drug target identification, and antibody-drug conjugation.
NATURE REVIEWS METHODS PRIMERS
(2021)
