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.
Review
Biochemistry & Molecular Biology
Francesca Camponeschi, Mario Piccioli, Lucia Banci
Summary: Despite limited knowledge about the mechanism of mitoNEET protein, its link to cancer suggests that targeting mitoNEET and its Fe-S clusters could inhibit cancer cell proliferation. Spectroscopic techniques, such as NMR, have been used to study mitoNEET and understand the differences in cluster stability and reactivity, as well as its cellular function. NMR assignment and characterization of the first coordination sphere can aid in drug design to interfere with cellular processes or participate in redox reactions or protein-protein recognition mechanisms.
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
Deborah Grifagni, Jose M. Silva, Francesca Cantini, Mario Piccioli, Lucia Banci
Summary: CISD3 is a mitochondrial protein with two [Fe2S2] clusters coordinated by CDGSH domains, belonging to the NEET proteins family. While little is known about its structure-function relationships, NMR can provide atomic level information on intermolecular interactions in solution. However, paramagnetic proteins limit the application of this technique due to signal broadening. This study demonstrates how paramagnetic relaxation can assist in signal assignment and identifies potential key players in the biological function of CISD3 protein.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
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
Muralidharan Shanmugam, Mussa Quareshy, Alexander D. Cameron, Timothy D. H. Bugg, Yin Chen
Summary: The oxidation of quaternary ammonium substrate, carnitine, by non-heme iron-containing Acinetobacter baumannii (Ab) oxygenase CntA/reductase CntB is associated with cardiovascular disease. A study using blue-light activation of NADH coupled with EPR measurements revealed that electron transfer from NADH to the oxidized [2Fe-2S] cluster in AbCntA only occurs in the presence of carnitine. The AbCntA-E205A mutant showed severely affected electron transfer, leading to a significant loss of catalytic activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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.
Review
Plant Sciences
Tatiana Monaretto, Tiago Bueno Moraes, Luiz Alberto Colnago
Summary: Time domain nuclear magnetic resonance (TD-NMR) has been widely used in plant science to measure various relaxation times, suitable for laboratory, greenhouse, and field studies. New pulse sequences can measure transverse relaxation time more effectively, and enhance signal-to-noise ratio using continuous wave free precession mode to obtain different correlation maps.
Article
Biochemistry & Molecular Biology
Jing Du, Zhaoyang Huang, Yanchun Li, Xueying Ren, Chaoting Zhou, Ruolan Liu, Ping Zhang, Guojie Lei, Jianxin Lyu, Jianghui Li, Guoqiang Tan
Summary: Copper is a necessary mineral nutrient but excess copper is cytotoxic. Wilson's disease is an autosomal recessive hereditary disease characterized by pathological copper accumulation in organs. The molecular mechanism of Wilson's disease is not fully understood and further research is needed to develop therapeutic strategies.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Yuri Hamanaka, Akira Tanimura, Takafumi Yokota, Sachiko Ezoe, Michiko Ichii, Yasuhiro Nagate, Kenji Oritani, Yuzuru Kanakura, Naoki Hosen, Hirohiko Shibayama
Summary: Anamorsin (AM) is a cloned molecule that confers resistance against apoptosis induced by growth factor deprivation. Conditional knockout of AM in mice showed its important role in the generation of mature B cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Sara Matteucci, Francesca Camponeschi, Martin Clemancey, Simone Ciofi-Baffoni, Genevieve Blondin, Lucia Banci
Summary: Studies have shown that human anamorsin protein binds two [2Fe-2S] clusters at both its cysteine-rich motifs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Leonardo Querci, Deborah Grifagni, Ines B. Trindade, Jose Malanho Silva, Ricardo O. Louro, Francesca Cantini, Mario Piccioli
Summary: The robustness of NMR coherence transfer near a paramagnetic center in Iron-Sulfur Proteins depends on the relaxation properties of the nuclei involved. Tailored experiments significantly enhance the number of observed connectivities and improve the overall knowledge of these systems. Different relaxation properties are exploited to obtain structural information.
JOURNAL OF BIOMOLECULAR NMR
(2023)
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
Biophysics
Aikaterini C. Tsika, Nikolaos K. Fourkiotis, Periklis Charalampous, Angelo Gallo, Georgios A. Spyroulias
Summary: The Macro Domains (MDs) of SARS-CoV and MERS-CoV exhibit topological and conformational features similar to the nsP3b macro domain of SARS-CoV-2, making them important drug targets for potential antiviral drugs.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Biochemistry & Molecular Biology
Aikaterini C. Tsika, Angelo Gallo, Nikolaos K. Fourkiotis, Aikaterini I. Argyriou, Sridhar Sreeramulu, Frank Loehr, Vladimir V. Rogov, Christian Richter, Verena Linhard, Santosh L. Gande, Nadide Altincekic, Robin Krishnathas, Isam Elamri, Harald Schwalbe, Jan Wollenhaupt, Manfred S. Weiss, Georgios A. Spyroulias
Summary: Viral infection triggers molecular defense mechanisms, including ADP-ribosylation. Viral macro domains, which can reverse ADP-ribosylation, are potential pharmaceutical targets. GS-441524, a metabolite of remdesivir, selectively inhibits viral macro domains.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Hannes Berg, Maria A. Wirtz Martin, Nadide Altincekic, Islam Alshamleh, Jasleen Kaur Bains, Julius Blechar, Betul Ceylan, Vanessa de Jesus, Karthikeyan Dhamotharan, Christin Fuks, Santosh L. Gande, Bruno Hargittay, Katharina F. Hohmann, Marie T. Hutchison, Sophie Marianne Korn, Robin Krishnathas, Felicitas Kutz, Verena Linhard, Tobias Matzel, Nathalie Meiser, Anna Niesteruk, Dennis J. Pyper, Linda Schulte, Sven Trucks, Kamal Azzaoui, Marcel J. J. Blommers, Yojana Gadiya, Reagon Karki, Andrea Zaliani, Philip Gribbon, Marcius da Silva Almeida, Cristiane Dinis Anobom, Anna L. Bula, Matthias Butikofer, Icaro Putinhon Caruso, Isabella Caterina Felli, Andrea T. Da Poian, Gisele Cardoso de Amorim, Nikolaos K. Fourkiotis, Angelo Gallo, Dhiman Ghosh, Francisco Gomes-Neto, Oksana Gorbatyuk, Bing Hao, Vilius Kurauskas, Lauriane Lecoq, Yunfeng Li, Nathane Cunha Mebus-Antunes, Miguel Mompean, Thais Cristtina Neves-Martins, Marti Ninot-Pedrosa, Anderson S. Pinheiro, Letizia Pontoriero, Yulia Pustovalova, Roland Riek, Angus J. Robertson, Marie Jose Abi Saad, Miguel A. Trevino, Aikaterini C. Tsika, Fabio C. L. Almeida, Ad Bax, Katherine Henzler-Wildman, Jeffrey C. Hoch, Kristaps Jaudzems, Douglas Laurents, Julien Orts, Roberta Pierattelli, Georgios A. Spyroulias, Elke Duchardt-Ferner, Jan Ferner, Boris Furtig, Martin Hengesbach, Frank Lohr, Nusrat Qureshi, Christian Richter, Krishna Saxena, Andreas Schlundt, Sridhar Sreeramulu, Anna Wacker, Julia E. Weigand, Julia Wirmer-Bartoschek, Jens Wohnert, Harald Schwalbe
Summary: This study explores novel drug design against SARS-CoV-2 through NMR screening and computational mapping. They identified multiple molecules that bind to SARS-CoV-2 proteins and studied their structural and chemical properties, providing new insights for drug development.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biophysics
Maria D. Politi, Angelo Gallo, Georgios Bouras, Maria Birkou, Bruno Canard, Bruno Coutard, Georgios A. Spyroulias
Summary: This study focused on the genome of Hepatitis E virus (HEV) and specifically on one of its proteins, HEV MD. The researchers found that HEV MD plays an important role in the interaction between the virus and the host, as well as in viral replication. They conducted a detailed structural analysis of HEV MD and discovered that its structure is similar to that of other viral macro domains.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biophysics
Jose Malanho Silva, Deborah Grifagni, Francesca Cantini, Mario Piccioli
Summary: CISD3 is a mitochondrial protein with two [2Fe-2S] clusters. It is overexpressed in certain cancers, making it a potential target for drug therapy. This study successfully characterized human CISD3 using isotopically labeled samples and NMR techniques, providing valuable information for understanding its role in cancer development.
BIOMOLECULAR NMR ASSIGNMENTS
(2023)
Article
Biochemistry & Molecular Biology
Deborah Grifagni, Jose M. Silva, Francesca Cantini, Mario Piccioli, Lucia Banci
Summary: CISD3 is a mitochondrial protein with two [Fe2S2] clusters coordinated by CDGSH domains, belonging to the NEET proteins family. While little is known about its structure-function relationships, NMR can provide atomic level information on intermolecular interactions in solution. However, paramagnetic proteins limit the application of this technique due to signal broadening. This study demonstrates how paramagnetic relaxation can assist in signal assignment and identifies potential key players in the biological function of CISD3 protein.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Onur Yildirim, Arshak Tsaturyan, Alessandro Damin, Stefano Nejrotti, Valentina Crocella, Angelo Gallo, Michele Remo Chierotti, Matteo Bonomo, Claudia Barolo
Summary: In this study, a novel 2D covalent organic polymer (COP), TAPB-QOT COP, is designed and synthesized. The polymer exhibits high iodine (I2) uptake capacity due to the presence of embedded sulfur sites and a conjugated scaffold. Characterization techniques confirm the high affinity between the sulfur atom in the COP and I2. The TAPB-QOT COP shows promising prospects for iodine capture with high volumetric uptake and reversibility.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Giacomo Parigi, Enrico Ravera, Mario Piccioli, Claudio Luchinat
Summary: Mobility is a crucial feature for the function of biomacromolecules, leading to a conformational ensemble rather than a single conformation. NMR paramagnetic data, especially when combined with other data sources, provide valuable information to monitor the conformational variability. By virtue of their long-range nature, paramagnetic data can demonstrate conformational rearrangements, reveal minor conformational states, indicate representative conformations, and provide upper limits for each conformation's weight.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Federica Bravetti, Raffaele E. E. Russo, Simone Bordignon, Angelo Gallo, Federica Rossi, Carlo Nervi, Roberto Gobetto, Michele R. R. Chierotti
Summary: Computational approaches like Crystal Structure Prediction (CSP) have been increasingly used in crystal structure determination, providing insights into the packing of atoms and molecules in the solid state without diffraction data. The coupling of CSP with solid-state NMR (SSNMR) enhances the accuracy and performance of the predictive method, known as CSP-NMRX. This paper successfully applies CSP-NMRX to determine the crystal structure of pyridine dicarboxylic acid isomers, using mono- and bidimensional SSNMR spectra and RMSEs between experimental and computed chemical shifts.
Article
Biochemistry & Molecular Biology
Ines B. Trindade, Maria O. Firmino, Sander J. Noordam, Alexandra S. Alves, Bruno M. Fonseca, Mario Piccioli, Ricardo O. Louro
Summary: In this study, the interactions between PioC, PioA, and LH-RC in Rhodopseudomonas palustris were mapped using NMR spectroscopy. It was found that PioA can directly reduce LH-RC, making it the most likely substitute for PioC upon deletion. By contrast, Rpal_4085 demonstrated significant electronic and structural differences from PioC, which likely explain its inability to reduce LH-RC.
Article
Chemistry, Multidisciplinary
Federica Bravetti, Lukas Tapmeyer, Kathrin Skorodumov, Edith Alig, Stefan Habermehl, Robert Huehn, Simone Bordignon, Angelo Gallo, Carlo Nervi, Michele R. Chierotti, Martin U. Schmidt
Summary: Leucopterin, a white pigment found in butterflies and insects, has a variable hydrate structure with 0.1 to 0.5 molecules of water per leucopterin molecule. The crystal structure of leucopterin was determined using techniques such as powder diffraction and solid-state NMR spectroscopy. The high density of leucopterin may contribute to the light-scattering properties of butterfly wings.
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
Leonardo Querci, Deborah Grifagni, Ines B. Trindade, Jose Malanho Silva, Ricardo O. Louro, Francesca Cantini, Mario Piccioli
Summary: The robustness of NMR coherence transfer near a paramagnetic center in Iron-Sulfur Proteins depends on the relaxation properties of the nuclei involved. Tailored experiments significantly enhance the number of observed connectivities and improve the overall knowledge of these systems. Different relaxation properties are exploited to obtain structural information.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Lauren A. Mcintosh, Jonathan D. Burns, Evgeny E. Tereshatov, Riccardo Muzzioli, Kris Hagel, Noimat A. Jinadu, Laura A. McCann, Gabriela A. Picayo, Federica Pisaneschi, David Piwnica-Worms, Steven J. Schultz, Gabriel C. Tabacaru, Austin Abbott, Brooklyn Green, Travis Hankins, Andrew Hannaman, Bryan Harvey, Kylie Lofton, Robert Rider, Maxwell Sorensen, Alexandra Tabacaru, Zachary Tobin, Sherry J. Yennello
Summary: This article presents a method for shipping At-211 radioisotope in a convenient form for further radiochemistry, addressing challenges in transportation for advanced reactions and other uses. The method is simple and efficient, and has been successfully implemented at multiple locations.
NUCLEAR MEDICINE AND BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Barbara Zambelli, Priyanka Basak, Heidi Hu, Mario Piccioli, Francesco Musiani, Valquiria Broll, Lionel Imbert, Jerome Boisbouvier, Michael J. Maroney, Stefano Ciurli
Summary: The maturation pathway for urease involves the protein UreE as a metallochaperone, and accessory proteins HypA and HypB are also required in H. pylori. A protein complex forms between HypA and the UreE(2) dimer, mediated by conserved motifs and extensive protein contacts. This complex contains a high-affinity Ni(II)-binding site and a six-coordinate, high-spin Ni(II) site with ligands from both component proteins.