Article
Chemistry, Multidisciplinary
Damien Sluysmans, Perrine Lussis, Charles-Andre Fustin, Andrea Bertocco, David A. Leigh, Anne-Sophie Duwez
Summary: This study used atomic force microscopy to identify and characterize an intermediate state in hydrogen bonded amide-based molecular shuttling. The research confirmed the presence of an intermediate state in shuttle motion and highlighted the significant influence of thread composition on shuttling dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Sahar Foroutannejad, Lydia L. L. Good, Changfan Lin, Zachariah I. I. Carter, Mahlet G. G. Tadesse, Aaron L. L. Lucius, Brian R. R. Crane, Rodrigo A. A. Maillard
Summary: Characterizing folding pathways of large proteins that bind complex cofactors is challenging. The authors use optical tweezers to study the folding mechanism of dCRY and identify the role of FAD moieties in folding. They show that FAD binds to unfolded intermediates and drives the folding process, but not all FAD moieties are necessary for complete folding.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Nicolas Altemose, Annie Maslan, Owen K. Smith, Kousik Sundararajan, Rachel R. Brown, Reet Mishra, Angela M. Detweiler, Norma Neff, Karen H. Miga, Aaron F. Straight, Aaron Streets
Summary: In this study, we developed a method called DiMeLo-seq, which utilizes long-read sequencing to perform in situ methylation of DNA and obtain genome-wide information about protein-DNA interactions. DiMeLo-seq involves methylating DNA near the binding sites of specific proteins using antibody-tethered enzymes, and simultaneously detecting the exogenous methylation marks along with the endogenous CpG methylation on unamplified DNA. Using DiMeLo-seq, researchers successfully mapped chromatin-binding proteins and histone modifications across the human genome, and identified the localization and density of centromere protein A in highly repetitive regions that were not readily mappable with short-read sequencing.
Article
Chemistry, Multidisciplinary
Jacob Bauer, Gabriel Zoldak
Summary: Single-molecule force spectroscopy experiments explore protein folding and unfolding using mechanical force. While steered molecular dynamics simulations are informative for understanding the structural aspects, they are computationally expensive. Normal mode analysis, a cheaper alternative, can provide insights that complement MD simulations for protein structural analysis in single-molecule force experiments.
Article
Chemistry, Analytical
Diana Soukarie, Philippe Rousseau, Maya Salhi, Alexia de Caro, Jean-Marc Escudier, Catherine Tardin, Vincent Ecochard, Laurence Salome
Summary: This study successfully developed an aptasensor based on high-throughput single-molecule techniques, which enables rapid, simple, and sensitive detection of single target molecules. The presence and concentration of the target molecules can be monitored in real time by combining videomicroscopy and image analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yang Liu, Yi He
Summary: This study investigates the dynamic interaction between acetic acid and covalent organic framework, and reveals the increased binding affinity of acetic acid towards iodine under nanoconfinement, resulting in improved adsorption performance.
ANALYTICAL CHEMISTRY
(2023)
Article
Biology
Yufeng Zhou, John H. Lewis, Zhe Lu, Kenton J. Swartz
Summary: This study successfully tracked the multistate conformational changes of the membrane protein AdiC using a high-resolution fluorescence-polarization-microscopy method. By monitoring the emission-polarization changes of a fluorophore label, four conformations of AdiC were resolved and their probabilities were quantified in the presence of different concentrations of the substrate arginine. The acquired data allowed for the determination of all equilibrium constants and provided insights into the energetic relations among the four states.
Article
Multidisciplinary Sciences
Pancheng Zhu, Vasileios A. Papadimitriou, Jeanne E. van Dongen, Julia Cordeiro, Yannick Neeleman, Albert Santoso, Shuyi Chen, Jan C. T. Eijkel, Hanmin Peng, Loes I. Segerink, Alina Y. Rwei
Summary: Here, we introduce an aptamer-based biosensor for real-time optical detection of endotoxin. The sensor utilizes the scattering of gold nanoparticles (AuNPs) coupled to a gold nanofilm, which is controlled by the conformational changes of an endotoxin-specific aptamer. It can be used in ensemble mode with a microspectrometer or single-particle mode with a color camera, achieving high sensitivity and resolution. This platform has the potential to enhance endotoxin detection and ensure the safety of medical, food, and pharmaceutical products.
Article
Chemistry, Multidisciplinary
Jialun Liang, Jiaxi Li, Zhensheng Zhong, Thitima Rujiralai, Jie Ma
Summary: The study quantitatively evaluated the hydrodynamic drag of DNA using the tethered-bead assay and demonstrated a linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system in a wide force range (0-110 pN). This research provides insights into the force in flow-cell based single-molecule stretching experiments and establishes flow-cells as a flexible and precise tool for single-molecule force measurements.
Article
Multidisciplinary Sciences
Jesper Levring, Daniel S. Terry, Zeliha Kilic, Gabriel Fitzgerald, Scott Blanchard, Jue Chen
Summary: The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that regulates salt and fluid homeostasis across epithelial membranes. Alterations in CFTR cause cystic fibrosis, a fatal disease without a cure. In this study, the authors investigate the structure and function of CFTR, specifically focusing on the dimerization of its nucleotide-binding domains (NBDs) and the allosteric gating mechanism that regulates chloride conductance. They also explore the effects of disease-causing substitutions on NBD dimerization and propose implications for potential clinical therapies.
Article
Chemistry, Physical
Oleg Opanasyuk, Anders Barth, Thomas-Otavio Peulen, Suren Felekyan, Stanislav Kalinin, Hugo Sanabria, Claus A. M. Seidel
Summary: This article introduces the importance of single-molecule Forster Resonance Energy Transfer (smFRET) experiments in resolving the structural dynamics of biomolecules. To overcome the challenges in these experiments, the authors propose a quantitative integrative analysis framework that accurately determines the number of states, their kinetic connectivity, transition rate constants, and species fractions in complex kinetic networks. They also provide a workflow for analysis and demonstrate the usefulness of this toolkit in dynamic structural biology.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Chemistry, Multidisciplinary
William Bro-Jorgensen, Joseph M. Hamill, Rasmus Bro, Gemma C. Solomon
Summary: This tutorial review describes the crucial aspects of applying machine learning to help users avoid common pitfalls. Examples based on single-molecule electron transport experiments demonstrate the application of machine learning and highlight the importance of careful application. The concepts explored are also applicable in other fields with similar data.
CHEMICAL SOCIETY REVIEWS
(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, Analytical
Marina Pons, Marine Perenon, Hugues Bonnet, Emilie Gillon, Celio Vallee, Liliane Coche-Guerente, Eric Defrancq, Nicolas Spinelli, Angeline Van der Heyden, Jerome Dejeu
Summary: In this study, negative or null SPR signals were observed for the recognition of a low molecular weight target by an aptamer. The introduction of a spacer group for aptamer immobilization led to a null SPR signal due to significant conformational transitions affecting the refractive index increment deviation. The unconventional signal was attributed to the positive contribution of aptamer recognition and folding, as well as the negative contribution from the refractive index increment deviation upon complex formation.
Article
Multidisciplinary Sciences
Amani A. Hariri, Sharon S. Newman, Steven Tan, Dan Mamerow, Alexandra M. Adams, Nicolo Maganzini, Brian L. Zhong, Michael Eisenstein, Alexander R. Dunn, H. Tom Soh
Summary: One major challenge in enzyme-linked immunosorbent assays (ELISAs) is distinguishing true signal from non-specific binding. The authors developed a Single-Molecule Colocalization Assay (SiMCA) that eliminates this issue and allows for reproducible detection of picomolar protein concentrations.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jacob S. Lewis, Lisanne M. Spenkelink, Grant D. Schauer, Olga Yurieva, Stefan H. Mueller, Varsha Natarajan, Gurleen Kaur, Claire Maher, Callum Kay, Michael E. O'Donnell, Antoine M. van Oijen
Article
Genetics & Heredity
Sarah S. Henrikus, Antoine M. van Oijen, Andrew Robinson
Summary: The study demonstrates that the formation of pol IV foci in E. coli cells with DNA damage is recB-dependent, and UmuD and UmuDMODIFIER LETTER PRIME play important roles in modulating pol IV activity.
Article
Biochemistry & Molecular Biology
Caitlin L. Johnston, Nicholas R. Marzano, Bishnu P. Paudel, George Wright, Justin L. P. Benesch, Antoine M. van Oijen, Heath Ecroyd
Summary: Research on small heat shock proteins (sHsps) focuses on their molecular mechanisms and interactions with misfolded proteins, utilizing single-molecule fluorescence to determine the stoichiometries of complexes formed with client proteins like chloride intracellular channel 1. This approach reveals a two-step mechanism by which sHsps like alphaB-crystallin prevent protein aggregation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
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
Chemistry, Multidisciplinary
Marta Urbanska, Annemarie Ludecke, Wilhelm J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez
Summary: This study introduces a highly-parallel, microfluidics-based method for rapid collection of force-dependent motility parameters of cytoskeletal motors, significantly improving throughput. DNA-tethered beads are used to apply tunable hydrodynamic forces to stepping kinesin-1 motors, allowing for simultaneous tracking of various motility parameters of hundreds of individual molecules. The approach, applicable to other molecular systems, represents a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
Article
Genetics & Heredity
Kelsey S. Whinn, Antoine M. van Oijen, Harshad Ghodke
Summary: Helicases are nucleic-acid dependent ATPases involved in genomic maintenance, converting ATP hydrolysis energy into physical work for DNA replication and repair. Understanding the catalytic properties and regulation mechanisms of these helicases is crucial for maintaining genomic integrity in cells. Recent single-molecule insights provide further understanding of the molecular mechanisms of prokaryotic helicases and translocases.
Editorial Material
Biochemistry & Molecular Biology
Michelle D. Wang, Mario Nicodemi, Nynke H. Dekker, Thomas Gregor, David Holcman, Antoine M. van Oijen, Suliana Manley
Article
Biochemistry & Molecular Biology
Richard R. Spinks, Lisanne M. Spenkelink, Sarah A. Stratmann, Zhi-Qiang Xu, N. Patrick J. Stamford, Susan E. Brown, Nicholas E. Dixon, Slobodan Jergic, Antoine M. van Oijen
Summary: In Escherichia coli, the helicase DnaB plays a crucial role in DNA replication by providing stability at the replication fork. Single-molecule experiments have shown that while DnaB is stable, it also has the ability to interact dynamically with other factors. This highlights the importance of DnaB as both a stable anchor and a dynamic player in the replication process.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Richard R. Spinks, Lisanne M. Spenkelink, Nicholas E. Dixon, Antoine M. van Oijen
Summary: Helicases are essential molecular motors that unwind DNA during replication. Recent advances in single-molecule methods have provided new insights into the mechanism of action of replicative helicases, revealing how they translocate and unwind DNA to facilitate DNA replication.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Bishnu P. Paudel, Zhi-Qiang Xu, Slobodan Jergic, Aaron J. Oakley, Nischal Sharma, Simon H. J. Brown, James C. Bouwer, Peter J. Lewis, Nicholas E. Dixon, Antoine M. van Oijen, Harshad Ghodke
Summary: Elongation by RNA polymerase can be dynamically modulated by accessory factors, and the transcription-repair coupling factor TRCF can choose to either rescue or terminate the paused/stalled RNAPs. The mechanism for TRCF's choice remains unclear. Using single-molecule assays with Escherichia coli as a model, it was found that nucleotide-bound Mfd, a bacterial TRCF, can convert the elongation complex (EC) into a catalytically poised state, allowing the EC to restart transcription. After a prolonged residence in this state, ATP hydrolysis by Mfd leads to a remodeling of the EC and loss of the RNA transcript. Biophysical studies also revealed that the motor domain of Mfd can bind and partially melt DNA with a template strand overhang.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Brian D. Reed, Michael J. Meyer, Valentin Abramzon, Omer Ad, Pat Adcock, Faisal R. Ahmad, Gun Alppay, James A. Ball, James Beach, Dominique Belhachemi, Anthony Bellofiore, Michael Bellos, Juan Felipe Beltran, Andrew Betts, Mohammad Wadud Bhuiya, Kristin Blacklock, Robert Boer, David Boisvert, Norman D. Brault, Aaron Buxbaum, Steve Caprio, Changhoon Choi, Thomas D. Christian, Robert Clancy, Joseph Clark, Thomas Connolly, Kathren Fink Croce, Richard Cullen, Mel Davey, Jack Davidson, Mohamed M. Elshenawy, Michael Ferrigno, Daniel Frier, Saketh Gudipati, Stephanie Hamill, Zhaoyu He, Sharath Hosali, Haidong Huang, Le Huang, Ali Kabiri, Gennadiy Kriger, Brittany Lathrop, An Li, Peter Lim, Stephen Liu, Feixiang Luo, Caixia Lv, Xiaoxiao Ma, Evan McCormack, Michele Millham, Roger Nani, Manjula Pandey, John Parillo, Gayatri Patel, Douglas H. Pike, Kyle Preston, Adeline Pichard-Kostuch, Kyle Rearick, Todd Rearick, Marco Ribezzi-Crivellari, Gerard Schmid, Jonathan Schultz, Xinghua Shi, Badri Singh, Nikita Srivastava, Shannon F. Stewman, T. R. Thurston, Philip Trioli, Jennifer Tullman, Xin Wang, Yen-Chih Wang, Eric A. G. Webster, Zhizhuo Zhang, Jorge Zuniga, Smita S. Patel, Andrew D. Griffiths, Antoine M. Van Oijen, Michael McKenna, Matthew D. Dyer, Jonathan M. Rothberg
Summary: This study presents a dynamic approach for single-molecule protein sequencing, where single peptides are probed in real time using a mixture of dye-labeled amino acid recognizers and simultaneously cleaved by aminopeptidases. The peptide sequence is identified by measuring fluorescence intensity, lifetime, and binding kinetics. This method enables discrimination of single amino acid substitutions and posttranslational modifications.
Article
Multidisciplinary Sciences
Yichen Zhong, Hakimeh Moghaddas Sani, Bishnu P. Paudel, Jason K. K. Low, Ana P. G. Silva, Stefan Mueller, Chandrika Deshpande, Santosh Panjikar, Xavier J. Reid, Max J. Bedward, Antoine M. van Oijen, Joel P. Mackay
Summary: CHD4 is an essential ATP-dependent translocase that alters chromatin accessibility by repositioning histone octamers. The N-terminal intrinsically disordered region (IDR) promotes remodelling integrity, while the C-terminal region harbours an auto-inhibitory region that is relieved by binding to substrate DNA.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Caitlin Keighley, Antoine M. van Oijen, Stuart J. Brentnall, Martina Sanderson-Smith, Peter Newton, Spiros Miyakis
Summary: The study found similar trends in antimicrobial resistance (AMR) among urinary Escherichia coli isolates from a private community-based laboratory and a public hospital-based laboratory in an Australian local health district. AMR rates increased over time in both settings, with consistently higher rates in the public hospital-based laboratory. Interventions targeting the community-based laboratory setting are crucial for addressing AMR in the community.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Article
Multidisciplinary Sciences
Nicholas R. Marzano, Bishnu P. Paudel, Antoine M. van Oijen, Heath Ecroyd
Summary: The study used total internal reflection fluorescence (TIRF) microscopy and single-molecule fluorescence resonance energy transfer (smFRET) to observe the folding process of firefly luciferase proteins mediated by the bacterial Hsp70 system. The researchers found that there are multiple cycles of chaperone binding and release to individual clients during refolding, and high rates of chaperone cycling improve refolding yield. Additionally, they discovered that DnaJ remodels misfolded proteins through a conformational selection mechanism, while DnaK resolves misfolded states through mechanical unfolding. This study elucidates important mechanistic details of chaperone-assisted folding that are inaccessible using other methods.
Review
Biochemistry & Molecular Biology
Lauren J. Rice, Heath Ecroyd, Antoine M. van Oijen
Summary: Single-molecule approaches have advantages in studying amyloid fibril formation, providing insights into the mechanism and interactions involved. Fluorescence-based single-molecule methods have proven to be particularly effective in studying amyloid fibril formation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
