Article
Chemistry, Inorganic & Nuclear
Leonardo Querci, Ines B. Trindade, Michele Invernici, Jose Malanho Silva, Francesca Cantini, Ricardo O. Louro, Mario Piccioli
Summary: In paramagnetic metalloproteins, C-13 ' and C-13(alpha) nuclei can be measured to obtain electron spin-nuclear spin distance restraints. These C-13 based restraints provide additional structural information that is not redundant with the more commonly used H-1 nuclei. This study demonstrates the complementarity of C-13 PRE restraints with H-1 PRE restraints, showing that C-13 R-1 values can be measured at short distances from the paramagnetic center and can be combined with other NMR restraints to improve the quality and quantity of the NMR information.
Article
Biochemistry & Molecular Biology
Ines B. Trindade, Michele Invernici, Francesca Cantini, Ricardo O. Louro, Mario Piccioli
Summary: Metalloproteins play vital roles in biology, and understanding their structure is crucial. A study utilized NMR to determine protein structure, finding that under favorable conditions, Paramagnetic Relaxation Enhancements (PREs) can efficiently complement and eventually replace Nuclear Overhauser Enhancements (NOEs) for structural characterization of small paramagnetic metalloproteins or de novo-designed metalloproteins.
Article
Multidisciplinary Sciences
Yuki Toyama, Atul Kaushik Rangadurai, Julie D. Forman-Kay, Lewis E. Kay
Summary: Electrostatic interactions and charge balance play important roles in the formation of biomolecular condensates. Using NMR spectroscopy, researchers measured the near-surface electrostatic potentials of CAPRIN1 and found that the addition of ATP changes the charge distribution and affects the protein's phase separation process. At high ATP concentrations, the electrostatic potential of CAPRIN1 is inverted, leading to re-entrance into a mixed phase.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Chandrashekhar Honrao, Nathalie Teissier, Bo Zhang, Robert Powers, Elizabeth M. O'Day
Summary: The addition of a gadolinium-based PRE agent can enhance the sensitivity of NMR spectral data, improve the detection of a wide range of metabolites, and increase the repeatability of intensity measurements in metabolomics samples.
Article
Chemistry, Multidisciplinary
Johannes Zehnder, Riccardo Cadalbert, Laurent Terradot, Matthias Ernst, Anja Boeckmann, Peter Guentert, Beat H. Meier, Thomas Wiegand
Summary: The study utilizes solid-state NMR and a structure-calculation protocol to determine the position of metal ions in the bacterial DnaB helicase from Helicobacter pylori complexed with ATP-analogue ADP:AlF4- and single-stranded DNA. The use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies is discussed and compared. P-31 PCSs induced in the Co2+-containing sample are then used to localize DNA phosphate groups and provide structural insights into DNA binding to the DnaB helicase.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Vlastimil Jirasko, Alons Lends, Nils-Alexander Lakomek, Marie-Laure Fogeron, Marco E. Weber, Alexander A. Malar, Susanne Penzel, Ralf Bartenschlager, Beat H. Meier, Anja Bockmann
Summary: NS5A, a membrane-associated protein involved in the life cycle of Hepatitis C virus, exhibits high flexibility in a lipidic environment, and organization of dimers in lipids requires a novel type of self-interaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Jonas C. Ott, Elizaveta A. Suturina, Ilya Kuprov, Joscha Nehrkorn, Alexander Schnegg, Markus Enders, Lutz H. Gade
Summary: In this study, experimental observations of P-31 and H-1 NMR resonances shifted by over 10 000 ppm in a square planar ferrous complex were reported. The influence of magnetic anisotropy and zero-field splitting on paramagnetic shift and relaxation enhancement was investigated using various techniques, and spin dynamics simulations showed the possibility of observing NMR signals of directly metal-bonded atoms even with relatively slow electron spin relaxation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Wenkai Zhu, Alex J. Guseman, Fatema Bhinderwala, Manman Lu, Xun-Cheng Su, Angela M. Gronenborn
Summary: In-cell NMR spectroscopy is a powerful tool for studying protein behavior in physiological environments. However, interactions with cellular components can often broaden resonances beyond detection in commonly used H-1-N-15 HSQC spectra of globular proteins. In contrast, F-19 spectra in mammalian cells readily show signals. By using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, F-19 paramagnetic relaxation enhancements provide an effective method for accurately assessing protein conformations in cellular milieu.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Andrew J. Pell
Summary: This paper discusses the paramagnetic shift in nuclear magnetic resonance (NMR) and shows that traditional Redfield theory fails to predict it, while the recently-introduced Lindbladian theory can accurately do so, applicable to dynamic nuclear polarization and beyond. The formalism is tested through simulations of various case studies, proving its effectiveness in predicting paramagnetic shifts and relaxation-induced linewidths in pNMR.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Biophysics
Frank Heinrich, Que N. Van, Frantz Jean-Francois, Andrew G. Stephen, Mathias Loesche
Summary: Research findings show that KRAS4B approximates an entropic ensemble of configurations in specific membrane environments, with interactions between the protein and lipid membrane having minimal impact on its shape. This challenges previous understanding of KRAS signaling and proposes a new model where the protein samples in a uniform manner and binds to effector proteins.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Sergio Rampino, Mirco Zerbetto, Antonino Polimeno
Summary: Stochastic modeling approaches can help interpret complex molecular dynamical behaviors in solution and extract structural and dynamical data from spectroscopic observables. In this paper, the authors propose a diffusive framework based on a systematic approach to construct stochastic models, and demonstrate the usefulness of a scaled diffusion tensor as an efficient gauge of molecular flexibility.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Biochemistry & Molecular Biology
Vitaly Volkov, Alexander Chernyak, Nikita A. Slesarenko, Irina A. Avilova
Summary: This review focuses on the progress of solvation and mobility studies in solid electrolyte, particularly ion-exchange membranes and composite materials, using NMR techniques. The applications of various NMR techniques are discussed, and comparisons are made between diffusion coefficients and ionic conductivity data. The microscopic mechanism of ionic transfer is also explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Physics, Multidisciplinary
William Beatrez, Otto Janes, Amala Akkiraju, Arjun Pillai, Alexander Oddo, Paul Reshetikhin, Emanuel Druga, Maxwell McAllister, Mark Elo, Benjamin Gilbert, Dieter Suter, Ashok Ajoy
Summary: This study reported the observation of long-lived Floquet prethermal states in a bulk solid composed of C-13 nuclei in diamond at room temperature, demonstrating the potential for quantum sensors constructed from hyperpolarized Floquet prethermal nuclei. The combination of continuous spin interrogation and hyperpolarization provides significant signal-to-noise ratio for clear detection of thermalization dynamics in the system.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemical Research Methods
Johannes Zehnder, Riccardo Cadalbert, Maxim Yulikov, Georg Kuenze, Thomas Wiegand
Summary: Labeling biomolecules with a paramagnetic probe for NMR spectroscopy allows determining long-range distance restraints, aiding in the structure determination of large proteins and protein complexes. The success of site-directed labeling of bacterial DnaB helicase with maleimide tags was confirmed through EPR experiments, leading to the extraction of site-specific PREs for further characterization. Comparison of experimental PREs and computational modeling of nitroxide and Gd3+ tags revealed differences in the blind sphere size around the paramagnetic center.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Chemistry, Multidisciplinary
Alejandro Bara-Estaun, Marie C. Harder, Catherine L. Lyall, John P. Lowe, Elizaveta Suturina, Ulrich Hintermair
Summary: Sensitivity in FlowNMR spectroscopy can be limited by low levels of pre-magnetisation, especially for low sensitivity nuclei at low concentrations. The use of paramagnetic relaxation agents (PRAs) can enhance polarisation and spin-lattice relaxation, mitigating the in-flow effect and improving the signal-to-noise ratio.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Rong Han, Yufei Yang, Shenlin Wang
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Biochemical Research Methods
Sergey Milikisiyants, Maxim A. Voinov, Antonin Marek, Morteza Jafarabadi, Jing Liu, Rong Han, Shenlin Wang, Alex I. Smirnov
JOURNAL OF MAGNETIC RESONANCE
(2019)
Article
Multidisciplinary Sciences
Florian Hamann, Andreas Schmitt, Filippo Favretto, Romina Hofele, Piotr Neumann, ShengQi Xiang, Henning Urlaub, Markus Zweckstetter, Ralf Ficner
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Yanzhang Luo, ShengQi Xiang, Peter Jan Hooikaas, Laura van Bezouwen, A. S. Jijumon, Carsten Janke, Friedrich Forster, Anna Akhmanova, Marc Baldus
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Nan Zhang, Jing Liu, Yajie Liu, Wenhao Wu, Jing Fang, Xiao-Di Da, Shenlin Wang, Wen-Bin Zhang
Article
Biochemistry & Molecular Biology
Xiaoli Zhao, Jenny (Jingxin) Tian, Hua Yu, Brian C. Bryksa, John H. Dupuis, Xiuyuan Ou, Zhaohui Qian, Chen Song, Shenlin Wang, Rickey Y. Yada
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Cell Biology
Hongchen Zhang, Shipeng Shao, Yong Zeng, Xiaotian Wang, Yizhi Qin, Qiunan Ren, Shengqi Xiang, Yuxin Wang, Junyu Xiao, Yujie Sun
Summary: This study reveals the mechanism by which heat-shock transcription factor 1 (HSF1) regulates transcriptional reprogramming through phase separation, enabling cells to quickly respond to heat shock. The study also demonstrates that heat-shock protein 70 (HSP70) disperses HSF1 condensates to regulate transcription.
NATURE CELL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
ShengQi Xiang, Cecilia Pinto, Marc Baldus
Summary: Membrane proteins play important biological roles by forming complexes in cell membranes. This study focuses on understanding the role of the lipoprotein BamC in the assembly of the beta-barrel assembly machinery (BAM) complex in lipid bilayers. By developing a selective preparation scheme and using proton-detected solid-state NMR methods, the researchers were able to investigate the structure and dynamics of BamC embedded in the entire BAM complex in lipid bilayers. This approach provides insights into the formation and functioning of membrane protein complexes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Sha Zhao, Xinming Li, Ziyang Wen, Mengbing Zou, Ge Yu, Xiangyang Liu, Jiafei Mao, Lixin Zhang, Yi Xue, Riqiang Fu, Shenlin Wang
Summary: Base pairs are essential units in RNA and their stability plays a crucial role in RNA functions. A solid-state NMR-based water-RNA exchange spectroscopy technique was developed to evaluate base pair stability. By applying this technique to a specific RNA complex, it was found that the U47.U51 base pair has low stability, indicating its involvement in the early stage of ligand release.
Article
Cell Biology
Xiaoyu Song, Fengrui Yang, Tongtong Yang, Yong Wang, Mingrui Ding, Linge Li, Panpan Xu, Shuaiyu Liu, Ming Dai, Changbiao Chi, Shengqi Xiang, Chao Xu, Dong Li, Zhikai Wang, Lin Li, Donald L. Hill, Chuanhai Fu, Kai Yuan, Pilong Li, Jianye Zang, Zhonghuai Hou, Kai Jiang, Yunyu Shi, Xing Liu, Xuebiao Yao
Summary: EB1 proteins form molecular condensates through liquid-liquid phase separation (LLPS) to constitute the microtubule plus-end machinery, which is crucial for cellular dynamics and organelle movements.
NATURE CELL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Shengnan Zhang, Juan Li, Qianhui Xu, Wencheng Xia, Youqi Tao, Chaowei Shi, Dan Li, ShengQi Xiang, Cong Liu
Summary: Many amyloid fibrils associated with neurodegenerative diseases consist of an ordered fibril core and disordered terminal regions. In this study, we used solid-state NMR and cryo-EM techniques to explore the intact structure of an alpha-syn fibril and studied its conformational dynamics upon binding to the LAG3 receptor. Our findings reveal the synergistic conformational transition of the intrinsically disordered terminal regions of alpha-syn, shedding light on the role of these regions in regulating amyloid fibril structure and pathology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Medicine, Research & Experimental
Mengzhen Jiang, Man Liu, Guodi Liu, Jiawen Ma, Lixin Zhang, Shenlin Wang
Summary: Antibody-based immune checkpoint blockade (ICB) is an effective clinical application for cancers. It can reverse the phenotype of depleted activated T cells and recover their anti-tumoral activities. High-resolution structures of the therapeutic monoclonal antibodies with PD-1 or PD-L1 have revealed the key inter-molecular interactions and provided valuable insights into the fundamental mechanisms by which these antibodies inhibit PD-L1-PD-1 binding.
Review
Biochemistry & Molecular Biology
Xiaole Liu, Xinyue Zhao, Jinhan He, Sishi Wang, Xinfei Shen, Qingfeng Liu, Shenlin Wang
Summary: This passage summarizes that the abnormal expansion of GGGGCC hexanucleotide repeats in the C9orf72 gene intron is the main genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). The transcribed r(GGGGCC)(n) RNA repeats form RNA foci, interfere with RNA binding proteins, and ultimately lead to fatal neurodegenerative disorders. The structural diversity of r(GGGGCC)(n) and its interactions with small molecules and proteins are emphasized, in order to facilitate the development of therapeutic interventions targeting r(GGGGCC)(n) RNA.
Article
Chemistry, Multidisciplinary
Sha Zhao, Yufei Yang, Yujie Zhao, Xinming Li, Yi Xue, Shenlin Wang
CHEMICAL COMMUNICATIONS
(2019)
Article
Materials Science, Biomaterials
Xiuxia Sun, Zhao Liu, Sha Zhao, Xiaojun Xu, Shenlin Wang, Chengchen Guo, Jianxi Xiao
JOURNAL OF MATERIALS CHEMISTRY B
(2019)