Article
Chemistry, Multidisciplinary
Naoya Kawakami, Hiroki Sato, Naohiro Terasaka, Kunio Matsumoto, Hiroaki Suga
Summary: The researchers have developed a ubiquitin-based protein ligand multimer, called U-bodies, as a surrogate agonist for the MET receptor. These U-body constructs have high binding affinity, thermal stability, and proteolytic stability. By assembling them into dimeric, tetrameric, and octameric structures, potent MET activation and cell proliferation-promoting activities are achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Kyoko Nakajima, Shota Araki, Masahiro Kawahara
Summary: In this study, minimal synthetic receptors were engineered by incorporating multiple tyrosine motifs to reconstitute signaling properties. These receptors, activated by synthetic small-molecule ligands, were able to recruit and activate up to four signaling molecules of interest, offering potential for analyzing and controlling cell fate.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Michael J. T. Senior, Carina Monico, Eve E. Weatherill, Robert J. Gilbert, Alejandro P. Heuck, Mark Wallace
Summary: By utilizing single-molecule tracking and optical single channel recording, we investigated the assembly pathway and pore formation of cholesterol-dependent cytolysin Perfringolysin O. Our results demonstrate a stepwise irreversible assembly dominated by monomer addition, with infrequent assembly from larger partial complexes.
Article
Multidisciplinary Sciences
Joy Sarkar, Yuncin Luo, Qiang Zhou, Evguenia Ivakhnitskaia, Daniel Lara, Eitan Katz, Michael G. Sun, Victor Guaiquil, Mark Rosenblatt
Summary: This study compared the interactions of VEGF receptors and ligands in neuronal cells and endothelial cells, revealing higher levels of VEGFR heterodimers in neuronal cells and higher levels of VEGFR homodimers in endothelial cells.
Article
Chemistry, Physical
Mirjam Kummerlin, Abhishek Mazumder, Achillefs N. Kapanidis
Summary: We present a general strategy to overcome photobleaching in single-molecule fluorescence measurements by replenishing fluorescent probes using transient binding of complementary DNA strands. This allows for near-continuous observation of single-molecule fluorescence for over an hour, much longer than typical photobleaching times. Our approach is adaptable to FRET and can be used to study the conformational dynamics of dynamic structures.
Article
Biochemical Research Methods
Lara Dresser, Patrick Hunter, Fatima Yendybayeva, Alex L. Hargreaves, Jamieson A. L. Howard, Gareth J. O. Evans, Mark C. Leake, Steven D. Quinn
Summary: Alzheimer's disease is characterized by misfolding and aggregation of Aβ, with small soluble Aβ oligomers now recognized as more toxic than larger fibrillar aggregates. Techniques to characterize oligomer stoichiometry and assembly are crucial for understanding neurodegeneration. By integrating biophysics techniques, new insights into oligomer formation at the single-molecule level can be gained, offering potential for investigating other protein aggregation systems.
Article
Biochemistry & Molecular Biology
Eric Santoni-Rugiu, Maya Jeje Schuang Lu, Jan Nyrop Jakobsen, Linea Cecilie Melchior, Jesper Ravn, Jens Benn Sorensen
Summary: The study found that MET overexpression occurs in a substantial fraction of predominantly epithelioid malignant mesotheliomas, but is poorly correlated with MET amplification status and may impact the likelihood of response to standard chemotherapy for mesothelioma. The predictive significance of MET-IHC and -FISH for possible MET-targeted therapy of mesothelioma remains to be elucidated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Chen Dong, Xinyue Fang, Jingrong Xiong, Jingjing Zhang, Hongyu Gan, Chunyuan Song, Lianhui Wang
Summary: A highly sensitive and specific surface-enhanced Raman scattering (SERS) strategy was proposed to simultaneously image dual homodimerizations of membrane proteins on single live cells. Networking of AuNPs-based dual-recognition probes (dual-RPs) and SERS tags via proximity ligation-assisted catalytic hairpin assembly (CHA) was used to enhance the SERS effect. This strategy provides a good method for high-sensitivity monitoring of membrane proteins dimerizations-based multiple intercellular signal transductions in a natural and complex cellular microenvironment.
Review
Biochemical Research Methods
Xia Zhang, Jiaqi Yin, Wei Pan, Yanhua Li, Na Li, Bo Tang
Summary: This review introduces the importance of receptor tyrosine kinases (RTKs) and their dimers in cell signal transduction pathways and highlights the strategies and advances in imaging RTK dimers. The visualization of RTK dimers is significant for monitoring physiological processes and expanding applications in biomedical areas.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Benjamin Vermeer, Sonja Schmid
Summary: Biomolecular systems rely on dynamic processes at the nanoscale, and detecting biomolecular nanodynamics is crucial for understanding the driving forces that control them. The technique of single-molecule fluorescence resonance energy transfer (smFRET) is limited by irreversible photobleaching, but the introduction of DyeCycling has the potential to break this limit and provide more information per single molecule. It has the ability to revolutionize time-resolved smFRET and uncover a wealth of biomolecular dynamics.
Article
Chemistry, Physical
G. Minervini, A. Panniello, A. Madonia, C. M. Carbonaro, F. Mocci, T. Sibillano, C. Giannini, R. Comparelli, C. Ingrosso, N. Depalo, E. Fanizza, M. L. Curri, M. Striccoli
Summary: Carbon dots are novel fluorescent nanoparticles composed of eco-friendly and inexpensive carbon-based materials. They exhibit intense emission of visible light and can be used in on/off sensors or stimulus-responding devices. The fluorescence of CDs is attributed to the presence of polycyclic aromatic hydrocarbons (PAHs) embedded in the carbon matrix.
Article
Biochemistry & Molecular Biology
Guglielmo Vesco, Marta Lualdi, Mauro Fasano, Luca Nardo, Tiziana Alberio
Summary: The study provides direct evidence of binding interaction between FcRn and fibrinogen at acidic pH, suggesting a protective mechanism for fibrinogen from degradation and regulation of its plasma levels. This interaction may also impact the levels of other FcRn binding partners, including clinically relevant plasma proteins.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Pia A. Lopez, Vy H. B. Pham, Suzanne A. Blum
Summary: A new autofluorescence technique was developed to monitor polymerization progress in real time/in line without typical fluorogenic groups. By harnessing the autofluorescence of dicyclopentadiene and polydicyclopentadiene, the reaction progress of ruthenium-catalyzed ring-opening metathesis polymerization could be quantitatively evaluated. This method has the potential to be extended to other polymerization reactions previously overlooked due to the lack of obvious fluorescence handles.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Rushita A. Bagchi, Emma L. Robinson, Tianjing Hu, Ji Cao, Jun Young Hong, Charles A. Tharp, Hanan Qasim, Kathleen M. Gavin, Julie Pires da Silva, Jennifer L. Major, Bradley K. McConnell, Edward Seto, Hening Lin, Timothy A. McKinsey
Summary: This article highlights the importance of lysine myristoylation in regulating protein localization and function, as well as its role in controlling G protein-coupled receptor signaling. Inhibiting HDAC11 may have therapeutic potential for manipulating adipocyte phenotypes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Optics
Raymundo Moya, Toru Kondo, Audrey C. Norris, Gabriela S. Schlau-Cohen
Summary: Single-molecule spectroscopy is widely used to study heterogeneity in behaviors on different timescales, with the recent emergence of single-molecule pump-probe spectroscopy for detecting heterogeneity on femtosecond and picosecond timescales. By developing a tunable apparatus, a bimodal distribution of energetic relaxation time constants was found for the fluorescent dye Atto647N, indicating dominance of specific processes within individual molecules and low heterogeneity. This spectrally-tunable single-molecule pump-probe spectroscopy has the potential to investigate heterogeneity in various biological and material systems.
Article
Biology
Edoardo L. M. Gelardi, Diego Caprioglio, Giorgia Colombo, Erika Del Grosso, Daniele Mazzoletti, Daiana Mattoteia, Stefano Salamone, Davide M. Ferraris, Eleonora Aronica, Giulia Nato, Annalisa Buffo, Menico Rizzi, Lorenzo Magrassi, Alberto Minassi, Silvia Garavaglia
Summary: Curcumin-based fluorescent probes are developed to selectively bind to ALDH1A3 and identify glioblastoma cells. These probes show high selectivity and specificity in vitro and in vivo, making them potential useful tools for glioblastoma cell detection.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Julian Kompa, Jorick Bruins, Marius Glogger, Jonas Wilhelm, Michelle S. Frei, Miroslaw Tarnawski, Elisa D'Este, Mike Heilemann, Julien Hiblot, Kai Johnsson
Summary: The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Chemistry, Multidisciplinary
Lorenzo Albertazzi, Mike Heilemann
Summary: The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy, which allows for a constant renewal of fluorescence signals at target sites. It has versatile use across microscopy methods and has shown potential in 3D, live, and many-target applications. Although some progress has been made in developing low-affinity labels, this research field still has a lot of untapped potential.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Claudia Catapano, Johanna V. Rahm, Marjan Omer, Laura Teodori, Jorgen Kjems, Marina S. Dietz, Mike Heilemann
Summary: HER2 belongs to the ErbB sub-family of receptor tyrosine kinases and is activated through heterodimerization with other ErbB receptors. This study found that HER2 is strongly activated by EGFR-targeting ligands EGF and TGFa, with a distinguishable temporal fingerprint. HER4-targeting ligands EREG and NRG beta 1 showed weaker activation of HER2, with a preference for EREG and a delayed response to NRG beta 1.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Marta Alberti, Stefano Sainas, Erika Ronchi, Marco L. Lolli, Donatella Boschi, Menico Rizzi, Davide M. Ferraris, Riccardo Miggiano
Summary: Researchers have characterized the full-length MTB DHODH and discovered the first selective inhibitor. This study has significant implications for drug treatment of tuberculosis.
Article
Biochemical Research Methods
Simon Gafe, Hartmut H. Niemann
Summary: This study reports the crystal structures of a single-component flavin-dependent halogenase AetF in complex with various substrates, representing the first experimental structures of a single-component FDH. AetF is structurally related to flavin-dependent monooxygenases, containing two dinucleotide-binding domains with unusual sequences. About half of the AetF protein forms additional structural elements containing the tryptophan binding site. A tunnel between the flavin adenine dinucleotide (FAD) and tryptophan allows the active halogenating agent to diffuse to the substrate.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Dominic Gilzer, Julia L. Kowal, Franziska Flottmann, Hartmut H. Niemann
Summary: Gram-negative bacteria can inhibit the immune defense of their host by injecting effector proteins into the host cytoplasm via type III secretion systems (T3SSs). The secretion of these effector proteins is tightly regulated by bacterial proteins such as SctX. Crystal structures of SctX in complex with SctY chaperones reveal that the positioning of the substrate is similar on different chaperones, but the C-terminal helices of SctX shift and tilt depending on the chaperone. In addition, an unprecedented kink in the C-terminus of the alpha 3 helix of SctX is observed. This kink may allow the chaperone to protect the hydrophobic C-terminus of SctX in solution.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Microbiology
Philipp Hansen, Thomas Haubenthal, Caroline Reiter, Jana Kniewel, Karla Bosse-Plois, Hartmut H. Niemann, Kristine von Bargen, Albert Haas
Summary: Rhodococcus equi is a major cause of life-threatening pneumonia in foals and occasionally in immunocompromised persons. VapA promotes the multiplication of Rhodococcus equi in lung macrophages, while VapN and VapB do not support intracellular multiplication.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Multidisciplinary
Laurell F. F. Kessler, Ashwin Balakrishnan, Nina S. S. Deussner-Helfmann, Yunqing Li, Maximilian Mantel, Marius Glogger, Hans-Dieter Barth, Marina S. S. Dietz, Mike Heilemann
Summary: Super-resolution techniques such as SMLM and STED microscopy are enhanced by using weak affinity-based transient labelling systems, such as DNA-based hybrid systems. However, these techniques suffer from high background fluorescence signal caused by unbound fluorophore-labelled oligonucleotides. This study introduces short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal and increase photon budget in the bound state.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Alon Saguy, Onit Alalouf, Nadav Opatovski, Soohyen Jang, Mike Heilemann, Yoav Shechtman
Summary: Single-molecule localization microscopy (SMLM) has significantly improved spatial resolution in biological imaging, but has limitations in observing dynamics at high temporal resolution. In this study, we introduce DBlink, a deep-learning-based method that reconstructs super spatiotemporal resolution videos from SMLM data. DBlink utilizes a convolutional neural network combined with a bidirectional long short-term memory network to capture long-term dependencies between different frames. Experimental results demonstrate the effectiveness of DBlink in various scenarios, including simulated structures and live-cell dynamic SMLM. This advancement in super-resolution imaging of dynamic processes in living cells is crucial.
Article
Biochemistry & Molecular Biology
Leila T. Alexander, Janani Durairaj, Andriy Kryshtafovych, Luciano A. Abriata, Yusupha Bayo, Gira Bhabha, Cecile Breyton, Simon G. Caulton, James Chen, Seraphine Degroux, Damian C. Ekiert, Benedikte S. Erlandsen, Peter L. Freddolino, Dominic Gilzer, Chris Greening, Jonathan M. Grimes, Rhys Grinter, Manickam Gurusaran, Marcus D. Hartmann, Charlie J. Hitchman, Jeremy R. Keown, Ashleigh Kropp, Petri Kursula, Andrew L. Lovering, Bruno Lemaitre, Andrea Lia, Shiheng Liu, Maria Logotheti, Shuze Lu, Sigurbjorn Markusson, Mitchell D. Miller, George Minasov, Hartmut H. Niemann, Felipe Opazo, George N. N. Phillips Jr, Owen R. Davies, Samuel Rommelaere, Monica Rosas-Lemus, Pietro Roversi, Karla Satchell, Nathan Smith, Mark A. Wilson, Kuan-Lin Wu, Xian Xia, Han Xiao, Wenhua Zhang, Z. Hong Zhou, Krzysztof Fidelis, Maya Topf, John Moult, Torsten Schwede
Summary: We conducted a thorough analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identified and discussed key protein features and evaluated the accuracy of the submitted predictions. While the overall ability to predict protein structures is impressive, reproducing uncommon features remains challenging. The need for novel scoring strategies to emphasize biologically relevant structural regions is highlighted, particularly when dealing with conformational flexibility and large multimeric complexes. Integration of computational and experimental techniques will play a crucial role in unraveling future challenges in structural molecular biology.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biophysics
Soohyen Jang, Kaarjel K. Narayanasamy, Johanna V. Rahm, Alon Saguy, Julian Kompa, Marina S. Dietz, Kai Johnsson, Yoav Shechtman, Mike Heilemann
Summary: Single-molecule localization microscopy achieves nanometer spatial resolution but faces challenges of long acquisition time and photobleaching. This study combines a neural network and a protein labeling method to improve acquisition speed and temporal resolution, enabling capturing of cellular structure dynamics in live cells.
BIOPHYSICAL REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Eugenio Ferrario, Riccardo Miggiano, Menico Rizzi, Davide M. Ferraris
Summary: Computational methods, such as AlphaFold, have improved protein structure prediction. In this study, we combined AlphaFold with crystal structures to investigate the structure of a previously unreported enzyme. We identified a functionally important structural element that was missing in the AlphaFold model but present in the crystal structure. We were able to reconstruct the protein oligomer using computational approaches and successfully solve the protein structure by phasing the diffraction data with the AlphaFold model. This work demonstrates the integration of AlphaFold with experimental data and its significance in protein analysis, crystallographic phasing, and structure solution.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Proceedings Paper
Cell Biology
Johanna Rahm, Sebastian Malkusch, Ulrike Endesfelder, Marina S. Dietz, Mike Heilemann
Summary: This study presents a pipeline for the analysis of single-particle tracking data, allowing for the determination of biomolecule mobility and diffusion state transitions. The application of this pipeline to receptor trajectories revealed that activated receptors move slower and more confined, with more transitions from free to confined diffusion states. The analysis also identified three diffusion states, with increased transition probabilities towards the less mobile and immobile states upon ligand activation.
SINGLE MOLECULE SPECTROSCOP AND SUPERRESOLUTION IMAGING XV
(2022)