Review
Chemistry, Multidisciplinary
Kiyohiko Kawai, Mamoru Fujitsuka, Atsushi Maruyama
Summary: Recent advances in fluorescence microscopy allow tracking of chemical reactions at the single-molecule level, minimizing sample amount needed for analysis and diagnosis, and enhancing efficiency. Single-molecule measurements show potential in ultralow-level biomarker detection, providing new perspectives in chemistry, physics, and life sciences.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Dan Zhao, Dingran Chang, Qiang Zhang, Yangyang Chang, Bo Liu, Changsen Sun, Zhonping Li, Chuan Dong, Meng Liu, Yingfu Li
Summary: In this study, a self-phosphorylating DNAzyme sensor was developed for fluorescence imaging of ATP, showing subsecond response kinetics, high specificity, and micromolar affinities. This sensor was demonstrated to be effective for visualizing ATP signaling in various cellular processes, such as stress-induced endogenous ATP release and mechanical stimulation-evoked ATP release.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
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.
Review
Biochemistry & Molecular Biology
Nibedita Pal
Summary: DNA nanostructures are self-assembled structures of DNA molecules at the nanoscale. Single-molecule FRET technology allows real-time observation and quantitative measurement of structural rearrangements and movements in DNA nanostructures. This technique not only plays an important role in the study of nanostructures, but also helps improve the design and performance of nanostructures and devices.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Byungju Kim, Jincheol Seol, Yoon Ki Kim, Jong-Bong Lee
Summary: Single-molecule fluorescence imaging allows for the observation of circular mRNA formation and the intricate interplay between messenger RNA and ribosomal proteins during translation. This detailed visualization method could potentially enable direct manipulation of interactions within mRNA-protein complexes.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Chemistry, Physical
Nicole Stephanie Galenkamp, Giovanni Maglia
Summary: The study demonstrates the dynamic exchange between five structural intermediates during DHFR catalysis in E. coli through nanopore currents. An endosteric effect promotes substrate binding to the enzyme and the chemical step switches the enzyme from closed to occluded conformation, leading to the release of the reduced cofactor. Only a few reactive complexes lead to catalysis, and second-long catalytic pauses were observed. Multiple cofactor binding events are required to release the product and switch DHFR back to the reactive conformer.
Article
Chemistry, Physical
Hector Vazquez
Summary: This method uses density functional theory to calculate the tunneling conductance of single molecule junctions, simplifying the model and reducing computational costs significantly, while also quantifying the relationship between molecular structure and conductance.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Review
Biochemistry & Molecular Biology
David P. Millar
Summary: This article describes the smFRET methods used to probe the conformational dynamics of DNA polymerases, with a focus on E. coli DNA polymerase I. The studies reviewed reveal the conformational dynamics underlying the nucleotide selection, proofreading, and 5' nuclease activities of Pol I, which are likely employed across the DNA polymerase family. smFRET methods have also been used to examine other aspects of DNA polymerase activity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
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
Chemistry, Multidisciplinary
Steffen Wolf, Benedikt Sohmen, Bjorn Hellenkamp, Johann Thurn, Gerhard Stock, Thorsten Hugel
Summary: The study investigates how ATP hydrolysis causes structural changes in proteins and the hierarchical dynamics process using Hsp90 as a model system.
The process involves timescales ranging from nanoseconds to milliseconds and length scales from angstroms to several nanometers, with conformational changes and structural information transfer leading to structural asymmetry in proteins.
The findings suggest that similar mechanisms may be fundamental for information transfer induced by ATP hydrolysis in many other proteins.
Article
Biochemistry & Molecular Biology
Yiming Zhang, Zongzhou Ji, Xin Wang, Yi Cao, Hai Pan
Summary: DNAzyme is a class of DNA molecules that can catalyze specific metal ions with high selectivity. Conformational changes in DNAzymes play an important role in catalysis, and these changes can be studied using the smFRET technique. In the case of a uranyl-specific DNAzyme 39E, conformational switches were observed to folded and extended states with the addition of Mg2+ and UO22+ respectively. The findings also showed that 39E can spontaneously undergo conformational changes between different configurations, with or without divalent metal ions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Biochemistry & Molecular Biology
Joseph Tibbs, Mohamed Ghoneim, Colleen C. Caldwell, Troy Buzynski, Wayne Bowie, Elizabeth M. Boehm, M. Todd Washington, S. M. Ali Tabei, Maria Spies
Summary: Molecular machines within cells exhibit dynamic assembly, disassembly, and reorganization, with molecular interactions between components being observed and quantified through single-molecule level studies and fluorescence microscopy techniques. Analyzing sequences of molecular interactions can reveal the structure and dynamic organization of complexes, providing important insights into complex biological systems.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Markus Goetz, Anders Barth, Soren S-R Bohr, Richard Boerner, Jixin Chen, Thorben Cordes, Dorothy A. Erie, Christian Gebhardt, Melodie C. A. S. Hadzic, George L. Hamilton, Nikos S. Hatzakis, Thorsten Hugel, Lydia Kisley, Don C. Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A. M. Seidel, Roland K. O. Sigel, Magnus Berg Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R. Weninger, Pengning Xu, Sonja Schmid
Summary: In this study, we compared the performance of 11 analysis tools in inferring kinetic rate constants from smFRET trajectories. The results highlight the current strengths and limitations in inferring kinetic information from smFRET data and provide recommendations for future developments.
NATURE COMMUNICATIONS
(2022)
Article
Hematology
Hongxia Fu, Yan Jiang, Wesley P. Wong, Timothy A. Springer
Summary: Von Willebrand factor (VWF) is an important ultra-long concatemeric protein in hemostasis and thrombosis. Self-association of VWF molecules in flow is reversible and has a self-limiting mechanism. The tension in tethered VWF plays a crucial role in mediating association between VWF molecules.