Correction
Chemistry, Multidisciplinary
Ming-Jie Han, Qing-tao He, Mengyi Yang, Chao Chen, Yirong Yao, Xiaohong Liu, Yuchuan Wang, Zhong-liang Zhu, Kong-kai Zhu, Changxiu Qu, Fan Yang, Cheng Hu, Xuzhen Guo, Dawei Zhang, Chunlai Chen, Jin-peng Sun, Jiangyun Wang
Summary: The study corrected and analyzed beta-arrestin-1 at the single-molecule level using genetic code expansion and a Se-click reaction, providing important insights into the function and structure of this protein for further research.
Article
Biochemistry & Molecular Biology
Busong Wang, Lu Zou, Liang Zhou
Summary: NMDAR is composed of GluN1 and GluN2, and/or GluN3 subunits, with GluN1 serving as the obligatory subunit containing variant N-terminal domain (NTD) and C-terminal domain (CTD). Through our study, we found that GluN1 CTD could bind to lipid bilayers and affect its antigen epitope, suggesting that membrane binding may determine the allosteric signal of GluN1 CTD. Additionally, we discovered that the membrane binding of GluN1 CTD can be regulated by the phosphorylation of GluN1 CTD C1 region.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Liang Zhou, Jingjing Duan
Summary: In this study, it was found that the positive charges of GluN1 C-terminus determine the translocation of CaM to the nucleus, regulating synaptic transmission and the gene expression of multiple cell surface receptors, consequently affecting NMDAR-mediated synaptic transduction.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Dagmar Klostermeier
Summary: Gyrase is an essential bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. Current inhibitors of gyrase often have severe side effects and lose antibiotic activity due to resistance mutations, highlighting the need for novel and improved inhibitors.
Review
Neurosciences
Simon Bossi, Lara Pizzamiglio, Pierre Paoletti
Summary: GluN3A is a subunit of the NMDA receptor family that can form glycine-activated receptors with GluN1 subunits. These excitatory glycine receptors (eGlyRs) have been discovered in specific brain regions and play a role in regulating neuronal excitability and behavior. The existence of eGlyRs expands our understanding of NMDAR diversity and glycinergic signaling, which was previously thought to be inhibitory. Given their concentration in brain regions regulating emotional responses, eGlyRs are potential therapeutic targets in neuropsychiatry.
TRENDS IN NEUROSCIENCES
(2023)
Article
Clinical Neurology
Alberto Imarisio, Elena Ferrari, Andrea Pilotto, Monica Di Luca, Alessandro Padovani, Fabrizio Gardoni
Summary: This study assessed the expression, synaptic abundance, and interaction of neurofilaments with NMDAR in experimental alpha-synucleinopathy models. The results demonstrated alterations in the striatal synaptic neurofilament pool in alpha-synucleinopathy models and suggested a potential role of neurofilament dysregulation in explaining glutamatergic synaptic dysfunction observed in diseases like Parkinson's.
NEURODEGENERATIVE DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Jake Zheng Chen, William Bret Church, Karine Bastard, Anthony P. Duff, Thomas Balle
Summary: This article investigates the molecular mechanisms of a mutation (Ser688Tyr) in the NMDAR GluN1 ligand binding domain that causes encephalopathies. The mutation leads to instability of ligands and changes in receptor activity.
Article
Immunology
Yuewen Ding, Zheye Zhou, Jinyu Chen, Yu Peng, Haitao Wang, Wei Qiu, Wei Xie, Jun Zhang, Honghao Wang
Summary: The study established a novel mouse model of anti-NMDAR encephalitis by actively immunizing against NMDARs with a peptide targeting the ATD of GluN1. Immunized mice showed significant memory loss and decreased surface NMDAR cluster density in hippocampal neurons, similar to effects observed in patients with anti-NMDAR encephalitis. These findings may contribute to further research on the pathogenesis of anti-NMDAR encephalitis and the development of new therapies for this disease.
JOURNAL OF NEUROINFLAMMATION
(2021)
Article
Medicine, Research & Experimental
Mihyun Bae, Junyeop Daniel Roh, Youjoung Kim, Seong Soon Kim, Hye Min Han, Esther Yang, Hyojin Kang, Suho Lee, Jin Yong Kim, Ryeonghwa Kang, Hwajin Jung, Taesun Yoo, Hyosang Kim, Doyoun Kim, Heejeong Oh, Sungwook Han, Dayeon Kim, Jinju Han, Yong Chul Bae, Hyun Kim, Sunjoo Ahn, Andrew M. Chan, Daeyoup Lee, Jin Woo Kim, Eunjoon Kim
Summary: Research has shown that SLC6A20A is an amino acid transporter that regulates proline and glycine balance in the brain and NMDAR function. Mutant PTEN protein may enhance abnormal expression of SLC6A20A transcript and protein by increasing binding to the Slc6a20a gene. Modulating SLC6A20A can normalize NMDAR currents and restore behavior in mice.
EMBO MOLECULAR MEDICINE
(2021)
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
Physiology
Nirvan Rouzbeh, Andrew R. Rau, Avery J. Benton, Feng Yi, Carly M. Anderson, Mia R. Johns, Loren Jensen, James S. Lotti, David C. Holley, Kasper B. Hansen
Summary: NMDA-type ionotropic glutamate receptors play important roles in brain function and CNS disorders. The mechanism by which GluN1-selective competitive antagonists potentiate GluN1/3 receptors and the allosteric interactions in these receptors were explored. The study revealed that CGP-78608 and L-689,560 prevent desensitization of GluN1/3 receptors, but CGP-78608-bound receptors display higher glycine potency at GluN3 subunits. Molecular dynamics simulations suggested that the conformation of GluN1 ABD influences agonist potency at GluN3 subunits. These findings provide insights into the activation mechanism of GluN1/3 receptors and its potential implications in brain function and disease.
JOURNAL OF GENERAL PHYSIOLOGY
(2023)
Article
Neurosciences
Irena Smaga, Karolina Wydra, Agata Suder, Malgorzata Frankowska, Marek Sanak, Lucia Caffino, Fabio Fumagalli, Malgorzata Filip
Summary: This study found changes in NMDA receptor subunit levels following cocaine abstinence with extinction training, particularly an increase in GluN2A subunit levels in the postsynaptic density fraction, without changing the expression of Grin1 and Grin2A genes in related brain structures. The modulation of NMDA receptor subunits observed after cocaine abstinence with extinction training may be a potential target for cocaine-seeking behavior.
NEUROTOXICITY RESEARCH
(2021)
Review
Engineering, Multidisciplinary
Yonglin Liu, Tianyuan Bian, Yan Liu, Zhimin Li, Yufeng Pei, Jie Song
Summary: DNA is not only a carrier of genetic information, but also a programmable and self-assembled nanomaterial. Different DNA structures are closely related to their biological and chemical functions. Single-molecule methods provide a powerful tool for studying the behavior and heterogeneity of individual DNA molecules. This review discusses the application of single-molecule methods in measuring the properties of DNA structures, including single-stranded/double-stranded DNA, DNA higher-order structures, and DNA nanostructures. The combination of DNA nanotechnology and single-molecule methods offers a new perspective for understanding the biophysical properties of DNA and other bio-matter and soft matter.
Article
Pharmacology & Pharmacy
Kai Langer, Adriana Mueller-Laengle, Jannik Wempe, Bodo Laube
Summary: Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels crucial for excitatory synaptic transmission in the central nervous system. Recent studies suggest that the architecture of all eukaryotic iGluRs may derive from a common prokaryotic ancestral receptor lacking M4. Deletions and mutations of M4 in NMDA receptor subfamily members affect receptor function, highlighting the importance of the evolutionarily newly evolved M4 for selective modulation of NMDARs.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Pharmacology & Pharmacy
Anna Pittaluga
Summary: This review summarizes the results from synaptosome studies over the past 40 years, supporting the existence of auto and hetero NMDA receptors controlling the release of transmitters in the CNS of mammals. Additionally, immunochemical studies in isolated nerve endings confirm these functional observations.
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Article
Chemistry, Physical
Flavia P. N. Inbanathan, Pawan Kumar, Kiran Dasari, Ram S. Katiyar, Jixin Chen, Wojciech M. Jadwisienczak
Summary: CdSe thin films were deposited on ITO glass substrates using PLD at different growth temperatures. AFM analysis showed an increase in surface roughness with deposition temperature, while optical constants and film thickness were obtained from ellipsometry analysis. The CdSe thin films had a band gap of approximately 1.71 eV and were suitable for photovoltaics with a refractive index of around 3.0 and extinction coefficient of around 1.0.
Article
Cell Biology
Lingyong Li, Shao-Rui Chen, Meng-Hua Zhou, Li Wang, De-Pei Li, Hong Chen, Garam Lee, Vasanthi Jayaraman, Hui-Lin Pan
Summary: The study reveals that nerve injury potentiates postsynaptic CP-AMPARs in the spinal dorsal horn via alpha 2 delta-1, which interacts with GluA1 and GluA2 to regulate the subunit composition and synaptic expression of AMPARs. Inhibition of alpha 2 delta-1 restores the intracellular assembly and synaptic dominance of heteromeric GluA1/GluA2 receptors, highlighting alpha 2 delta-1 as a key regulator of AMPAR function.
Editorial Material
Biophysics
Vasanthi Jayaraman
BIOPHYSICAL JOURNAL
(2022)
Article
Engineering, Electrical & Electronic
Juvinch R. Vicente, Wojciech M. Jadwisienczak, Savas Kaya, Jixin Chen
Summary: Photovoltaics based on lead halide perovskite (LHP) materials have gained interest for their high conversion efficiency and low cost. However, current fabrication methods require inert environments. This study investigates the effect of lead source and device architecture on the quality of LHP films prepared under ambient conditions. Results show that LHP prepared from PbI2 has poor material morphology, while LHP prepared from PbCl2 and PbAc2 on a mesoporous TiO2 scaffold show superior quality. A full perovskite solar cell with over 8.0% PCE is fabricated using an ambient-compatible hole transport layer.
JOURNAL OF ELECTRONIC MATERIALS
(2022)
Article
Nanoscience & Nanotechnology
Jixin Chen
Summary: This report uses Monte Carlo simulations to investigate the connection between stochastic single-molecule and ensemble surface adsorption of molecules from dilute solutions. It identifies discrepancies between simulation results and traditional methods, and proposes a way to correct the results. Simulations of self-assembled monolayers (SAM) and biosensing systems show different levels of accuracy in the adsorption rates, depending on the conditions and uncertainties.
Article
Chemistry, Applied
Juvinch R. Vicente, Martin E. Kordesch, Jixin Chen
Summary: This study demonstrates the stabilization of mixed-halide lead perovskites (MHLPs) photoluminescence peak through photothermal heating, providing a potential approach to obtain MHLP with stable emission peaks under operating conditions.
JOURNAL OF ENERGY CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kelle D. Hart, Chelsea Thompson, Clay Burger, Dylan Hardwick, Amanda H. Michaud, Abdul H. M. Al Bulushi, Cole Pridemore, Carson Ward, Jixin Chen
Summary: The COVID-19 pandemic has led to the online transition of laboratory courses, allowing students to remotely analyze data and apply kinetic techniques to successfully solve real-world problems.
Article
Chemistry, Physical
Annik Bernhardt, Tharushi D. Ambagaspitiya, Martin E. Kordesch, Katherine Leslee A. Cimatu, Jixin Chen
Summary: Methylammonium lead iodide bromides are a class of mixed halide lead perovskite materials with tunable bandgap and high-power conversion efficiencies. However, their use in solar cells is limited due to factors such as phase segregation and complex kinetics.
Article
Chemistry, Multidisciplinary
Dylan K. Smith, Kristin Lauro, Dymond Kelly, Joel Fish, Emma Lintelman, David McEwen, Corrin Smith, Max Stecz, Tharushi D. Ambagaspitiya, Jixin Chen
Summary: This report describes a physical chemistry lab for undergraduate students that involves applying kinetic models to analyze the spread of COVID-19 in the United States and obtain reproduction numbers. The lab explains the SIR and SIRV models and uses them to analyze COVID-19 spread data from the CDC. By fitting the data with the models, the lab extracts the basic reproduction number R0 and real-time reproduction number Rt of COVID-19, providing insights into spreading kinetics and predicting trends. The lab also demonstrates the differences between the SIR and SIRV models, with the latter considering vaccination effects and explaining the later stages of the pandemic.
JOURNAL OF CHEMICAL EDUCATION
(2022)
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
Chemistry, Physical
Jixin Chen
Summary: Predicting reaction kinetics is crucial for many processes, and the collision theory is commonly used. However, for reactions in diluted gas or liquid solutions, diffusion is important. This report presents a different collision model derived from molecular adsorption and reveals a surprising result of fractal reaction kinetics.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Multidisciplinary Sciences
Xiaolong Gao, Philipp A. M. Schmidpeter, Vladimir Berka, Ryan J. Durham, Chen Fan, Vasanthi Jayaraman, Crina M. Nimigean
Summary: This study reveals the importance of visualizing conformational changes and voltage sensor movements during ion channel gating. Multiple gating intermediates and subtle voltage sensor movements were captured in a CNG channel, providing insights into the regulation of ion channels. The ligand-gating trajectory of SthK was defined, showing allosteric couplings between voltage sensor, cyclic nucleotide-binding, and pore domains. The findings shed light on the physiological roles of ion channels and their potential as therapeutic targets in pathophysiological conditions.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Dinesh Gautam, Srijana Pandey, Jixin Chen
Summary: Single-molecule DNA studies have enhanced our understanding of DNA structure and its interactions with other molecules. YOYO-1 and YO-PRO-1, which are highly-affine and bright DNA labeling dyes, were investigated for their behavior in DNA molecules under high ionic strength and strong buffer flow. It was found that higher flow rate and ionic strength resulted in faster washing away of the intercalated dyes from the DNAs, with YOYO-1 and YO-PRO-1 mostly being washed away within 2 minutes in a buffer with 1 M ionic strength.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Nabina Paudyal, Anindita Das, Elisa Carrillo, Vladimir Berka, Vasanthi Jayaraman
Summary: In this study, the mechanism of partial agonism in heteromeric GluK2/K5 receptors was investigated. It was found that the partial agonist AMPA-bound receptor occupied intermediate cleft closure conformational states at the GluK2 cleft, while in the full agonist glutamate-bound form, more open cleft conformations were observed. There was no significant difference in cleft closure states at the GluK5 agonist-binding domain between the partial agonist AMPA- and full agonist glutamate-bound states. Our findings suggest that partial agonism observed with AMPA binding is primarily mediated by differences in the GluK2 subunit.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Meeting Abstract
Biophysics
Elisa Carrillo, Cuauhtemoc U. Gonzalez, Vasanthi Jayaraman
BIOPHYSICAL JOURNAL
(2023)