Article
Biochemistry & Molecular Biology
Szymon Radzin, Anna Wisniewska-Becker, Michal Markiewicz, Sebastian Betkowski, Justyna Furso, Joanna Waresiak, Jaroslaw Grolik, Tadeusz Sarna, Anna M. Pawlak
Summary: Photoreceptor membranes have a unique lipid composition, with high levels of polyunsaturated fatty acids and phosphatidylethanolamines. These membranes are sensitive to oxidative stress and lipid peroxidation due to their high degree of lipid unsaturation, extended exposure to intensive irradiation, and high respiratory demands.
Article
Chemistry, Physical
Nir Dayan, Yaron Artzi, Moamen Jbara, David Cristea, Aharon Blank
Summary: Nuclear magnetic resonance (NMR) spectroscopy provides atomic-level molecular structural information. However, in molecules containing unpaired electron spins, direct measurement of NMR signals is difficult. In this study, we demonstrate the use of miniature microwave resonators and miniature NMR coils to excite and detect a wide bandwidth of electron-nuclear double resonance (ENDOR) data in a single pulse. This approach improves spectral resolution and allows for the measurement of ENDOR spectra with narrow lines spread over a large frequency range, revealing previously inaccessible details of the paramagnetic molecules' chemical structure.
Article
Chemistry, Analytical
Hideo Utsumi, Toshiki Masumizu, Ryoma Kobayashi, Tomoko Tahira, Fuminori Hyodo, Tatsuya Shimizu, Tatsuya Naganuma, Kazunori Anzai
Summary: Free radicals are key substances in organisms but can also cause oxidative diseases. Dynamic nuclear polarization- magnetic resonance imaging is a noninvasive imaging method that can be used for in vivo free radical imaging.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Toshinobu Nakajo, Jun Kumagai, Shinpei Kusaka, Akihiro Hori, Yuh Hijikata, Jenny Pirillo, Yunsheng Ma, Ryotaro Matsuda
Summary: Triplet carbenes (TCs) are highly reactive species with unique electronic states, making it challenging to balance reactivity and stability. By confining TCs in the nanospace of a metal-organic framework (MOF), it is possible to enhance their thermal stability while maintaining reactivity, allowing for the stabilization of highly reactive species.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Michal J. Sabat, Anna M. Wisniewska-Becker, Michal Markiewicz, Katarzyna M. Marzec, Jakub Dybas, Justyna Furso, Pawel Pabisz, Mariusz Duda, Anna M. Pawlak
Summary: TUDCA is a hydrophilic bile acid that has been used as a therapeutic compound in traditional Chinese medicine. It has gained interest as a neuroprotective agent and has antioxidant activity, as well as stabilizing effects on mitochondrial and plasma membranes. Additionally, TUDCA induces slight changes in the polarity and fluidity of model membranes.
Review
Crystallography
Valentin G. Grachev, Galina Malovichko
Summary: Intrinsic and extrinsic defects, especially paramagnetic ions of transition metals and rare-earth elements, have a significant impact on the properties of lithium niobate (LN) and tantalate (LT), determining their suitability for various applications. Discussions on the structures of defects in LN/LT have been ongoing for decades, with experimental methods facilitating progress in determining the structures of impurity centers. Symmetry and charge compensation considerations restrict the number of possible structures, and comparison of measured angular dependences of ENDOR frequencies with calculated ones allows for the accurate determination of the exact location of paramagnetic impurities. Self-compensation of excessive charges in stoichiometric LN/LT leads to the appearance of interstitial Li+ in the structural vacancy near paramagnetic ions Me3+(Nb5+).
Article
Chemistry, Inorganic & Nuclear
Anthony J. Campanella, Manh-Thuong Nguyen, Jun Zhang, Thacien Ngendahimana, William E. Antholine, Gareth R. Eaton, Sandra S. Eaton, Vassiliki-Alexandra Glezakou, Joseph M. Zadrozny
Summary: This work investigates how variations in ligand structures affect the EPR spectroscopic properties of five Cr(III) complexes, indicating that the spectral broadening is correlated to rigidity in the inner coordination sphere and reflected in ligand-dependent distribution of Cr-N bond distances.
DALTON TRANSACTIONS
(2021)
Article
Chemistry, Multidisciplinary
Kin Kuan Hoi, Juan Francisco Bada Juarez, Peter J. Judge, Hsin-Yung Yen, Di Wu, Javier Vinals, Garrick F. Taylor, Anthony Watts, Carol Robinson
Summary: The study used native MS to investigate the spectra of membrane proteins in different membrane mimetics, revealing that SMA may favor selective solubilization of correctly folded proteins. The results provide insights into the correlation between PTMs, lipid interactions, and protein folding states.
Article
Multidisciplinary Sciences
Jessica E. Besaw, Jorg Reichenwallner, Paolo De Guzman, Andrejs Tucs, Anling Kuo, Takefumi Morizumi, Koji Tsuda, Adnan Sljoka, R. J. Dwayne Miller, Oliver P. Ernst
Summary: In this study, the crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) was determined under low pH conditions. The structure revealed the accommodation of a chloride anion in the hydrophilic Schiff base cavity (SBC), stabilizing the protonated retinal Schiff base. Computational studies further supported an intramolecular signaling transduction pathway, with allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space. These findings suggest the potential sensory role of TaHeR as a rhodopsin.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Juvinch R. Vicente, Amanda Durkin, Kristina Shrestha, Mihaela Balu
Summary: Melanin plays a significant role in skin homeostasis and protection. The two-photon excited fluorescence lifetime detection method allows for selective and quantitative measurement of melanin. Previous studies lacked consideration of skin heterogeneity due to limited field of view. In this work, a fast large-area multiphoton exoscope was used to evaluate the 3D distribution of epidermal melanin content, improving measurement reliability.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Peng Huang, Manju Sheokand, David Payno Zarceno, Samrana Kazim, Luis Lezama, Mohammad Khaja Nazeeruddin, Rajneesh Misra, Shahzada Ahmad
Summary: To solve the toxicity issues related to lead-based halide perovskite solar cells, a lead-free double halide perovskite Cs2AgBiBr6 is proposed. However, the reduced rate of charge transfer affects the optoelectronic performance of double perovskites. By using interface engineering, a series of pyridine-based small molecules with different arms attached to the pyridine core are designed as hole-selective materials. The solar cells fabricated using Cs2AgBiBr6 as a light harvester and the designed hole-selective layer showed an unprecedented 2.9% power conversion efficiency. Our findings provide guidance for designing small molecules for electro-optical applications and developing lead-free perovskite materials for solar applications.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
S. A. Rodriguez, S. S. Gomez, J. Fernandez-Rossier, A. Ferron
Summary: Electron-spin resonance carried out with scanning tunneling microscopes (ESR-STM) is a recently developed experimental technique that is attracting enormous interest on account of its potential to carry out single-spin on-surface resonance with subatomic resolution. In this theoretical study, we investigate the role of tip-adatom interactions in order to optimize spin resonance measurements. We provide guidelines for optimizing the tip-sample distance to cancel the effective magnetic field created by the tip on the surface spin, for reducing the voltage dependence of the surface-spin resonance frequency, and for inferring the detuning angle between the applied field and the tip magnetization.
Article
Physics, Applied
T. D. Gustafson, N. C. Giles, B. C. Holloway, C. A. Lenyk, J. Jesenovec, J. S. McCloy, M. D. McCluskey, L. E. Halliburton
Summary: In this study, electron paramagnetic resonance (EPR) and optical absorption were used to characterize Cu2+ and Cu3+ ions in Cu-doped beta-Ga2O3. Different EPR spectra and optical absorption bands were observed for Cu2+ and Cu3+ ions. The results showed that Cu2+(A) ions occupy defect-free octahedral Ga sites, while Cu2+(B) ions have adjacent defects, possibly OH- ions, oxygen vacancies, or H- ions trapped within oxygen vacancies. Additionally, exposure of the crystals to 275 nm light at room temperature produced Cu3+ ions and reduced the number of Cu2+(A) and Cu2+(B) ions. Thermal annealing studies showed that Cu3+ ions decay, and Cu2+ ions recover.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Ameen Uddin Ammar, Ipek Deniz Yildirim, Mohamad Hasan Aleinawi, Merve Buldu-Akturk, Nur Selin Turhan, Shankari Nadupalli, Arpad Mihai Rostas, Emre Erdem
Summary: The doping of Mn, Fe, and Cu ions into ZnO nanocrystals adds magnetic phenomena to their semiconducting property. However, there is a lack of research on the local lattice structure, spin-exchange phenomena, and interaction between defects and doped metal ions in TM ion-doped ZnO. This study uses multi-frequency (EPR) techniques to investigate ZnO:TM, revealing the localization of the dopant ion, site symmetry, and the formation of intrinsic-extrinsic defect complexes. The incorporation of TM ions modifies the intrinsic defect structure of ZnO nanocrystals, with the appearance of peculiar spin-exchange phenomena from intrinsic-extrinsic defect complexes, and charge selective substitutions in the matrix are observed for Cu2+ compared to Mn2+ and Fe3+.
MATERIALS RESEARCH BULLETIN
(2023)
Article
Chemistry, Multidisciplinary
Santina S. Cruz, Vadim Tanygin, Benjamin J. Lear
Summary: Using electron spin resonance spectroscopy, it has been demonstrated that morphological asymmetries in small spheroidal metallic nanoparticles significantly affect the electronic behavior of states near the metal's Fermi energy. The study found that morphological effects were more important than size distributions in explaining the asymmetry in electronic behavior, and this was consistent across various particles made from different metals. Additionally, the study also showed that morphological changes can tune the electronic properties of even small particles, as evidenced by the modeling used to explain asymmetries in both electron spin resonance spectra and plasmon spectra.
Article
Physics, Atomic, Molecular & Chemical
Hannah Russell, Rachel Stewart, Christopher Prior, Vasily S. Oganesyan, Thembaninkosi G. Gaule, Janet E. Lovett
Summary: PDS techniques such as DEER and RIDME were used to measure spin-spin distances in the copper amine oxidase, revealing two distinct distances with the longer one around 5 nm, where RIDME showed potential superiority over DEER. Modeling methods demonstrated the consistency of the obtained distances with the AGAO structure after data analysis.
APPLIED MAGNETIC RESONANCE
(2021)
Article
Microbiology
Sofia Banchenko, Ferdinand Krupp, Christine Gotthold, Joerg Buerger, Andrea Graziadei, Francis J. O'Reilly, Ludwig Sinn, Olga Ruda, Juri Rappsilber, Christian M. T. Spahn, Thorsten Mielke, Ian A. Taylor, David Schwefel
Summary: Viruses rely on host cell components for replication, with certain viral factors altering the specificity of host ubiquitin ligases to down-regulate antiviral factors. Studies have shown how viruses exploit the dynamic assembly of the CRL4(DCAF1) complex to optimize SAMHD1 ubiquitylation.
Article
Chemistry, Multidisciplinary
Matthieu Starck, Jack D. Fradgley, Davide F. De Rosa, Andrei S. Batsanov, Maria Papa, Michael J. Taylor, Janet E. Lovett, Jacob C. Lutter, Matthew J. Allen, David Parker
Summary: A series of cationic and neutral p-Br and p-NO2 pyridine substituted Eu(III) and Gd(III) coordination complexes serve as versatile synthetic intermediates. The introduction of various substituents is made possible through nucleophilic aromatic substitution reactions, leading to the tuning of absorption and emission spectral properties in Eu(III) complexes. The p-substituent in Gd(III) complexes does not significantly affect EPR properties, making them suitable as EPR spin probes for biomolecules.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Andrea Graziadei, Juri Rappsilber
Summary: Crosslinking mass spectrometry is a versatile tool that provides structural insights into protein conformation and protein-protein interactions. It has been used for protein structure validation and integrative modeling, and complements the resolution revolution in electron microscopy. Its flexibility and high-throughput nature make it valuable in protein research.
Article
Biochemical Research Methods
Jake Keeley, Tajwar Choudhury, Laura Galazzo, Enrica Bordignon, Akiva Feintuch, Daniella Goldfarb, Hannah Russell, Michael J. Taylor, Janet E. Lovett, Andrea Eggeling, Luis Fabregas Ibanez, Katharina Kelle, Maxim Yulikov, Gunnar Jeschke, Ilya Kuprov
Summary: This paper is a methodological guide to using deep neural networks for processing pulsed dipolar spectroscopy (PDS) data in various fields such as structural biology, organic photovoltaics, and photosynthesis research. The paper discusses the advantages and challenges of neural networks in handling this type of data, including training against simulated databases, network architecture choices, options for handling specific experiment types, and providing a practical data processing flowchart.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Biochemistry & Molecular Biology
Hannah Russell, Robyn Cura, Janet E. Lovett
Summary: This study compares and reviews six software packages for analyzing DEER data to extract distance distributions, providing a brief getting started guide for each.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Andrew M. Stewart, Muralidharan Shanmugam, Roger J. Kutta, Nigel S. Scrutton, Janet E. Lovett, Sam Hay
Summary: This study investigates the conformational changes of calmodulin (CaM) using PELDOR measurements. The results support a three-state conformational model of CaM, including an open apo-state, an extended Ca2+-replete state, and a compact target protein-bound state. Molecular dynamics simulations suggest that the presence of molecular crowding agents affects the stability of different conformational states.
Article
Chemistry, Multidisciplinary
Shiny Maity, Brad D. D. Price, C. Blake Wilson, Arnab Mukherjee, Matthieu Starck, David Parker, Maxwell Z. Z. Wilson, Janet E. E. Lovett, Songi Han, Mark S. S. Sherwin
Summary: We propose a time-resolved Gd-Gd electron paramagnetic resonance (TiGGER) technique at 240 GHz to monitor inter-residue distances in proteins' mechanical cycles in solution state. TiGGER utilizes Gd-sTPATCN spin labels with favorable properties, including spin-7/2 EPR-active center, short linker, narrow intrinsic linewidth, and minimal anisotropy at high fields. By applying TiGGER, we observed that the C-terminus and N-terminus of AsLOV2 separate within 1 s upon light activation and relax back to equilibrium with a time constant of approximately 60 s. TiGGER also revealed that the light-induced long-range mechanical motion is decelerated in the Q513A variant of AsLOV2, which is correlated with the slowed relaxation of the optically excited chromophore as reported in recent literature. TiGGER has the potential to complement existing methods for studying triggered functional dynamics in proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Marcin Jaciuk, David Scherf, Karol Kaszuba, Monika Gaik, Alexander Rau, Anna Koscielniak, Roscislaw Krutyholowa, Michal Rawski, Paulina Indyka, Andrea Graziadei, Andrzej Chramiec-Glabik, Anna Biela, Dominika Dobosz, Ting-Yu Lin, Nour-el-Hana Abbassi, Alexander Hammermeister, Juri Rappsilber, Jan Kosinski, Raffael Schaffrath, Sebastian Glatt
Summary: The Elongator complex is responsible for modifying tRNAs in eukaryotes by adding a carboxymethyl group to wobble uridines. This modification is crucial for maintaining cellular proteome integrity and protecting against neurodegenerative diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Vu Thuy Khanh Le-Trilling, Sofia Banchenko, Darius Paydar, Pia Madeleine Leipe, Lukas Binting, Simon Lauer, Andrea Graziadei, Robin Klingen, Christine Gotthold, Joerg Buerger, Thilo Bracht, Barbara Sitek, Robert Jan Lebbink, Anna Malyshkina, Thorsten Mielke, Juri Rappsilber, Christian M. T. Spahn, Sebastian Voigt, Mirko Trilling, David Schwefel
Summary: This study revealed that rat cytomegalovirus infection induces the loss of transcription factor STAT2, which is crucial for antiviral interferon signaling. It was found that viral protein E27 exploits the host-cell CRL4 complexes to degrade STAT2 through poly-ubiquitylation. Furthermore, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, partially overlapping with the IRF9 binding site.
Article
Biochemistry & Molecular Biology
Francis J. O'Reilly, Andrea Graziadei, Christian Forbrig, Rica Bremenkamp, Kristine Charles, Swantje Lenz, Christoph Elfmann, Lutz Fischer, Joerg Stuelke, Juri Rappsilber
Summary: Accurately modeling protein structures and their complexes using AI is revolutionizing molecular biology. In this study, we used a combination of crosslinking mass spectrometry and CoFrac-MS to identify protein-protein interactions in a Gram-positive bacterium. By predicting the structures of these interactions and validating them with crosslinking MS data, we proposed novel structural models of protein assemblies and identified new interactors of important cellular machineries. This approach provides insights into protein-protein interactions inside intact cells and is applicable to genetically intractable organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Kolja Stahl, Andrea Graziadei, Therese Dau, Oliver Brock, Juri Rappsilber
Summary: Limitations of Alphafold2 structure prediction are overcome by incorporating experimentally determined distance constraints using AlphaLink. This modified version improves prediction for challenging targets by utilizing sparse experimental contacts and can predict distinct protein conformations. Experimental data on residue-residue contacts obtained through crosslinking mass spectrometry validates the improved performance. The noise-tolerant framework for integrating data allows accurate characterization of protein structures from in-cell data.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mateusz P. P. Sowinski, Sahil Gahlawat, Bjarte A. A. Lund, Anna-Luisa Warnke, Kathrin H. H. Hopmann, Janet E. E. Lovett, Marius M. M. Haugland
Summary: This study presents a strategy for enhancing the stability of nitroxides under reducing conditions. By incorporating additional substituents on the nitroxide ring, the authors tuned the conformation of the spirocyclic nitroxide scaffold to a highly stable closed spirocyclic conformation. The closed spirocyclohexyl nitroxides showed significantly improved stability towards reduction and maintained long relaxation times in electron paramagnetic resonance spectroscopy.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Organic
Emmanouil Broumidis, Christopher G. Thomson, Brendan Gallagher, Lia Sotorrios, Kenneth G. Mckendrick, Stuart A. Macgregor, Martin J. Paterson, Janet E. Lovett, Gareth O. Lloyd, Georgina M. Rosair, Andreas S. Kalogirou, Panayiotis A. Koutentis, Filipe Vilela
Summary: This study discovered that 1,2,6-thiadiazines can be converted into 1,2,5-thiadiazole 1-oxides using visible light and oxygen under ambient conditions, which was previously difficult to achieve. Experimental and theoretical studies revealed that 1,2,6-thiadiazines act as triplet photosensitizers and undergo a selective cycloaddition reaction to form an endoperoxide.
Article
Multidisciplinary Sciences
Anokhi Shah, Michael J. Taylor, Giulia Molinaro, Sellamuthu Anbu, Margaux Verdu, Lucy Jennings, Iuliia Mikulska, Sofia Diaz-Moreno, Hassane EL Mkami, Graham M. Smith, Melanie M. Britton, Janet E. Lovett, Anna F. A. Peacock
Summary: We report the creation of a new copper-binding site within a protein scaffold, which shows promise as an MRI contrast agent despite the general belief that copper is unsuitable for this purpose. The copper coiled coil displays relaxivity values equal to or better than those of the Gd(III) analog, challenging the current consensus. This study demonstrates the power of de novo peptide design in accessing abiological chemistry for practical applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
