Article
Multidisciplinary Sciences
Anne-Bart Seinen, Dian Spakman, Antoine M. van Oijen, Arnold J. M. Driessen
Summary: SecA predominantly associates with the cytoplasmic membrane as a homodimer in three distinct diffusional populations. Disruption of the proton-motive-force results in the re-localization of SecA to the cytoplasm and transient location at specific membrane sites. This supports a model in which SecA diffuses along the membrane surface to access the SecYEG translocon.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jinrun Dong, Yuxian Lu, Yang Xu, Fanfan Chen, Jinmei Yang, Yuang Chen, Jiandong Feng
Summary: Optical imaging of single-molecule electrochemical reactions in aqueous solution enables super-resolution electrochemiluminescence microscopy, providing high spatiotemporal resolution for monitoring adhesion dynamics of live cells. Single-molecule methods go beyond ensemble averages and reveal statistical distribution of reaction positions, pathways, and dynamics, advancing fundamental understanding of electrochemical reactions and proving useful for bioassays and cell-imaging applications.
Article
Nanoscience & Nanotechnology
Jeffrey A. Ivie, Nathan D. Bamberger, Keshaba N. Parida, Stuart Shepard, Dylan Dyer, Aldilene Saraiva-Souza, Roland Himmelhuber, Dominic McGrath, Manuel Smeu, Oliver L. A. Monti
Summary: This study investigates the relationship between chemical substituents and the conductance of metal-single-molecule-metal junctions, revealing complex effects on energy-level alignment in the junction. The proposed design principles are capable of predicting conductance trends and aid in suggesting novel strategies for maximizing conductance tunability in single-molecule systems.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Review
Biochemistry & Molecular Biology
Anna Svirina, Neharika Chamachi, Michael Schlierf
Summary: Outer membrane proteins (OMPs) play important roles in maintaining the viability of Gram-negative bacteria through various functions. Previous studies have identified proteins and mechanisms involved in OMP biogenesis, but the mechanisms of action of these molecular machines without ATP as an energy source are still not fully understood. Single-molecule studies can provide additional insights into the mechanisms and kinetics of OMP biogenesis.
Article
Physics, Fluids & Plasmas
Ting Liang, Chao Yang, Xiaoya Song, Yuyu Feng, Yanhui Liu, Hu Chen
Summary: This study systematically investigated the kinetics and thermodynamics of the folding-unfolding transition of an individual DNA hairpin in a crowded environment using a combination of high-resolution magnetic tweezers and an extended crowder-oxDNA model. The results demonstrated a linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration, highlighting the importance of excluded volume effects in the interaction between PEG and the DNA hairpin. The method provides insights into accurately mimicking cytosolic environments using mixtures of different inert molecules. Overall rating: 9/10.
Review
Biochemistry & Molecular Biology
Shashank Dadsena, Andreas Jenner, Ana J. Garcia-Saez
Summary: Apoptotic cell death plays a crucial role in development and tissue homeostasis, and MOMP is a central event in this process. Researchers focus on the interaction network of Bcl-2 family proteins and other regulatory elements, emphasizing the importance of single-molecule techniques in uncovering apoptosis regulation mechanisms.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Chemistry, Physical
Philip Daniel Maret, Devika Sasikumar, Ebin Sebastian, Mahesh Hariharan
Summary: This study aims to explore the excited-state dynamics of chiral organic bichromophores and provide guidance for the development of efficient chiral organic semiconductors and their applications in charge transport materials.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biophysics
Dalton R. Gibbs, Roaa Mahmoud, Anisa Kaur, Soma Dhakal
Summary: This study used an optical-tweezers-based single-molecule manipulation assay to investigate the mechanical and thermodynamic properties of the RuvA-Holliday junction complex. The results showed that RuvA protein stabilizes the Holliday junction and increases its unfolding force, facilitating refolding under high force. This approach can be applied to study other junction-binding proteins involved in critical DNA repair processes.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Yongyao Wang, Xiao Hu, Jiangang Long, Jiajie Diao
Summary: Researchers have developed a chemical labeling-based single-molecule imaging method, known as SMEL, which enables the detection and study of epigenetic modifications, specifically 5-hydroxymethylcytosine. They successfully applied this method to mouse embryonic stem cell genomic DNA and demonstrated its potential clinical applications.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Nuno Bustorff, Joerg Fitter
Summary: In this study, the denaturant-induced unfolded states of the protein PGK were investigated using single-molecule FRET. In addition to the known two-state transition, a transition with a compact folding intermediate was also identified. The results provide clear evidence that the domain topology plays an important role in determining the observed structural changes.
Article
Chemistry, Multidisciplinary
Yuna Bae, Min Young Ha, Ki-Taek Bang, Sanghee Yang, Sung Yun Kang, Joodeok Kim, Jongbaek Sung, Sungsu Kang, Dohun Kang, Won Bo Lee, Tae-Lim Choi, Jungwon Park
Summary: This paper utilizes liquid-phase transmission electron microscopy to track the real-time dynamics of single-chain polymers, revealing the conformational characteristics of these polymers and their dependence on intrachain interactions and environmental factors.
ADVANCED MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Michael Trumpp, Anna Oliveras, Hannes Gonschior, Julia Ast, David J. Hodson, Petra Knaus, Martin Lehmann, Melissa Birol, Johannes Broichhagen
Summary: In this study, the near-infrared ATTO700 was evaluated as an acceptor in SNAP- and Halo-tag protein labeling for Forster Resonance Energy Transfer (FRET) using ensemble and single molecule measurements. Microscopy was performed to observe cell surface proteins in live cells, including super-resolution stimulated emission by depletion (STED) nanoscopy technique.
CHEMICAL COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Liang Li, Claudia R. R. Prindle, Wanzhuo Shi, Colin Nuckolls, Latha Venkataraman
Summary: Radicals, with their open-shell electronic structures, are unique molecular systems for electronic devices, capable of functioning as conductors and switches in molecular circuits and holding promise in molecular spintronics. However, creating stable and persistent radicals and understanding their properties in molecular junctions pose challenges. This Perspective provides design principles for synthesizing stable radicals relevant to molecular junctions and offers insight into the electronic properties of radicals in single-molecule devices, aiming to facilitate further exploration and development of radical-based molecular systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Jinyang Liu, Bingjie Zhao, Xuebo Zhang, Daoming Guan, Kuangshi Sun, Yunxiang Zhang, Qian Liu
Summary: In this study, we developed a novel thiolation strategy for squaraine dyes to improve their photostability and extend their application in single-molecule imaging. By introducing thiolation of the central cyclobutene of squaraine, we observed a significant increase in photobleaching lifetime, allowing for stable single-molecule tracking of membrane protein CD56 and monitoring mitochondria movements in live neurons. This research contributes to the advancement of single-molecule imaging probes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Wang Xiao, Wang Xingwen, Xiao Lehui
Summary: This review discusses the use of single-molecule fluorescence imaging (SMFI) in studying nanocatalysis at the single-particle level. By adopting fluorogenic reactions and monitoring the fluorescence signal, SMFI allows for real-time tracking of reaction processes on individual nanoparticles and revealing various factors influencing catalytic mechanisms.
ACTA CHIMICA SINICA
(2023)
Article
Biochemistry & Molecular Biology
Michael Kamel, Maryna Loewe, Stephan Schott-Verdugo, Holger Gohlke, Alexej Kedrov
Summary: Unsaturated fatty acids (UFAs) play a crucial role in enhancing protein translocation mediated by SecA: SecYEG in bacterial cytoplasmic membranes. UFAs increase lipid area and cause loose packing of lipid head groups, promoting SecA binding and improving translocation efficiency. This discovery highlights the importance of fatty acid structure in protein secretion mechanisms in bacteria, which respond to environmental changes by altering their membrane composition.
Article
Immunology
Richel J. C. Bilderbeek, Maksim V. Baranov, Geert van den Bogaart, Frans Bianchi
Summary: This study reveals the over-presentation of membrane protein fragments in cytolytic and helper T cell responses. It also demonstrates the evolutionary conservation and lower frequency of mutations in transmembrane helices, suggesting that T cells are more tuned to respond to membrane proteins to avoid evasion by pathogens.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrea J. Weiler, Olivia Spitz, Mirja Gudzuhn, Stephan N. Schott-Verdugo, Michael Kamel, Wolfgang R. Streit, Alexej Kedrov, Lutz Schmitt, Holger Gohlke, Filip Kovacic
Summary: This study reveals the role of a novel phospholipase B, PaPlaB, in Pseudomonas aeruginosa. PaPlaB is involved in biofilm formation and cell localization, and may serve as a potential therapeutic target.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2022)
Article
Biochemistry & Molecular Biology
Sjors Maassen, Harry Warner, Melina Ioannidis, Jack Jansma, Hugo Markus, Sahar El Aidy, Maria-Dolores Chiara, Jose Luis Chiara, Larissa Maierhofer, Helen Weavers, Geert van den Bogaart
Summary: 5-MTP alters the metabolism and function of macrophages by affecting their mitochondria. It changes the physical and chemical properties of mitochondrial membranes, leading to increased glucose import and reduced mitochondrial import of acyl-carnitines. This results in increased endocytosis of collagen by macrophages. However, 5-MTP does not affect macrophages following pathogenic stimulation.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Review
Cell Biology
Harry Warner, Shweta Mahajan, Geert van den Bogaart
Summary: Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are membrane-associated trafficking proteins that facilitate membrane fusion through posttranslational modifications (PTMs). These PTMs provide cells with functional plasticity to respond to changing extracellular environments.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Sjors Maassen, Britt Coenen, Sara Dulk, Martijn van Der Werff, Harry Warner, Fabio Spada, Thomas Frischmuth, Danny Incarnato, Geert van den Bogaart
Summary: A new uridine analogue, 5-ethynyluridine (EU), has been identified as a potential candidate for mRNA-based vaccines and therapeutics. It does not cause immune activation and allows for prolonged expression. Although EU-modified mRNA is expressed at lower levels, it exhibits similar stability and low immunogenicity to other uridine analogues.
Article
Biochemistry & Molecular Biology
Sjors Maassen, Britt Coenen, Melina Ioannidis, Karl Harber, Pieter Grijpstra, Jan Van den Bossche, Geert van den Bogaart
Summary: Pathological conditions associated with dysfunctional wound healing are characterized by impaired remodelling of extracellular matrix (ECM), increased macrophage infiltration, and chronic inflammation. Macrophages play an important role in wound healing through secretion of molecules like transforming growth factor beta-1 (TGF-beta). This study investigated the effects of 4-octyl itaconate (4-OI) on macrophage wound healing functions, and found that it reduced inflammation, increased expression of TGF-beta, and promoted scavenging of ECM by macrophages.
Review
Cell Biology
Myrthe T. Frans, Ella M. Kuipers, Frans Bianchi, Geert van den Bogaart
Summary: The Golgi membrane protein GOLM1/GP73/GOLPH2 is involved in cytokine production in both infectious disease and cancer. It can reduce the production of type I interferons and other inflammatory cytokines during viral infections, but increased expression levels of GOLM1 due to mutations can lead to higher interleukin-6 production during Candida infections. In cancer, GOLM1 promotes the production of the chemokine CCL2 and suppresses the production of inflammatory cytokines such as IL-12 and interferon gamma.
IMMUNOLOGY AND CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alka Rao, Niels A. W. de Kok, Arnold J. M. Driessen
Summary: Cellular membranes play essential roles in compartmentalization, permeability maintenance, and fluidity in all three domains of life. Archaea, as the third domain of life, have unique phospholipid compositions. The study focuses on Sulfolobus acidocaldarius, an archaeon with a membrane dominated by glycerol dialkyl glycerol tetraethers (GDGTs), and the effects of the antifungal terbinafine on its lipidome and transcriptome. The results show that terbinafine treatment leads to growth phase-dependent depletion of GDGTs and the accumulation of bilayer-forming dialkyl glycerol diethers (DGDs). Transcriptomic analysis reveals significant differential expression of genes involved in respiratory stress, isoprenoid biosynthesis, and saturation. Overall, terbinafine inhibition affects the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization in S. acidocaldarius.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Femmy C. Stempels, Muwei Jiang, Harry M. Warner, Magda-Lena Moser, Maaike H. Janssens, Sjors Maassen, Iris H. Nelen, Rinse de Boer, William F. Jiemy, David Knight, Julian Selley, Ronan O'Cualain, Maksim V. Baranov, Thomas C. Q. Burgers, Roberto Sansevrino, Dragomir Milovanovic, Peter Heeringa, Matthew C. Jones, Rifka Vlijm, Martin ter Beest, Geert van den Bogaart
Summary: Stempels et al. discovered large ESCRT structures in migratory cell types that wrap around clusters of integrins lacking actin. These structures are involved in membrane repair and extracellular vesicle formation. The ESCRT structures are tightly connected to the cellular support and are left behind by the cells with surrounding patches of membrane. The presence of ESCRT structures indicates membrane damage and extracellular shedding.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Polymer Science
Guus van der Borg, Harry Warner, Melina Ioannidis, Geert van den Bogaart, Wouter H. Roos
Summary: 3D printing with polylactic acid (PLA) filament is shown to be a cheaper and more easily accessible alternative to resin printing for manufacturing PDMS molds. A method using chloroform vapor treatment is introduced to smoothen the printed PLA mold, which was successfully used to cast PDMS rings. The PDMS-glass well created with the PLA mold showed no leakage and was suitable for cell culturing, as tested with monocyte-derived dendritic cells (moDCs).
Article
Biochemistry & Molecular Biology
Maryna Loewe, Sebastian Haensch, Eymen Hachani, Lutz Schmitt, Stefanie Weidtkamp-Peters, Alexej Kedrov
Summary: Biochemical processes in crowded cellular environments, such as membranes, are affected by macromolecular crowding. Researchers developed a fluorescence-based sensor to quantify macromolecular crowding at membrane interfaces, and validated its dynamics in Escherichia coli inner membrane vesicles.
Article
Multidisciplinary Sciences
Adela Melcrova, Sourav Maity, Josef Melcr, Niels A. W. de Kok, Mariella Gabler, Jonne van der Eyden, Wenche Stensen, John S. M. Svendsen, Arnold J. M. Driessen, Siewert J. Marrink, Wouter H. Roos
Summary: This study investigates the mechanism of action of the antimicrobial cationic tripeptide AMC-109. It was found that AMC-109 self-assembles into stable aggregates with a cationic surface, and then inserts into the bacterial membrane disrupting membrane nanodomains, thus affecting membrane function without forming pores. The results suggest that AMC-109 is a peptide with enhanced selectivity for bacterial membranes.
NATURE COMMUNICATIONS
(2023)
Article
Polymer Science
Lorand Bonda, Janita Mueller, Lukas Fischer, Maryna Loewe, Alexej Kedrov, Stephan Schmidt, Laura Hartmann
Summary: The straightforward synthesis of polyamide-derived statistical copolymers with catechol, amine, amide and hydroxy residues via free radical polymerization is presented in this study. The research aims to investigate whether synergistic effects exist in statistical copolymer systems that lack the sequence-defined positioning of functional groups in mussel foot proteins.
Article
Multidisciplinary Sciences
Sjors Maassen, Harry M. Warner, Pieter Grijpstra, Geert van den Bogaart
Summary: Collagen remodelling is a crucial process in both embryonic development and maintenance of the adult body. This study presents a protocol for quantifying the uptake of collagen by cells, using polymerisation of collagen type I-FITC conjugate in cell culture plate wells, followed by cell detachment using the protease accutase and quantification of FITC signal via microscopy and/or flow cytometry. This easy-to-use protocol allows for quantitative measurement of collagen uptake in cells.