Article
Microbiology
Joshua R. Prindle, Yibo Wang, Julian M. Rocha, Andreas Diepold, Andreas Gahlmann
Summary: This study used three-dimensional single-molecule tracking to elucidate the interaction of injectisome proteins in the cytosol and found that different cytosolic complexes of these proteins can form prior to injectisome binding, which has significant implications for the functional regulation of injectisomes.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Prabhat Tripathi, Arash Firouzbakht, Martin Gruebele, Meni Wanunu
Summary: Translocation of proteins is influenced by structural fluctuations and electric fields at the solid-state nanopore can control this process. By studying the change in occupancy of protein conformations as a function of electric field, we can determine the number of accessible conformational states and evaluate the ruggedness of their free energy landscapes. We also found that translocation becomes faster at higher electric fields, while folding rates are not correlated with ease of translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Nathan Ponzar, Nicola Pozzi
Summary: Disulfide bonds are essential for protein folding and stability, and dysregulation of this process can lead to various disorders. Thiol-isomerases (TIs) are a family of enzymes that oversee this process in human cells. However, our understanding of how TIs select and interact with their substrates, as well as their response to changes in redox environment, remains limited.
Article
Chemistry, Multidisciplinary
Lauren A. Mayse, Ali Imran, Yazheng Wang, Mohammad Ahmad, Rebecca A. Oot, Stephan Wilkens, Liviu Movileanu
Summary: Nanopores are powerful tools for single-molecule protein sensing, but their use outside the nanopore presents challenges in transducing physical interactions into electrical signatures. This limits their widespread adoption. Researchers have developed single-polypeptide-chain nanopores that can be integrated with an optical platform, accelerating their optimization process and providing insights into their performance.
Article
Microbiology
Joshua R. Prindle, Yibo Wang, Julian M. Rocha, Andreas Diepold, Andreas Gahlmann
Summary: Injectisome proteins in the cytosol form distinct complexes with each other prior to binding to injectisomes, and these interactions have important implications for the functional regulation of injectisomes.
MICROBIOLOGY SPECTRUM
(2022)
Article
Chemistry, Multidisciplinary
Tengyang Gao, Zhichao Pan, Zhuanyun Cai, Jueting Zheng, Chun Tang, Saisai Yuan, Shi Qiang Zhao, Hua Bai, Yang Yang, Jia Shi, Zongyuan Xiao, Junyang Liu, Wenjing Hong
Summary: The study reports the switching among multiple conductance pathways achieved by sliding the scanning tunneling microscope tip among different binding sites under different electric fields, leading to the appearance of high molecular conductance states. The switch can be operated in situ and reversibly, with apparent conductance conversion in I-V measurements. Theoretical simulations agree well with experimental results, indicating the possibility of triggering switching in single-molecule junctions with electric fields.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Aleksandr Alekseev, Natalia Morozova, Alexey Vedyaykin, Alexander Yakimov, Mikhail Khodorkovskii, Georgii Pobegalov
Summary: RecA is a central enzyme in bacteria that is involved in homologous recombination, DNA repair, natural transformation, and SOS-response activation. This study explores the features of inactive RecA nucleoprotein filaments formed without nucleotide cofactors, demonstrating that compressed RecA-DNA filaments can exist with different binding stoichiometry and only the 3:1 stoichiometry allows direct interconvertibility with the active ATP-bound conformation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Neeraj Soni, Noam Freundlich, Shilo Ohayon, Diana Huttner, Amit Meller
Summary: Utilizing heat denaturation and sodium dodecyl sulfate (SDS) as aids, nanopore sensing can detect and distinguish unfolded proteins, aiding in single-cell proteomics research.
Review
Biochemistry & Molecular Biology
Dylan R. Weaver, Gavin M. King
Summary: The translocation of specific polypeptide chains across membranes is a vital process in all life forms. Atomic force microscopy (AFM) can be used to directly visualize the dynamic structure of the membrane-external protein topography of Sec system components, providing insights into the translocation process. AFM investigations have revealed the association of SecA with SecYEG, forming membrane-bound translocases, and suggested that the mechanism of translocation may vary depending on the hydrophobic content of precursor sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Boris I. Godoy, Nicholas A. Vickers, Sean B. Andersson
Summary: Single Particle Tracking (SPT) is a powerful method for studying biomolecular dynamics in living cells, revealing trajectories of individual particles and motion model parameters. However, existing algorithms assume constant parameters, while this study proposes an estimation algorithm to determine time-varying parameters in systems that switch between different linear models of motion.
Article
Multidisciplinary Sciences
Fushi Wang, Chunxiao Zhao, Pinlong Zhao, Fanfan Chen, Dan Qiao, Jiandong Feng
Summary: This study reports the direct identification of single amino acids in MoS2 nanopores, as well as the discrimination of amino acid isomers and phosphorylation. This is a significant breakthrough for protein sequencing.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Hongliang Chen, Vitor Brasiliense, Jingshan Mo, Long Zhang, Yang Jiao, Zhu Chen, Leighton O. Jones, Gen He, Qing-Hui Guo, Xiao-Yang Chen, Bo Song, George C. Schatz, J. Fraser Stoddart
Summary: This study introduces a new electrostatic anchoring strategy that forms robust gold-molecule-gold structures and demonstrates electron injection-induced redox switching in single-molecule junctions. These mechanisms could lay the foundation for a new class of redox-activated single-molecule switches.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Izabela Kaminska, Johann Bohlen, Renukka Yaadav, Patrick Schueler, Mario Raab, Tim Schroeder, Jonas Zaehringer, Karolina Zielonka, Stefan Krause, Philip Tinnefeld
Summary: Graphene is a game-changing material with unique mechanical and electrical properties. This study highlights its application as a transparent yet fluorescence-quenching energy transfer acceptor, showcasing its versatility in various fields such as molecular height determination, DNA structure visualization, and orientation determination of energy transfer pairs.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Vanni Doffini, Haipei Liu, Zhaowei Liu, Michael A. Nash
Summary: This study reports the application of machine learning techniques to classify and analyze protein unfolding trajectories. It demonstrates the potential of machine learning to accelerate data analysis and generate new insights.