Review
Biochemistry & Molecular Biology
Nitesh Kumar Podh, Sheetal Paliwal, Partha Dey, Ayan Das, Shruti Morjaria, Gunjan Mehta
Summary: Single-molecule imaging in live yeast cells has become a powerful tool for researchers to quantitatively measure cellular activities in real time, with significant progress made in recent years to provide important references for studying biological processes. Different labs have tailored imaging setups and data analysis pipelines to estimate biophysical parameters for various biological processes, reflecting a rich variety of experimental experiences.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biophysics
Yukun Wang, Avinash Kumar, Huaizhou Jin, Yongli Zhang
Summary: The study demonstrates that optical tweezers are able to stably trap GUVs and control membrane tension, serving as force sensors. Additionally, SUVs are rigid enough to resist large pulling forces, making them suitable for detecting force-induced protein conformational changes.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Yi Wang, Bo Jiang, Yan Wang, Wei Wei, Ben Niu, Hongyuan Chen, Hui Wang
Summary: Single-molecule localization technique reveals the transient states of single biomolecules and nanoparticles, as well as the dynamic details and intrinsic mechanisms of single-molecule binding pairs with high specificity and accuracy. Additionally, it can uncover the characteristic behavior of nanoscale liposomes influenced by surface chemistry.
ANALYTICAL CHEMISTRY
(2021)
Article
Optics
Oumeng Zhang, Zijian Guo, Yuanyuan He, Tingting Wu, Michael D. Vahey, Matthew D. Lew
Summary: Single-molecule orientation-localization microscopy is a powerful tool for studying biochemical processes, but the limited photon budget poses challenges for high-dimensional imaging. A raMVR microscope has been developed with isotropic 3D spatial resolution and precision in measuring molecular orientations, enabling detailed imaging of molecular dynamics within biological and chemical systems.
Article
Multidisciplinary Sciences
Mackenzie W. Turvey, Kristin N. Gabriel, Wonbae Lee, Jeffrey J. Taulbee, Joshua K. Kim, Silu Chen, Calvin J. Lau, Rebecca E. Kattan, Jenifer T. Pham, Sudipta Majumdar, Davil Garcia, Gregory A. Weiss, Philip G. Collins
Summary: In this study, the motions and reactions of Taq DNA polymerase at different temperatures were recorded using single-walled carbon nanotube transistors. The results showed that the reaction rate and duration of Taq DNA polymerase had almost no temperature dependence, with its temperature sensitivity primarily determined by its open state.
Article
Biology
Marko Usaj, Luisa Moretto, Venukumar Vemula, Aseem Salhotra, Alf Mansson
Summary: The benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies, with key reasons being complexities due to dye photophysics and fluorescent contaminants. After eliminating these complexities, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, providing new insights into ATP turnover mechanisms.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Analytical
Xueqin Chen, Yan Gao, Jiayin Zhan, Qing Xia, Zixuan Chen, Jun-Jie Zhu
Summary: This paper proposes a spatiotemporal-resolved Raman spectroscopy (STRS) technology for fast and high spatial resolution hyperspectral Raman imaging of single nanostructures. By utilizing the outstanding electromagnetic field enhancement factor by surface plasmon resonance and the snapshot hyperspectral imaging strategy, the observation of stepwise Raman signals from single-particle plasmon-assisted reactions is demonstrated. The results reveal the impact of both surface plasmon-polariton generation and Raman molecule density on the reaction kinetics.
ANALYTICAL CHEMISTRY
(2022)
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.
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, Multidisciplinary
Pengfei Zhang, Guangzhong Ma, Zijian Wan, Shaopeng Wang
Summary: Single-molecule-based measurement can distinguish specific and nonspecific binding processes by quantifying the mass and binding dynamics of individual-bound analyte molecules, providing a convenient solution for high-resolution imaging on widely used prism-coupled SPR systems.
Review
Chemistry, Analytical
Hui Wang, Cuilin Zhu, Di Li
Summary: The emergence of single-molecule techniques has greatly advanced research in enzymology. Single-molecule enzymology studies the individual behavior of a single enzyme molecule, which is hidden under the overall average. This review summarizes the emerging developments of several single-molecule techniques, such as TIRFM, confocal microscopy, FCS, and magnetic/optical tweezers, in real-time monitoring of the catalytic process of single enzymes. It explores various enzymatic catalytic behaviors and mechanisms that differ from bulk experiments, providing a deeper understanding of enzymatic reaction mechanisms through the analysis of single-molecule enzymatic kinetics coupled with conformational changes. Additionally, this review critically discusses the future challenges of imaging and monitoring single enzymatic reactions in cellular environments.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Katarzyna Makasewicz, Stefan Wennmalm, Bjorn Stenqvist, Marco Fornasier, Alexandra Andersson, Peter Jonsson, Sara Linse, Emma Sparr
Summary: Cooperative binding is a crucial feature in metabolic pathways, signaling, and transport processes, allowing for tight regulation over a narrow concentration range. The study shows strong positive cooperativity of alpha-synuclein binding to phospholipid membranes, indicating that the protein has a higher affinity for a membrane where there is already bound protein, compared to a bare membrane.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Jie Xu, Shuya Fan, Lei Xu, Atsushi Maruyama, Mamoru Fujitsuka, Kiyohiko Kawai
Summary: By measuring fluorescence blinking, the dynamics of triplet-triplet energy transfer (TTET) governed by oligonucleotide dynamics at the single-molecule level were studied. TTET kinetics measurement allowed access to length- and sequence-dependent dynamics of oligos and enabled single-molecule detection.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
Chemistry, Multidisciplinary
Jinrun Dong, Yang Xu, Ziqing Zhang, Jiandong Feng
Summary: Here, we demonstrate super-resolution imaging of Ru(bpy)(3)(2+) reactions on Au plates using single-molecule electrochemiluminescence microscopy, achieving high spatial resolution and sensitivity to single photons. The spatiotemporally resolved dynamic structure-activity relationship on Au plates reveals the importance of catalyst restructuring in determining reactivity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Meeting Abstract
Biophysics
Rujin Cheng, Marina Grossi, Jun Liu, Peter R. Hoffmann, Sharon Rozovsky
BIOPHYSICAL JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Jun Liu, Oshini Ekanayake, Dominic Santoleri, Kelsi Walker, Sharon Rozovsky
Article
Chemistry, Physical
Qingqing Chen, Shiping Xu, Xingyu Lu, Michael Boeri, Yuliya Pepelyayeva, Elizabeth L. Diaz, Sunil-Datta Soni, Marc Allaire, Martin B. Forstner, Brian J. Bahnson, Sharon Rozovsky
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Multidisciplinary
Jun Liu, Rujin Cheng, Ned Van Eps, Nanxi Wang, Takefumi Morizumi, Wei-Lin Ou, Paul C. Klauser, Sharon Rozovsky, Oliver P. Ernst, Lei Wang
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Endocrinology & Metabolism
Chi Ma, FuKun W. Hoffmann, Michael P. Marciel, Kathleen E. Page, Melodie A. Williams-Aduja, Ellis N. L. Akana, Greg S. Gojanovich, Mariana Gerschenson, Johann Urschitz, Stefan Moisyadi, Vedbar S. Khadka, Sharon Rozovsky, Youping Deng, F. David Horgen, Peter R. Hoffmann
Summary: T cell activation triggers metabolic reprogramming for energy demands and cell proliferation. Ethanolamine phospholipid synthesis plays a crucial role during this process as a regulator of metabolic shifts in stem cells and cancer cells.
MOLECULAR METABOLISM
(2021)
Article
Biochemistry & Molecular Biology
Li Cao, Jun Liu, Farid Ghelichkhani, Sharon Rozovsky, Lei Wang
Summary: Researchers have developed orthogonal tRNA(Pyl)-MaBzKRS pairs for site-specific modification of proteins, allowing for efficient incorporation of epsilon-N-benzoyllysine (BzK) into proteins in E. coli and mammalian cells. MaBzKRS variants with mutations at different positions in the amino acid binding pocket have been identified for incorporating BzK, which could have broad utility in studying the biological effects of lysine benzoylation.
Article
Chemistry, Multidisciplinary
Jun Liu, Li Cao, Paul C. Klauser, Rujin Cheng, Viktoriya Y. Berdan, Wei Sun, Nanxi Wang, Farid Ghelichkhani, Bingchen Yu, Sharon Rozovsky, Lei Wang
Summary: Introducing novel chemical bonds into proteins offers innovative possibilities, with the incorporation of latent bioreactive unnatural amino acids providing a powerful system for covalent targeting of natural residues. This approach has potential applications in biochemical research and protein engineering.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Microbiology
Jessica L. Keffer, Sean M. McAllister, Arkadiy I. Garber, Beverly J. Hallahan, Molly C. Sutherland, Sharon Rozovsky, Clara S. Chan
Summary: Iron (Fe) oxidation is a crucial biogeochemical process on Earth, with microbial iron oxidizers playing a significant role. Studies on Cyc2 in neutrophilic iron oxidizers suggest that it functions as an iron oxidase, providing new insights into the metabolism of these organisms. The presence of Cyc2 in a wide variety of iron oxidizers indicates its importance in iron oxidation processes.
Meeting Abstract
Biochemistry & Molecular Biology
Fabio A. Gonzalez-Arias, Sharon Rozovsky
Meeting Abstract
Biochemistry & Molecular Biology
Farid Ghelichkhani, Sharon Rozovsky
Article
Biochemistry & Molecular Biology
Caitlin M. Quinn, Shiping Xu, Guangjin Hou, Qingqing Chen, Deepak Sail, R. Andrew Byrd, Sharon Rozovsky
Summary: Sulfur-containing sites in proteins play crucial roles in protein structure and function. Selenium-77 can replace sulfur and be introduced into proteins without significant structural changes. However, there is currently no established method to accurately map the local environment around selenium sites. This study explores a method using correlations between selenium and carbon-13 to characterize the local environment of selenium sites in a model protein variant.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Biochemistry & Molecular Biology
Geneva Maddison Crump, Sharon Rozovsky, Catherine L. Grimes
Summary: The evolutionarily conserved leucine rich repeat (LRR) protein domain is a unique structural motif found in many viral, bacterial, archaeal, and eukaryotic proteins. The LRR domain serves various roles, including being a signaling domain and a pathogen recognition receptor. Through new experimental methods, researchers have demonstrated that the LRR domain of Cyr1p can bind bacterial peptidoglycan fragments under native conditions, paving the way for the development of antifungal agents.
Review
Biochemistry & Molecular Biology
Farid Ghelichkhani, Fabio A. Gonzalez, Mariia A. Kapitonova, Stephanie Schaefer-Ramadan, Jun Liu, Rujin Cheng, Sharon Rozovsky
Summary: Selenoprotein S (selenos) is a membrane protein associated with various cellular functions, including ER-associated degradation, transcription factor control, and cytokine level regulation. Genetic polymorphisms of selenos are linked to increased risk for diseases, while high expression levels are associated with poor prognosis in certain cancers.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Janusz Koscielniak, Jess Li, Deepak Sail, Rolf Swenson, Clemens Anklin, Sharon Rozovsky, R. Andrew Byrd
Summary: NMR spectroscopy has been widely used in proteins and biomolecules, but observing sulfur sites has been challenging. Recent studies have explored the use of Se-77 as a replacement for sulfur and applied Se-77 NMR in both solution and solid states. A double-labeling method using C-13 and Se-77 in proteins has been developed, enabling more sensitive triple-resonance schemes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)