Article
Chemistry, Multidisciplinary
Yusuke Takashima, Yuki Komoto, Takahito Ohshiro, Kazuhiko Nakatani, Masateru Taniguchi
Summary: Chemical properties have been determined using statistical averages, but the lack of suitable counting methods for single molecules has been a challenge. This study presents a new approach using single-molecule electrical measurements and AI to quantify important parameters like binding selectivity and microscopic hydrogen bonds. The results provide insights into the nature of DNA and its interaction with small molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Huajun Zhang, Shuyan Dai, Xujun Liang, Jun Li, Yongheng Chen
Summary: This study demonstrates that FOXM1 prefers binding tandem DNA sites, and this binding preference may be driven by intermolecular protein-protein interactions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Ilya A. Vakser
Summary: Structural characterization of protein interactions is crucial for understanding and manipulating physiological processes. Computational modeling of protein complexes using Deep Learning techniques has revolutionized protein structure prediction and interaction prediction. Schweke et al.'s study presents a community-wide investigation into distinguishing physiological protein-protein complexes/interfaces from non-physiological ones, providing a benchmark set and evaluating various scoring functions and AlphaFold predictions.
Review
Microbiology
Eugen Pfeifer, Jorge M. Sousa, Marie Touchon, Eduardo P. C. Rocha
Summary: Interactions between viruses, cells, and other genetic elements play a crucial role in the success of infections. These interactions can involve antagonism, competition, cooperation, or parasitism. Rapid evolution through genetic exchanges and functional diversification shapes multilayered networks of interactions that determine the outcome of viral infections.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Xiaohan Chen, Youwen Zhang, Pearl Arora, Xiyun Guan
Summary: Different species can be detected using nanopores engineered with various recognition sites based on non-covalent interactions. This strategy allows for differentiation between species, making it potentially useful for molecular detection in medical and environmental applications.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Alan Fernando Rodriguez Serrano, I-Ming Hsing
Summary: Understanding the interactions between aptamers and ligands is important for designing aptamer-based systems. This study used independent simulations and multiple metastable conformations to accurately predict binding sites, providing valuable insights for aptamer design and applications.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Review
Chemistry, Physical
Izabella Brand
Summary: Proteins in the cytoplasm bind selectively and sensitively to DNA, leading to structural changes in both biomolecules. Detection of these changes requires sophisticated analytical methods, with electrochemical detection being particularly suitable. This has laid the foundations for the development of biosensors.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Arivazhagan Rajendran, Kirankumar Krishnamurthy, Seojeong Park, Eiji Nakata, Youngjoo Kwon, Takashi Morii
Summary: DNA minicircles are important for studying DNA-protein interactions, and their topological features play a significant role in these interactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Mengyi Yang, Ruirui Sun, Pujuan Deng, Yuzhuo Yang, Wenjuan Wang, Jun-Jie Gogo Liu, Chunlai Chen
Summary: Research has revealed the unique searching mechanism of Cas9 under physiological salt conditions, involving both three-dimensional and one-dimensional diffusion, as well as the presence of apparent asymmetric target search regions flanking PAM sites.
Article
Biochemistry & Molecular Biology
Bharath Srinivasan, Krzysztof Kus, Alekos Athanasiadis
Summary: DNA/RNA molecules adopting the left-handed conformation (Z-form) have immunogenic properties and play important roles in immunity and self/non-self-discrimination. Z alpha domains in different proteins recognize and bind left-handed Z-DNA/RNA in a conformation-specific manner, and have been implicated in virus recognition.
BIOCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Pinghua Ling, Shan Cheng, Linyu Wang, Xinyu Sun, Xianping Gao, Feng Gao
Summary: In this study, the differential binding ability of aminoglycosides to DNA structures was investigated using electrochemical method and principal component analysis (PCA). It was found that the structure and sequence of DNA, as well as the size and structure of small molecules, can affect the binding ability between aminoglycosides and DNA. This research presents a new approach for classifying DNA structure and designing targeted drugs.
BIOELECTROCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Shu-Qin Qin, Wei Xu, Wen-Cai Ye, Ren-Wang Jiang
Summary: In this study, Guanidinium-naphthalenedisulfonic acid (GNPS) was used as a molecular catcher to encapsulate liquid guests 1-8. The aromatic cavity of GNPS, with hydrogen bonding and enhanced C-H center dot center dot center dot pi interactions, proved to be a useful tool for the structural determination of liquid molecules.
Article
Biochemical Research Methods
Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marin-Lopez, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva
Summary: The study introduces SPServer, a web server that utilizes Split-Statistical Potentials to analyze protein folds and interfaces. SPServer provides global scores and residue/residue pair profiles for users to identify problematic regions, disruptive amino acid pairs, and compare structural quality.
BMC BIOINFORMATICS
(2021)
Article
Plant Sciences
Jun Takeuchi, Kosuke Fukui, Yoshiya Seto, Yousuke Takaoka, Masanori Okamoto
Summary: Small-molecule plant hormones play a crucial role in controlling plant growth, development, differentiation, and environmental responses. Through genomic decoding of model plants with genetic mutants, scientists have elucidated the molecular mechanisms of nine types of plant hormones and identified the structure of hormone receptors. Studies on the three-dimensional structure of ligand-receptor complexes have revealed the details of ligand perception mechanisms.
Article
Multidisciplinary Sciences
Jiri Wald, Dirk Fahrenkamp, Nikolaus Goessweiner-Mohr, Wolfgang Lugmayr, Luciano Ciccarelli, Oliver Vesper, Thomas C. Marlovits
Summary: This study provides insights into the structure and mechanism of the ATP-hydrolysing RuvAB complex during the assembly and processing of the Holliday junction. The findings reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange, and conformational changes, and elucidate the mechanistic basis for DNA recombination.
Article
Chemistry, Multidisciplinary
Annabelle Hoegl, Matthew B. Nodwell, Volker C. Kirsch, Nina C. Bach, Martin Pfanzelt, Matthias Stahl, Sabine Schneider, Stephan A. Sieber
Review
Biochemistry & Molecular Biology
Christopher M. Scheidler, Leonhard M. Kick, Sabine Schneider
Article
Plant Sciences
Shuaijun Wang, Florian A. Gegenfurtner, Alvaro H. Crevenna, Christoph Ziegenhain, Zane Kliesmete, Wolfgang Enard, Rolf Mueller, Angelika M. Vollmar, Sabine Schneider, Stefan Zahler
JOURNAL OF NATURAL PRODUCTS
(2019)
Article
Cell Biology
Anita Wagner, Olga Hofmeister, Stephane G. Rolland, Andreas Maiser, Koit Aasumets, Sabine Schmitt, Kenji Schorpp, Annette Feuchtinger, Kamyar Hadian, Sabine Schneider, Hans Zischka, Heinrich Leonhardt, Barbara Conradt, Joachim M. Gerhold, Alexander Wolf
JOURNAL OF CELL SCIENCE
(2019)
Article
Biochemical Research Methods
Christopher M. Scheidler, Milan Vrabel, Sabine Schneider
ACS SYNTHETIC BIOLOGY
(2020)
Article
Cell Biology
Bruno Pinheiro, Christopher M. Scheidler, Pavel Kielkowski, Marina Schmid, Ignasi Forne, Suhui Ye, Norbert Reiling, Eriko Takano, Axel Imhof, Stephan A. Sieber, Sabine Schneider, Kirsten Jung
Article
Biochemistry & Molecular Biology
Ines Huebner, Jan-Niklas Dienemann, Julia Friederich, Sabine Schneider, Stephan A. Sieber
ACS CHEMICAL BIOLOGY
(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
Chemistry, Multidisciplinary
Cornelia A. Karg, Shuaijun Wang, Nader Al Danaf, Ryan P. Pemberton, Denzil Bernard, Maibritt Kretschmer, Sabine Schneider, Themistoklis Zisis, Angelika M. Vollmar, Don C. Lamb, Stefan Zahler, Simone Moser
Summary: Chlorophyll and heme are essential pigments in life, and their metabolites have important biological activities. Recent studies have shown that phyllobilins, a derivative of chlorophyll, can target actin, a major component of the cytoskeleton, affecting actin dynamics and related processes in cancer cells. This discovery opens up new possibilities for research in plant science, ecology, and physiology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
David Schmidl, Niko S. W. Lindlar ne Jonasson, Annika Menke, Sabine Schneider, Lena J. Daumann
Summary: The activation of molecular oxygen for selective functionalization and repair of DNA and RNA nucleobases is achieved by alpha-ketoglutarate/iron-dependent dioxygenases. This article focuses on the human homologues AlkBH and TET enzymes, discussing the importance of studying enzyme-substrate interactions and turnover for understanding their mode of action. Various analytical methods have been employed to study changes in the active site and overall enzyme structure, and several methods are available to assess enzyme activity. The article aims to provide a comprehensive synopsis for researchers in the field of epigenetic processes and DNA/RNA repair and modification.
Article
Chemistry, Multidisciplinary
Hulya Aldemir, Shuangjie Shu, Francoise Schaefers, Hanna Hong, Rene Richarz, Sabrina Harteis, Manuel Einsiedler, Tobias M. Milzarek, Sabine Schneider, Tobias A. M. Gulder
Summary: The arylomycin antibiotics are potent inhibitors of bacterial type I signal peptidase, containing a biaryl structural motif reminiscent of glycopeptide antibiotics. AryC, a cytochrome P450 enzyme, performs biaryl coupling in arylomycin biosynthesis without the need for any protein interaction partner, due to its strongly hydrophobic cavity at the surface pointing to the substrate tunnel. This unique reactivity enables chemo-enzymatic assembly of arylomycin A2 combining liquid- and solid-phase peptide synthesis advantages.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemical Research Methods
Dmytro Makarov, Andras Telek, Tobias Becker, Marie-Kristin Wrisberg, Sabine Schneider, Pavel Kielkowski
Summary: The identification and quantification of modified peptides are important for understanding the biological function of protein modifications. This study introduces a synthesized tandem mass spectrometry tag for direct peptide-PTM quantification.
JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Biology
Leonhard M. Kick, Marie-Kristin Von Wrisberg, Leander S. Runtsch, Sabine Schneider
Summary: Cas13a is a single-molecule effector of the CRISPR-Cas system that plays a role in bacterial and archaeal defense. It has the ability to cleave target RNAs and bystander RNAs, providing protection to the bacterial population. This study focuses on the Cas13a enzyme from the purple bacteria Rhodobacter capsulatus, and reveals its structural and functional characteristics. The research provides insights into the molecular mechanisms and function of this family of RNA-dependent RNA endonucleases.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Franziska R. Traube, Marcel Stern, Annika J. Toelke, Martina Rudelius, Ernesto Mejias-Perez, Nada Raddaoui, Beate M. Kuemmerer, Celine Douat, Filipp Streshnev, Manuel Albanese, Paul R. Wratil, Yasmin Gaertner, Milda Nainyte, Grazia Giorgio, Stylianos Michalakis, Sabine Schneider, Hendrik Streeck, Markus Mueller, Oliver T. Keppler, Thomas Carell
Summary: In this study, chemically stabilized siRNA against SARS-CoV-2 was synthesized and modified with peptides, reducing viral loads and virus-induced cytotoxicity. The siRNA was also able to reduce virus replication and virus-induced apoptosis in 3D mucociliary lung microtissues. The adjustment of siRNA sequence allows rapid adaptation to different variants, and conjugation with receptor ligands via click-chemistry enables the construction of targeted siRNAs for a flexible antiviral defense strategy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
David Ranava, Christopher M. Scheidler, Martin Pfanzelt, Michaela Fiedler, Stephan A. Sieber, Sabine Schneider, Mee-Ngan F. Yap
Summary: A previously unrecognized binding partner of the hibernation-promoting factor (HPF) in Staphylococcus aureus has been discovered, which is functionally linked to cold adaptation and glucose metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
