1
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Nguyen UTT, Youn E, Le TAN, Ha NM, Tran SH, Lee S, Cha JW, Park JS, Kwon HC, Kang K. Photodynamic treatment increases the lifespan and oxidative stress resistance of Caenorhabditis elegans. Free Radic Biol Med 2024; 221:98-110. [PMID: 38754743 DOI: 10.1016/j.freeradbiomed.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Photodynamic therapy is a noninvasive treatment in which specific photosensitizers and light are used to produce high amounts of reactive oxygen species (ROS), which can be employed for targeted tissue destruction in cancer treatment or antimicrobial therapy. However, it remains unknown whether lower amounts of ROS produced by mild photodynamic therapy increase lifespan and stress resistance at the organism level. Here, we introduce a novel photodynamic treatment (PDTr) that uses 20 μM hypericin, a photosensitizer that originates from Hypericum perforatum, and orange light (590 nm, 5.4 W/m2, 1 min) to induce intracellular ROS formation (ROS), thereby resulting in lifespan extension and improved stress resistance in C. elegans. The PDTr-induced increase in longevity was abrogated by N-acetyl cysteine, suggesting the hormetic response was driven by prooxidative mechanisms. PDTr activated the translocation of SKN-1/NRF-2 and DAF-16/FOXO, leading to elevated expression of downstream oxidative stress-responsive genes, including ctl-1, gst-4, and sod-3. In summary, our findings suggest a novel PDTr method that extends the lifespan of C. elegans under both normal and oxidative stress conditions through the activation of SKN-1 and DAF-16 via the involvement of many antioxidant genes.
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Affiliation(s)
- Uyen Tran Tu Nguyen
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea
| | - Esther Youn
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea
| | - Tram Anh Ngoc Le
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea
| | - Ngoc Minh Ha
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea
| | - Son Hung Tran
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea
| | - Sohyun Lee
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea
| | - Jin Wook Cha
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea
| | - Jin-Soo Park
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea
| | - Hak Cheol Kwon
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea
| | - Kyungsu Kang
- Natural Product Informatics Research Center, Gangneung Institute of Natural Products, Korea Institute of Science and Technology, Gangwon-do, 25451, Republic of Korea; Natural Product Applied Science, KIST School, University of Science and Technology (UST), Gangneung, Gangwon-do, 25451, Republic of Korea.
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2
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Pankratova Y, McKay MJ, Ma C, Tan H, Wang J, Hong M. Structure and dynamics of the proton-selective histidine and the gating tryptophan in an inward rectifying hybrid influenza B and A virus M2 proton channel. Phys Chem Chem Phys 2024. [PMID: 39037444 DOI: 10.1039/d4cp01648c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
The M2 proteins of influenza A and B viruses form acid-activated proton channels that are essential for the virus lifecycle. Proton selectivity is achieved by a transmembrane (TM) histidine whereas gating is achieved by a tryptophan residue. Although this functional apparatus is conserved between AM2 and BM2 channels, AM2 conducts protons exclusively inward whereas BM2 conducts protons in either direction depending on the pH gradient. Previous studies showed that in AM2, mutations of D44 abolished inward rectification of AM2, suggesting that the tryptophan gate is destabilized. To elucidate how charged residues C-terminal to the tryptophan regulates channel gating, here we investigate the structure and dynamics of H19 and W23 in a BM2 mutant, GDR-BM2, in which three BM2 residues are mutated to the corresponding AM2 residues, S16G, G26D and H27R. Whole-cell electrophysiological data show that GDR-BM2 conducts protons with inward rectification, identical to wild-type (WT) AM2 but different from WT-BM2. Solid-state NMR 15N and 13C spectra of H19 indicate that the mutant BM2 channel contains higher populations of cationic histidine and neutral τ tautomers compared to WT-BM2 at acidic pH. Moreover, 19F NMR spectra of 5-19F-labeled W23 resolve three peaks at acidic pH, suggesting three tryptophan sidechain conformations. Comparison of these spectra with the tryptophan spectra of other M2 peptides suggests that these indole sidechain conformations arise from interactions with the C-terminal charged residues and with the N-terminal cationic histidine. Taken together, these solid-state NMR data show that inward rectification in M2 proton channels is accomplished by tryptophan interactions with charged residues on both its C-terminal and N-terminal sides. Gating of these M2 proton channels is thus accomplished by a multi-residue complex with finely tuned electrostatic and aromatic interactions.
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Affiliation(s)
- Yanina Pankratova
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, 85721, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA.
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3
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Ito K, Yamamoto R, Sekiyama Y. Tracking Metabolite Variations during the Degradation of Vegetables in Rice Bran Bed with Intact-State Nuclear Magnetic Resonance Spectroscopy. Metabolites 2024; 14:391. [PMID: 39057714 DOI: 10.3390/metabo14070391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Fermentation-a process of compound degradation by microorganisms-is a traditional food processing method utilized worldwide for the long-term preservation of fresh foods. In recent years, fermented foods have gained attention as health foods. Fermentation increases the nutritional value of ingredients, producing complex flavors and aromas. To identify unknown components in fermented foods, it is necessary to analyze compounds and conditions nondestructively and comprehensively. We performed intact-state nuclear magnetic resonance (NMR) spectroscopy using intermolecular single quantum coherence (iSQC) to detect the degradation of vegetables directly and nondestructively. We used two types of vegetables and a rice bran bed (nukazuke), which is used for traditional vegetable fermentation in Japan. Major metabolites such as saccharides, organic acids, and amino acids were identified in iSQC-sliced spectra. Comparing NMR signal intensities during degradation revealed the transition of metabolites characteristic of lactic acid fermentation. A pathway-based network analysis showed pathways involved in amino acid metabolism and lactic acid fermentation. Our analytical approach with intact-state NMR spectroscopy using iSQC demonstrated that it may be effective in other experimental systems, allowing for the evaluation of phenomena that have been conventionally overlooked in their true state.
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Affiliation(s)
- Kengo Ito
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba 305-0856, Japan
| | - Ryusei Yamamoto
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Yasuyo Sekiyama
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
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4
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Weber DK, Reddy UV, Robia SL, Veglia G. Pathological mutations in the phospholamban cytoplasmic region affect its topology and dynamics modulating the extent of SERCA inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184370. [PMID: 38986894 DOI: 10.1016/j.bbamem.2024.184370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Phospholamban (PLN) is a 52 amino acid regulin that allosterically modulates the activity of the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) in the heart muscle. In its unphosphorylated form, PLN binds SERCA within its transmembrane (TM) domains, approximately 20 Å away from the Ca2+ binding site, reducing SERCA's apparent Ca2+ affinity (pKCa) and decreasing cardiac contractility. During the enzymatic cycle, the inhibitory TM domain of PLN remains anchored to SERCA, whereas its cytoplasmic region transiently binds the ATPase's headpiece. Phosphorylation of PLN at Ser16 by protein kinase A increases the affinity of its cytoplasmic domain to SERCA, weakening the TM interactions with the ATPase, reversing its inhibitory function, and augmenting muscle contractility. How the structural changes caused by pathological mutations in the PLN cytoplasmic region are transmitted to its inhibitory TM domain is still unclear. Using solid-state NMR spectroscopy and activity assays, we analyzed the structural and functional effects of a series of mutations and their phosphorylated forms located in the PLN cytoplasmic region and linked to dilated cardiomyopathy. We found that these missense mutations affect the overall topology and dynamics of PLN and ultimately modulate its inhibitory potency. Also, the changes in the TM tilt angle and cytoplasmic dynamics of PLN caused by these mutations correlate well with the extent of SERCA inhibition. Our study unveils new molecular determinants for designing variants of PLN that outcompete endogenous PLN to regulate SERCA in a tunable manner.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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5
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Nawrocka EK, Jadwiszczak M, Leszczyński PJ, Kazimierczuk K. Supporting the assignment of NMR spectra with variable-temperature experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:479-485. [PMID: 38303612 DOI: 10.1002/mrc.5433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful tools in analytical chemistry. An important step in the analysis of NMR data is the assignment of resonance frequencies to the corresponding atoms in the molecule being investigated. The traditional approach considers the spectrum's characteristic parameters: chemical shift values, internuclear couplings, and peak intensities. In this paper, we show how to support the process of assigning a series of spectra of similar organic compounds by using temperature coefficients, that is, the rates of change in chemical shift values associated with given changes in temperature.
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Affiliation(s)
- Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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6
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Furuita K, Kojima C. Improved analysis of NMR chemical shift perturbations through an error estimation method. Biophys Chem 2024; 310:107255. [PMID: 38728808 DOI: 10.1016/j.bpc.2024.107255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
In solution NMR, chemical shift perturbation (CSP) experiments are widely employed to study intermolecular interactions. However, excluding the nonsignificant peak shift is difficult because little is known about errors in CSP. Here, to address this issue, we introduce a method for estimating errors in CSP based on the noise level. First, we developed a technique that involves line shape fitting to estimate errors in peak position via Monte Carlo simulations. Second, this technique was applied to estimate errors in CSP. In intermolecular interaction analysis of VAP-A with SNX2, error estimation of CSP enabled the evaluation of small but significant changes in peak position and yielded detailed insights that are unattainable with conventional CSP analysis. Third, this technique was successfully applied to estimate errors in residual dipolar couplings. In conclusion, our error estimation method improves CSP analysis by excluding the nonsignificant peak shift.
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Affiliation(s)
- Kyoko Furuita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Engineering Science, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501, Japan.
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7
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Toyama Y, Shimada I. Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'- 19F probe in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00446-7. [PMID: 38918317 DOI: 10.1007/s10858-024-00446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.
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Affiliation(s)
- Yuki Toyama
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, 739-8528, Japan.
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8
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Karunanithy G, Shukla VK, Hansen DF. Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks. Nat Commun 2024; 15:5073. [PMID: 38871714 PMCID: PMC11176362 DOI: 10.1038/s41467-024-49378-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Methyl-TROSY nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterising large biomolecules in solution. However, preparing samples for these experiments is demanding and entails deuteration, limiting its use. Here we demonstrate that NMR spectra recorded on protonated, uniformly 13C labelled samples can be processed using deep neural networks to yield spectra that are of similar quality to typical deuterated methyl-TROSY spectra, potentially providing information for proteins that cannot be produced in bacterial systems. We validate the methodology experimentally on three proteins with molecular weights in the range 42-360 kDa. We further demonstrate the applicability of our methodology to 3D NOESY spectra of Escherichia coli Malate Synthase G (81 kDa), where observed NOE cross-peaks are in good agreement with the available structure. The method represents an advance in the field of using deep learning to analyse complex magnetic resonance data and could have an impact on the study of large biomolecules in years to come.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, London, NW1 1BF, UK
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
- The Francis Crick Institute, London, NW1 1BF, UK.
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9
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Ianc O, Teleanu F, Ciumeică A, Lupulescu A, Sadet A, Vasos PR. Improved detection of magnetic interactions in proteins based on long-lived coherences. Commun Chem 2024; 7:112. [PMID: 38755276 PMCID: PMC11099074 DOI: 10.1038/s42004-024-01195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Living systems rely on molecular building blocks with low structural symmetry. Therefore, constituent amino acids and nucleotides yield short-lived nuclear magnetic responses to electromagnetic radiation. Magnetic signals are at the basis of molecular imaging, structure determination and interaction studies. In solution state, as the molecular weight of analytes increases, coherences with long lifetimes are needed to yield advantageous through-space magnetisation transfers. Interactions between magnetic nuclei can only be detected provided the lifetimes of spin order are sufficient. In J-coupled pairs of nuclei, long-lived coherences (LLC's) connect states with different spin-permutation symmetry. Here in, we show sustained LLC's in protein Lysozyme, weighing 14.3 kDa, with lifetimes twice as long as those of classical magnetisation for the aliphatic protons of glycine residues. We found for the first time that, in a protein of significant molecular weight, LLC's yield substantial through-space magnetisation transfers: spin-order transfer stemming from LLC's overcame transfers from classical coherences by factors > 2. Furthermore, in agreement with theory, the permutation symmetry of LLC-based transfers allows mapping interacting atoms in the protein structure with respect to the molecular plane of glycine residues in a stereospecific manner. These findings can extend the scope of liquid-state high-resolution biomolecular spectroscopy.
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Affiliation(s)
- Octavian Ianc
- Biophysics and Biomedical Applications Laboratory and Group, LGED, ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania
- Faculty of Physics, University of Bucharest, 405 Atomiștilor Street, 050663, Măgurele, Romania
| | - Florin Teleanu
- Biophysics and Biomedical Applications Laboratory and Group, LGED, ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania
- Interdisciplinary School of Doctoral Studies, University of Bucharest, 36-46 Mihail Kogălniceanu Bd, 050107, Bucharest, Romania
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Andrei Ciumeică
- Interdisciplinary School of Doctoral Studies, University of Bucharest, 36-46 Mihail Kogălniceanu Bd, 050107, Bucharest, Romania
| | - Adonis Lupulescu
- Biophysics and Biomedical Applications Laboratory and Group, LGED, ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania
| | - Aude Sadet
- Biophysics and Biomedical Applications Laboratory and Group, LGED, ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania.
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria.
| | - Paul R Vasos
- Biophysics and Biomedical Applications Laboratory and Group, LGED, ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, 077125, Bucharest-Măgurele, Romania.
- Interdisciplinary School of Doctoral Studies, University of Bucharest, 36-46 Mihail Kogălniceanu Bd, 050107, Bucharest, Romania.
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria.
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10
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Basford AR, Bennett SK, Xiao M, Turcani L, Allen J, Jelfs KE, Greenaway RL. Streamlining the automated discovery of porous organic cages. Chem Sci 2024; 15:6331-6348. [PMID: 38699265 PMCID: PMC11062116 DOI: 10.1039/d3sc06133g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/12/2024] [Indexed: 05/05/2024] Open
Abstract
Self-assembly through dynamic covalent chemistry (DCC) can yield a range of multi-component organic assemblies. The reversibility and dynamic nature of DCC has made prediction of reaction outcome particularly difficult and thus slows the discovery rate of new organic materials. In addition, traditional experimental processes are time-consuming and often rely on serendipity. Here, we present a streamlined hybrid workflow that combines automated high-throughput experimentation, automated data analysis, and computational modelling, to accelerate the discovery process of one particular subclass of molecular organic materials, porous organic cages. We demonstrate how the design and implementation of this workflow aids in the identification of organic cages with desirable properties. The curation of a precursor library of 55 tri- and di-topic aldehyde and amine precursors enabled the experimental screening of 366 imine condensation reactions experimentally, and 1464 hypothetical organic cage outcomes to be computationally modelled. From the screen, 225 cages were identified experimentally using mass spectrometry, 54 of which were cleanly formed as a single topology as determined by both turbidity measurements and 1H NMR spectroscopy. Integration of these characterisation methods into a fully automated Python pipeline, named cagey, led to over a 350-fold decrease in the time required for data analysis. This work highlights the advantages of combining automated synthesis, characterisation, and analysis, for large-scale data curation towards an accessible data-driven materials discovery approach.
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Affiliation(s)
- Annabel R Basford
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Steven K Bennett
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Muye Xiao
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Lukas Turcani
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Jasmine Allen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
| | - Rebecca L Greenaway
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London White City Campus, 82 Wood Lane W12 0BZ UK
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11
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Toyama Y, Shimada I. NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity. Nat Commun 2024; 15:3303. [PMID: 38664397 PMCID: PMC11045745 DOI: 10.1038/s41467-024-47659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The DEAD-box RNA helicase (DDX) plays a central role in many aspects of RNA metabolism by remodeling the defined structure of RNA molecules. While a number of structural studies have revealed the atomistic details of the interaction between DDX and RNA ligands, the molecular mechanism of how this molecule unwinds a structured RNA into an unstructured single-stranded RNA (ssRNA) has largely remained elusive. This is due to challenges in structurally characterizing the unwinding intermediate state and the lack of thermodynamic details underlying this process. In this study, we use solution nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction of human DDX3X, a member of the DDX family, with various RNA ligands. Our results show that the inherent binding affinity of DDX3X for ssRNA is significantly higher than that for structured RNA elements. This preferential binding, accompanied by the formation of a domain-closed conformation in complex with ssRNA, effectively stabilizes the denatured ssRNA state and thus underlies the unwinding activity of DDX3X. Our results provide a thermodynamic and structural basis for the DDX function, whereby DDX can recognize and remodel a distinct set of structured RNAs to participate in a wide range of physiological processes.
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Affiliation(s)
- Yuki Toyama
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.
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12
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Sučec I, Pankratova Y, Parasar M, Hong M. Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63. Protein Sci 2024; 33:e4923. [PMID: 38501465 PMCID: PMC10949323 DOI: 10.1002/pro.4923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 03/20/2024]
Abstract
The envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured 13 C and 15 N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone (ϕ, ψ) torsion angles. We further measured the water accessibility of NL63 ETM at neutral pH versus acidic pH in the presence of Ca2+ ions. These data show that NL63 ETM adopts a regular α-helical conformation that is unaffected by pH and the N-terminal ectodomain. Interestingly, the water accessibility of NL63 ETM increases only modestly at acidic pH in the presence of Ca2+ compared to neutral pH, in contrast to SARS ETM, which becomes much more hydrated at acidic pH. This difference suggests a structural basis for the weaker channel conductance of α-CoV compared to β-CoV E proteins. The weaker E channel activity may in turn contribute to the reduced virulence of hCoV-NL63 compared to SARS-CoV viruses.
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Affiliation(s)
- Iva Sučec
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Yanina Pankratova
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mriganka Parasar
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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13
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Harkness RW, Zhao H, Toyama Y, Schuck P, Kay LE. Exploring Host-Guest Interactions within a 600 kDa DegP Protease Cage Complex Using Hydrodynamics Measurements and Methyl-TROSY NMR. J Am Chem Soc 2024; 146:8242-8259. [PMID: 38477967 DOI: 10.1021/jacs.3c13247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The DegP protease-chaperone operates within the periplasm of Gram-negative bacteria, where it assists in the regulation of protein homeostasis, promotes virulence, and is essential to survival under stress. To carry out these tasks, DegP forms a network of preorganized apo oligomers that facilitate the capture of substrates within distributions of cage-like complexes which expand to encapsulate clients of various sizes. Although the architectures of DegP cage complexes are well understood, little is known about the structures, dynamics, and interactions of client proteins within DegP cages and the relationship between client structural dynamics and function. Here, we probe host-guest interactions within a 600 kDa DegP cage complex throughout the DegP activation cycle using a model α-helical client protein through a combination of hydrodynamics measurements, methyl-transverse relaxation optimized spectroscopy-based solution nuclear magnetic resonance studies, and proteolytic activity assays. We find that in the presence of the client, DegP cages assemble cooperatively with few intermediates. Our data further show that the N-terminal half of the bound client, which projects into the interior of the cages, is predominantly unfolded and flexible, and exchanges between multiple conformational states over a wide range of time scales. Finally, we show that a concerted structural transition of the protease domains of DegP occurs upon client engagement, leading to activation. Together, our findings support a model of DegP as a highly cooperative and dynamic molecular machine that stabilizes unfolded states of clients, primarily via interactions with their C-termini, giving rise to efficient cleavage.
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Affiliation(s)
- Robert W Harkness
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuki Toyama
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto M5G 0A4, Canada
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14
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Dorst KM, Widmalm G. Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures. Chemistry 2024; 30:e202304047. [PMID: 38180821 DOI: 10.1002/chem.202304047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/07/2024]
Abstract
Glycans are central to information content and regulation in biological systems. These carbohydrate molecules are active either as oligo- or polysaccharides, often in the form of glycoconjugates. The monosaccharide entities are joined by glycosidic linkages and stereochemical arrangements are of utmost importance in determining conformation and flexibility of saccharides. The conformational preferences and population distributions at the glycosidic torsion angles φ and ψ have been investigated for O-methyl glycosides of three disaccharides where the substitution takes place at a secondary alcohol, viz., in α-l-Fucp-(1→3)-β-d-Glcp-OMe, α-l-Fucp-(1→3)-α-d-Galp-OMe and α-d-Glcp-(1→4)-α-d-Galp-OMe, corresponding to disaccharide structural elements present in bacterial polysaccharides. Stereochemical differences at or adjacent to the glycosidic linkage were explored by solution state NMR spectroscopy using one-dimensional 1 H,1 H-NOESY NMR experiments to obtain transglycosidic proton-proton distances and one- and two-dimensional heteronuclear NMR experiments to obtain 3 JCH transglycosidic coupling constants related to torsion angles φ and ψ. Computed effective proton-proton distances from molecular dynamics (MD) simulations showed excellent agreement to experimentally derived distances for the α-(1→3)-linked disaccharides and revealed that for the bimodal distribution at the ψ torsion angle for the α-(1→4)-linked disaccharide experiment and simulation were at variance with each other, calling for further force field developments. The MD simulations disclosed a highly intricate inter-residue hydrogen bonding pattern for the α-(1→4)-linked disaccharide, including a nonconventional hydrogen bond between H5' in the glucosyl residue and O3 in the galactosyl residue, supported by a large downfield 1 H NMR chemical shift displacement compared to α-d-Glcp-OMe. Comparison of population distributions of the glycosidic torsion angles φ and ψ in the disaccharide entities to those of corresponding crystal structures highlighted the potential importance of solvation on the preferred conformation.
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Affiliation(s)
- Kevin M Dorst
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
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15
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Gopinath T, Shin K, Tian Y, Im W, Struppe J, Perrone B, Hassan A, Marassi FM. Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite. J Struct Biol 2024; 216:108061. [PMID: 38185342 PMCID: PMC10939839 DOI: 10.1016/j.jsb.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The low sensitivity of nuclear magnetic resonance (NMR) is a major bottleneck for studying biomolecular structures of complex biomolecular assemblies. Cryogenically cooled probe technology overcomes the sensitivity limitations enabling NMR applications to challenging biomolecular systems. Here we describe solid-state NMR studies of the human blood protein vitronectin (Vn) bound to hydroxyapatite (HAP), the mineralized form of calcium phosphate, using a CryoProbe designed for magic angle spinning (MAS) experiments. Vn is a major blood protein that regulates many different physiological and pathological processes. The high sensitivity of the CryoProbe enabled us to acquire three-dimensional solid-state NMR spectra for sequential assignment and characterization of site-specific water-protein interactions that provide initial insights into the organization of the Vn-HAP complex. Vn associates with HAP in various pathological settings, including macular degeneration eyes and Alzheimer's disease brains. The ability to probe these assemblies at atomic detail paves the way for understanding their formation.
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Affiliation(s)
- T Gopinath
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kyungsoo Shin
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ye Tian
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, PA 18015, USA
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | | | - Alia Hassan
- Bruker Switzerland AG, Fallanden, Switzerland
| | - Francesca M Marassi
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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16
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Xu Y, Chen J, Aydt AP, Zhang L, Sergeyev I, Keeler EG, Choi B, He S, Reichman DR, Friesner RA, Nuckolls C, Steigerwald ML, Roy X, McDermott AE. Electron and Spin Delocalization in [Co 6 Se 8 (PEt 3 ) 6 ] 0/+1 Superatoms. Chemphyschem 2024; 25:e202300064. [PMID: 38057144 DOI: 10.1002/cphc.202300064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 11/01/2023] [Indexed: 12/08/2023]
Abstract
Molecular clusters can function as nanoscale atoms/superatoms, assembling into superatomic solids, a new class of solid-state materials with designable properties through modifications on superatoms. To explore possibilities on diversifying building blocks, here we thoroughly studied one representative superatom, Co6 Se8 (PEt3 )6 . We probed its structural, electronic, and magnetic properties and revealed its detailed electronic structure as valence electrons delocalize over inorganic [Co6 Se8 ] core while ligands function as an insulated shell. 59 Co SSNMR measurements on the core and 31 P, 13 C on the ligands show that the neutral Co6 Se8 (PEt3 )6 is diamagnetic and symmetric, with all ligands magnetically equivalent. Quantum computations cross-validate NMR results and reveal degenerate delocalized HOMO orbitals, indicating aromaticity. Ligand substitution keeps the inorganic core nearly intact. After losing one electron, the unpaired electron in [Co6 Se8 (PEt3 )6 ]+1 is delocalized, causing paramagnetism and a delocalized electron spin. Notably, this feature of electron/spin delocalization over a large cluster is attractive for special single-electron devices.
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Affiliation(s)
- Yunyao Xu
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Jia Chen
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Alexander P Aydt
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Lichirui Zhang
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Ivan Sergeyev
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Eric G Keeler
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Bonnie Choi
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Shoushou He
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - David R Reichman
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Colin Nuckolls
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | | | - Xavier Roy
- Department of Chemistry, Columbia University New York, New York, 10027, USA
| | - Ann E McDermott
- Department of Chemistry, Columbia University New York, New York, 10027, USA
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17
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Bruni GO, Qi Y, Terrell E, Dupre RA, Mattison CP. Characterization of Levan Fructan Produced by a Gluconobacter japonicus Strain Isolated from a Sugarcane Processing Facility. Microorganisms 2024; 12:107. [PMID: 38257935 PMCID: PMC10819292 DOI: 10.3390/microorganisms12010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
During raw sugarcane processing, a significant portion of lost sucrose is attributable to microbial degradation. Sucrose consumption by many bacteria is also linked to the production of exopolysaccharides (EPS) such as dextrans and fructans. These resulting EPS cause operational challenges during raw sugar manufacturing. Here, we report the characterization of EPS from a fructan-forming Gluconobacter japonicus bacterium that we previously isolated from a Louisiana sugarcane factory. The genome sequencing revealed the presence of two encoded levansucrase genes, lsrA and lsrB. One levansucrase, LsrB, was detected in the secreted protein fraction of G. japonicus LASM12 by QTOF LC-MS. The spotting assays indicated that G. japonicus produces EPS using sucrose and raffinose as substrates. The G. japonicus EPS correlated with levan fructan commercial standards by 1H-NMR, and with the characteristic carbohydrate fingerprint region for FTIR spectra, confirming that the G. japonicus EPS is levan fructan. The glycosyl composition and glycosyl linkage analysis revealed a linear β-2,6-fructofuranosyl polysaccharide with occasional (5.7%) β-2,1-fructofuranosyl branches. The gel permeation chromatography of the levan fructan EPS showed two main peaks at 4.5 kDa and 8 kDa and a very minor peak at 500 kDa. G. japonicus was identified as a producer of levan fructan. These findings will be useful for future studies aimed at evaluating the impact of levan fructans on sugar crop processing, which have been historically underestimated in industry.
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Affiliation(s)
- Gillian O. Bruni
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA
| | - Yunci Qi
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA
| | - Evan Terrell
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA
| | - Rebecca A. Dupre
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA
- U.S. Department of Energy, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Christopher P. Mattison
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA
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18
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Bhai L, Thomas JK, Conroy DW, Xu Y, Al-Hashimi HM, Jaroniec CP. Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements. Front Mol Biosci 2023; 10:1286172. [PMID: 38111464 PMCID: PMC10726973 DOI: 10.3389/fmolb.2023.1286172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 12/20/2023] Open
Abstract
Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments.
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Affiliation(s)
- Lakshmi Bhai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Daniel W. Conroy
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
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19
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Xu J, Yang B, Kelley D, Magnotta VA. Automated High-Order Shimming for Neuroimaging Studies. Tomography 2023; 9:2148-2157. [PMID: 38133072 PMCID: PMC10748357 DOI: 10.3390/tomography9060168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
B0 inhomogeneity presents a significant challenge in MRI and MR spectroscopy, particularly at high-field strengths, leading to image distortion, signal loss, and spectral broadening. Existing high-order shimming methods can alleviate these issues but often require time-consuming and subjective manual selection of regions of interest (ROIs). To address this, we proposed an automated high-order shimming (autoHOS) method, incorporating deep-learning-based brain extraction and image-based high-order shimming. This approach performs automated real-time brain extraction to define the ROI of the field map to be used in the shimming algorithm. The shimming performance of autoHOS was assessed through in vivo echo-planar imaging (EPI) and spectroscopic studies at both 3T and 7T field strengths. AutoHOS outperforms linear shimming and manual high-order shimming, enhancing both the image and spectral quality by reducing the EPI image distortion and narrowing the MRS spectral lineshapes. Therefore, autoHOS demonstrated a significant improvement in correcting B0 inhomogeneity while eliminating the need for additional user interaction.
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Affiliation(s)
- Jia Xu
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA
| | | | - Douglas Kelley
- GE Corporate Consultant, Contracted through Kelly Services, Fairfax, CA 94930, USA;
| | - Vincent A. Magnotta
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
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20
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Rout M, Lipfert M, Lee BL, Berjanskii M, Assempour N, Fresno RV, Cayuela AS, Dong Y, Johnson M, Shahin H, Gautam V, Sajed T, Oler E, Peters H, Mandal R, Wishart DS. MagMet: A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:681-704. [PMID: 37265034 DOI: 10.1002/mrc.5371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectral analysis of biofluids can be a time-consuming process, requiring the expertise of a trained operator. With NMR becoming increasingly popular in the field of metabolomics, there is a growing need to change this paradigm and to automate the process. Here we introduce MagMet, an online web server, that automates the processing and quantification of 1D 1 H NMR spectra from biofluids-specifically, human serum/plasma metabolites, including those associated with inborn errors of metabolism (IEM). MagMet uses a highly efficient data processing procedure that performs automatic Fourier Transformation, phase correction, baseline optimization, chemical shift referencing, water signal removal, and peak picking/peak alignment. MagMet then uses the peak positions, linewidth information, and J-couplings from its own specially prepared standard metabolite reference spectral NMR library of 85 serum/plasma compounds to identify and quantify compounds from experimentally acquired NMR spectra of serum/plasma. MagMet employs linewidth adjustment for more consistent quantification of metabolites from higher field instruments and incorporates a highly efficient data processing procedure for more rapid and accurate detection and quantification of metabolites. This optimized algorithm allows the MagMet webserver to quickly detect and quantify 58 serum/plasma metabolites in 2.6 min per spectrum (when processing a dataset of 50-100 spectra). MagMet's performance was also assessed using spectra collected from defined mixtures (simulating other biofluids), with >100 previously measured plasma spectra, and from spiked serum/plasma samples simulating known IEMs. In all cases, MagMet performed with precision and accuracy matching the performance of human spectral profiling experts. MagMet is available at http://magmet.ca.
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Affiliation(s)
- Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Matthias Lipfert
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mark Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nazanin Assempour
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rosa Vazquez Fresno
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Arnau Serra Cayuela
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ying Dong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Mathew Johnson
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Honeya Shahin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tanvir Sajed
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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21
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Klein A, Vasa SK, Linser R. 5D solid-state NMR spectroscopy for facilitated resonance assignment. JOURNAL OF BIOMOLECULAR NMR 2023; 77:229-245. [PMID: 37943392 PMCID: PMC10687145 DOI: 10.1007/s10858-023-00424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023]
Abstract
1H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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22
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Lee BL, Rout M, Mandal R, Wishart DS. Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:705-717. [PMID: 37265043 DOI: 10.1002/mrc.5372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
We report the development of a software program, called MagMet-F, that automates the processing and quantification of 1D 1 H NMR of human fecal extracts. To optimize the program, we identified 82 potential fecal metabolites using 1D 1 H NMR of six human fecal extracts using manual profiling and a literature review of known fecal metabolites. We acquired pure versions of those metabolites and then acquired their 1D 1 H NMR spectra at 700 MHz to generate a fecal metabolite spectral library for MagMet-F. The fitting of these metabolites by MagMet-F was iteratively optimized to replicate manual profiling. We validated MagMet-F's automated profiling using a test set of six fecal extracts. It correctly identified 80% of the compounds and quantified those within <20% of the values determined by manual profiling using Chenomx. We also compared MagMet-F's profiling performance to two other open-access NMR profiling tools, Bayesil and Batman. MagMet-F outperformed both. Bayesil repeatedly overestimated metabolite concentrations by 10% to 40% while Batman was unable to properly quantify any compounds and took 10-20× longer. We have implemented MagMet-F as a freely accessible web server to enable automated, fast and convenient 1D 1 H NMR spectral profiling of fecal samples. MagMet-F is available at https://www.magmet.ca.
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Affiliation(s)
- Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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23
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Tamaki H, Matsuki Y. Optimal-Control-Based Cβ Chemical Shift Encoding for Efficient Signal Assignment of Solid Proteins. J Phys Chem B 2023; 127:10118-10128. [PMID: 37975835 DOI: 10.1021/acs.jpcb.3c05914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fast magic-angle spinning (MAS) solid-state NMR spectroscopy is a powerful tool for gaining structural and dynamic information on solid proteins. To access such information site-specifically, the signal assignment process is unavoidable. In the assignment process, Cα and Cβ chemical shifts are of paramount importance in identifying the type of amino acid residues. Conventionally, however, recording the Cβ chemical shift of solid proteins with relatively short transverse relaxation time is often limited by the long delay required for the magnetization transfer to Cβ spins and its evolution, that is, by the sensitivity drop. In this article, we propose a new method that encodes the Cβ chemical shifts onto the intensities of the scalar-coupled Cα signals by combining an optimal control-based spin manipulation pulse and a spin-state filter. This reduces the total required transverse evolution to less than half of that for the previously proposed method, opening up the concept of the Cβ-encoding nearest-neighbor NMR, for the first time, to solid proteins. Also, the total measurement time was shorter than that required for the explicit Cβ shift evolution. We demonstrate the sequential signal assignment for microcrystalline protein GB1, and then discuss the prospects for more challenging proteins.
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Affiliation(s)
- Hajime Tamaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Osaka, Suita 565-0871, Japan
| | - Yoh Matsuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Osaka, Suita 565-0871, Japan
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24
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Wang Y, Wei W, Du W, Cai J, Liao Y, Lu H, Kong B, Zhang Z. Deep-Learning-Based Mixture Identification for Nuclear Magnetic Resonance Spectroscopy Applied to Plant Flavors. Molecules 2023; 28:7380. [PMID: 37959799 PMCID: PMC10648966 DOI: 10.3390/molecules28217380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Nuclear magnetic resonance (NMR) is a crucial technique for analyzing mixtures consisting of small molecules, providing non-destructive, fast, reproducible, and unbiased benefits. However, it is challenging to perform mixture identification because of the offset of chemical shifts and peak overlaps that often exist in mixtures such as plant flavors. Here, we propose a deep-learning-based mixture identification method (DeepMID) that can be used to identify plant flavors (mixtures) in a formulated flavor (mixture consisting of several plant flavors) without the need to know the specific components in the plant flavors. A pseudo-Siamese convolutional neural network (pSCNN) and a spatial pyramid pooling (SPP) layer were used to solve the problems due to their high accuracy and robustness. The DeepMID model is trained, validated, and tested on an augmented data set containing 50,000 pairs of formulated and plant flavors. We demonstrate that DeepMID can achieve excellent prediction results in the augmented test set: ACC = 99.58%, TPR = 99.48%, FPR = 0.32%; and two experimentally obtained data sets: one shows ACC = 97.60%, TPR = 92.81%, FPR = 0.78% and the other shows ACC = 92.31%, TPR = 80.00%, FPR = 0.00%. In conclusion, DeepMID is a reliable method for identifying plant flavors in formulated flavors based on NMR spectroscopy, which can assist researchers in accelerating the design of flavor formulations.
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Affiliation(s)
- Yufei Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Weiwei Wei
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Wen Du
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Jiaxiao Cai
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Yuxuan Liao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Bo Kong
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
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25
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Dorst KM, Widmalm G. NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER. Carbohydr Res 2023; 533:108937. [PMID: 37734222 DOI: 10.1016/j.carres.2023.108937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.
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Affiliation(s)
- Kevin M Dorst
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
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26
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Paul S, Bouleau E, Reynard-Feytis Q, Arnaud JP, Bancel F, Rollet B, Dalban-Moreynas P, Reiter C, Purea A, Engelke F, Hediger S, De Paëpe G. Sustainable and cost-effective MAS DNP-NMR at 30 K with cryogenic sample exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 356:107561. [PMID: 37837749 DOI: 10.1016/j.jmr.2023.107561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/16/2023]
Abstract
We report here instrumental developments to achieve sustainable, cost-effective cryogenic Helium sample spinning in order to conduct dynamic nuclear polarisation (DNP) and solid-state NMR (ssNMR) at ultra-low temperatures (<30 K). More specifically, we describe an efficient closed-loop helium system composed of a powerful heat exchanger (95% efficient), a single cryocooler, and a single helium compressor to power the sample spinning and cooling. The system is integrated with a newly designed triple-channel NMR probe that minimizes thermal losses without compromising the radio frequency (RF) performance and spinning stability (±0.05%). The probe is equipped with an innovative cryogenic sample exchange system that allows swapping samples in minutes without introducing impurities in the closeloop system. We report that significant gain in sensitivity can be obtained at 30-40 K on large micro-crystalline molecules with unfavorable relaxation timescales, making them difficult or impossible to polarize at 100 K. We also report rotor-synchronized 2D experiments to demonstrate the stability of the system.
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Affiliation(s)
- Subhradip Paul
- Univ. Grenoble. Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France
| | - Eric Bouleau
- Univ. Grenoble Alpes, CEA, IRIG, DSBT, 38000 Grenoble, France
| | | | | | - Florian Bancel
- Univ. Grenoble Alpes, CEA, IRIG, DSBT, 38000 Grenoble, France
| | - Bertrand Rollet
- Univ. Grenoble Alpes, CEA, IRIG, DSBT, 38000 Grenoble, France
| | | | | | | | | | - Sabine Hediger
- Univ. Grenoble. Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble. Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
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27
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Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023; 9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
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Affiliation(s)
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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28
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Estelle AB, Forsythe HM, Yu Z, Hughes K, Lasher B, Allen P, Reardon PN, Hendrix DA, Barbar EJ. RNA structure and multiple weak interactions balance the interplay between RNA binding and phase separation of SARS-CoV-2 nucleocapsid. PNAS NEXUS 2023; 2:pgad333. [PMID: 37901441 PMCID: PMC10605006 DOI: 10.1093/pnasnexus/pgad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 binds viral RNA, condensing it inside the virion, and phase separating with RNA to form liquid-liquid condensates. There is little consensus on what differentiates sequence-independent N-RNA interactions in the virion or in liquid droplets from those with specific genomic RNA (gRNA) motifs necessary for viral function inside infected cells. To identify the RNA structures and the N domains responsible for specific interactions and phase separation, we use the first 1,000 nt of viral RNA and short RNA segments designed as models for single-stranded and paired RNA. Binding affinities estimated from fluorescence anisotropy of these RNAs to the two-folded domains of N (the NTD and CTD) and comparison to full-length N demonstrate that the NTD binds preferentially to single-stranded RNA, and while it is the primary RNA-binding site, it is not essential to phase separation. Nuclear magnetic resonance spectroscopy identifies two RNA-binding sites on the NTD: a previously characterized site and an additional although weaker RNA-binding face that becomes prominent when binding to the primary site is weak, such as with dsRNA or a binding-impaired mutant. Phase separation assays of nucleocapsid domains with double-stranded and single-stranded RNA structures support a model where multiple weak interactions, such as with the CTD or the NTD's secondary face promote phase separation, while strong, specific interactions do not. These studies indicate that both strong and multivalent weak N-RNA interactions underlie the multifunctional abilities of N.
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Affiliation(s)
- Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Heather M Forsythe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Brittany Lasher
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Allen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick N Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, OR 97331, USA
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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29
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Altenhof AR, Kaseman DC, Mason HE, Alvarez MA, Malone MW, Williams RF. On the effects of quadrupolar relaxation in Earth's field NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107540. [PMID: 37722217 DOI: 10.1016/j.jmr.2023.107540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
There is growing interest in using low-field magnetic resonance experiments for routine chemical characterization. Earth's field NMR is one such technique that can garner structural information and enable sample differentiation with low cost and highly portable designs. The resulting NMR spectra are primarily influenced by J-couplings, resulting in so-called J-coupled spectra (JCS). Many small molecules include atoms with NMR-active nuclei that are quadrupolar either at natural abundance or are often isotopically enriched (e.g.,2H, 6Li, 11B, 14N, 17O, etc.) where the effects of quadrupolar J-couplings and relaxation on JCS of strongly- and weakly-coupled spin systems have not been explored to date. Herein, using a set of seven fluoropyridine samples with unique substitution and J-couplings, we demonstrate that the 14N relaxation rates can induce drastic line-broadening in the JCS. This includes a previously unexplored unique line broadening mechanism enabled by strongly coupled spins at low-field. Numerical simulations are used to model and refine the magnitudes and signs of J-couplings, as well as indirectly determine the 14N relaxation rates in a single 1D experiment that has a higher fidelity than observed in high-field NMR experiments.
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Affiliation(s)
- Adam R Altenhof
- MPA-Q, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | | | - Harris E Mason
- C-IIAC, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Marc A Alvarez
- B-TEK, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael W Malone
- MPA-Q, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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30
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Hommel U, Hurth K, Rondeau JM, Vulpetti A, Ostermeier D, Boettcher A, Brady JP, Hediger M, Lehmann S, Koch E, Blechschmidt A, Yamamoto R, Tundo Dottorello V, Haenni-Holzinger S, Kaiser C, Lehr P, Lingel A, Mureddu L, Schleberger C, Blank J, Ramage P, Freuler F, Eder J, Bornancin F. Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1β. Nat Commun 2023; 14:5497. [PMID: 37679328 PMCID: PMC10484922 DOI: 10.1038/s41467-023-41190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Human interleukin-1β (hIL-1β) is a pro-inflammatory cytokine involved in many diseases. While hIL-1β directed antibodies have shown clinical benefit, an orally available low-molecular weight antagonist is still elusive, limiting the applications of hIL-1β-directed therapies. Here we describe the discovery of a low-molecular weight hIL-1β antagonist that blocks the interaction with the IL-1R1 receptor. Starting from a low affinity fragment-based screening hit 1, structure-based optimization resulted in a compound (S)-2 that binds and antagonizes hIL-1β with single-digit micromolar activity in biophysical, biochemical, and cellular assays. X-ray analysis reveals an allosteric mode of action that involves a hitherto unknown binding site in hIL-1β encompassing two loops involved in hIL-1R1/hIL-1β interactions. We show that residues of this binding site are part of a conformationally excited state of the mature cytokine. The compound antagonizes hIL-1β function in cells, including primary human fibroblasts, demonstrating the relevance of this discovery for future development of hIL-1β directed therapeutics.
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Affiliation(s)
- Ulrich Hommel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Konstanze Hurth
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
| | - Jean-Michel Rondeau
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Daniela Ostermeier
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Boettcher
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jacob Peter Brady
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Michael Hediger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Elke Koch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Rina Yamamoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | | | | | - Christian Kaiser
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Philipp Lehr
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Luca Mureddu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christian Schleberger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Felix Freuler
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Joerg Eder
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland
| | - Frédéric Bornancin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002, Basel, Switzerland.
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31
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Enders L, Siklos M, Borggräfe J, Gaussmann S, Koren A, Malik M, Tomek T, Schuster M, Reiniš J, Hahn E, Rukavina A, Reicher A, Casteels T, Bock C, Winter GE, Hannich JT, Sattler M, Kubicek S. Pharmacological perturbation of the phase-separating protein SMNDC1. Nat Commun 2023; 14:4504. [PMID: 37587144 PMCID: PMC10432564 DOI: 10.1038/s41467-023-40124-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
SMNDC1 is a Tudor domain protein that recognizes di-methylated arginines and controls gene expression as an essential splicing factor. Here, we study the specific contributions of the SMNDC1 Tudor domain to protein-protein interactions, subcellular localization, and molecular function. To perturb the protein function in cells, we develop small molecule inhibitors targeting the dimethylarginine binding pocket of the SMNDC1 Tudor domain. We find that SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation behavior is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction and can be recapitulated in vitro. Inhibitors of the protein's Tudor domain drastically alter protein-protein interactions and subcellular localization, causing splicing changes for SMNDC1-dependent genes. These compounds will enable further pharmacological studies on the role of SMNDC1 in the regulation of nuclear condensates, gene regulation and cell identity.
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Affiliation(s)
- Lennart Enders
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jan Borggräfe
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Gaussmann
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Sloan Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währinger Straße 25a, 1090, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
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Dunlap JH, Ethier JG, Putnam-Neeb AA, Iyer S, Luo SXL, Feng H, Garrido Torres JA, Doyle AG, Swager TM, Vaia RA, Mirau P, Crouse CA, Baldwin LA. Continuous flow synthesis of pyridinium salts accelerated by multi-objective Bayesian optimization with active learning. Chem Sci 2023; 14:8061-8069. [PMID: 37538827 PMCID: PMC10395269 DOI: 10.1039/d3sc01303k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023] Open
Abstract
We report a human-in-the-loop implementation of the multi-objective experimental design via a Bayesian optimization platform (EDBO+) towards the optimization of butylpyridinium bromide synthesis under continuous flow conditions. The algorithm simultaneously optimized reaction yield and production rate (or space-time yield) and generated a well defined Pareto front. The versatility of EDBO+ was demonstrated by expanding the reaction space mid-campaign by increasing the upper temperature limit. Incorporation of continuous flow techniques enabled improved control over reaction parameters compared to common batch chemistry processes, while providing a route towards future automated syntheses and improved scalability. To that end, we applied the open-source Python module, nmrglue, for semi-automated nuclear magnetic resonance (NMR) spectroscopy analysis, and compared the acquired outputs against those obtained through manual processing methods from spectra collected on both low-field (60 MHz) and high-field (400 MHz) NMR spectrometers. The EDBO+ based model was retrained with these four different datasets and the resulting Pareto front predictions provided insight into the effect of data analysis on model predictions. Finally, quaternization of poly(4-vinylpyridine) with bromobutane illustrated the extension of continuous flow chemistry to synthesize functional materials.
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Affiliation(s)
- John H Dunlap
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- UES, Inc. Dayton OH 45431 USA
| | - Jeffrey G Ethier
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- UES, Inc. Dayton OH 45431 USA
| | - Amelia A Putnam-Neeb
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
- National Research Council Research Associate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Sanjay Iyer
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Shao-Xiong Lennon Luo
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Haosheng Feng
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | | | - Abigail G Doyle
- Department of Chemistry and Biochemistry, University of California Los Angeles CA 90095 USA
| | - Timothy M Swager
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Richard A Vaia
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Peter Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Christopher A Crouse
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
| | - Luke A Baldwin
- Materials and Manufacturing Directorate, Air Force Research Laboratory Wright-Patterson AFB OH 45433 USA
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van Aalst EJ, Jang J, Halligan TC, Wylie BJ. Strategies for acquisition of resonance assignment spectra of highly dynamic membrane proteins: a GPCR case study. JOURNAL OF BIOMOLECULAR NMR 2023; 77:191-202. [PMID: 37493866 PMCID: PMC10838152 DOI: 10.1007/s10858-023-00421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
In protein nuclear magnetic resonance (NMR), chemical shift assignment provides a wealth of information. However, acquisition of high-quality solid-state NMR spectra depends on protein-specific dynamics. For membrane proteins, bilayer heterogeneity further complicates this observation. Since the efficiency of cross-polarization transfer is strongly entwined with protein dynamics, optimal temperatures for spectral sensitivity and resolution will depend not only on inherent protein dynamics, but temperature-dependent phase properties of the bilayer environment. We acquired 1-, 2-, and 3D homo- and heteronuclear experiments of the chemokine receptor CCR3 in a 7:3 phosphatidylcholine:cholesterol lipid environment. 1D direct polarization, cross polarization (CP), and T2' experiments indicate sample temperatures below - 25 °C facilitate higher CP enhancement and longer-lived transverse relaxation times. T1rho experiments indicate intermediate timescales are minimized below a sample temperature of - 20 °C. 2D DCP NCA experiments indicated optimal CP efficiency and resolution at a sample temperature of - 30 °C, corroborated by linewidth analysis in 3D NCACX at - 30 °C compared to - 5 °C. This optimal temperature is concluded to be directly related the lipid phase transition, measured to be between - 20 and 15 °C based on rINEPT signal of all-trans and trans-gauche lipid acyl conformations. Our results have critical implications in acquisition of SSNMR membrane protein assignment spectra, as we hypothesize that different lipid compositions with different phase transition properties influence protein dynamics and therefore the optimal acquisition temperature.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Jun Jang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Ty C Halligan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA.
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34
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Laursen KR, Christensen NV, Mulder FA, Schullehner J, Hoffmann HJ, Jensen A, Møller P, Loft S, Olin AC, Rasmussen BB, Rosati B, Strandberg B, Glasius M, Bilde M, Sigsgaard T. Airway and systemic biomarkers of health effects after short-term exposure to indoor ultrafine particles from cooking and candles - A randomized controlled double-blind crossover study among mild asthmatic subjects. Part Fibre Toxicol 2023; 20:26. [PMID: 37430267 DOI: 10.1186/s12989-023-00537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND There is insufficient knowledge about the systemic health effects of exposure to fine (PM2.5) and ultrafine particles emitted from typical indoor sources, including cooking and candlelight burning. We examined whether short-term exposure to emissions from cooking and burning candles cause inflammatory changes in young individuals with mild asthma. Thirty-six non-smoking asthmatics participated in a randomized controlled double-blind crossover study attending three exposure sessions (mean PM2.5 µg/m3; polycyclic aromatic hydrocarbons ng/m3): (a) air mixed with emissions from cooking (96.1; 1.1), (b) air mixed with emissions from candles (89.8; 10), and (c) clean filtered air (5.8; 1.0). Emissions were generated in an adjacent chamber and let into a full-scale exposure chamber where participants were exposed for five hours. Several biomarkers were assessed in relation to airway and systemic inflammatory changes; the primary outcomes of interest were surfactant Protein-A (SP-A) and albumin in droplets in exhaled air - novel biomarkers for changes in the surfactant composition of small airways. Secondary outcomes included cytokines in nasal lavage, cytokines, C-reactive protein (CRP), epithelial progenitor cells (EPCs), genotoxicity, gene expression related to DNA-repair, oxidative stress, and inflammation, as well as metabolites in blood. Samples were collected before exposure start, right after exposure and the next morning. RESULTS SP-A in droplets in exhaled air showed stable concentrations following candle exposure, while concentrations decreased following cooking and clean air exposure. Albumin in droplets in exhaled air increased following exposure to cooking and candles compared to clean air exposure, although not significant. Oxidatively damaged DNA and concentrations of some lipids and lipoproteins in the blood increased significantly following exposure to cooking. We found no or weak associations between cooking and candle exposure and systemic inflammation biomarkers including cytokines, CRP, and EPCs. CONCLUSIONS Cooking and candle emissions induced effects on some of the examined health-related biomarkers, while no effect was observed in others; Oxidatively damaged DNA and concentrations of lipids and lipoproteins were increased in blood after exposure to cooking, while both cooking and candle emissions slightly affected the small airways including the primary outcomes SP-A and albumin. We found only weak associations between the exposures and systemic inflammatory biomarkers. Together, the results show the existence of mild inflammation following cooking and candle exposure.
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Affiliation(s)
- Karin Rosenkilde Laursen
- Environment, Occupation and Health, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Nichlas Vous Christensen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Frans Aa Mulder
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jörg Schullehner
- Environment, Occupation and Health, Department of Public Health, Aarhus University, Aarhus, Denmark
- Geological Survey of Denmark and Greenland, Aarhus, Denmark
| | - Hans Jürgen Hoffmann
- Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | - Annie Jensen
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Aarhus, Denmark
| | - Peter Møller
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Aarhus, Denmark
| | - Steffen Loft
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Aarhus, Denmark
| | - Anna-Carin Olin
- Department of Public Health and Community Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Bernadette Rosati
- Department of Chemistry, Aarhus University, Aarhus, Denmark
- Faculty of Physics, University of Vienna, Vienna, Austria
| | - Bo Strandberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | | | - Merete Bilde
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Torben Sigsgaard
- Environment, Occupation and Health, Department of Public Health, Aarhus University, Aarhus, Denmark.
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35
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Ikari M, Yagi H, Kasai T, Inomata K, Ito M, Higuchi K, Matsuda N, Ito Y, Kigawa T. Direct Observation of Membrane-Associated H-Ras in the Native Cellular Environment by In-Cell 19F-NMR Spectroscopy. JACS AU 2023; 3:1658-1669. [PMID: 37388687 PMCID: PMC10302746 DOI: 10.1021/jacsau.3c00108] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 07/01/2023]
Abstract
Ras acts as a molecular switch to control intracellular signaling on the plasma membrane (PM). Elucidating how Ras associates with PM in the native cellular environment is crucial for understanding its control mechanism. Here, we used in-cell nuclear magnetic resonance (NMR) spectroscopy combined with site-specific 19F-labeling to explore the membrane-associated states of H-Ras in living cells. The site-specific incorporation of p-trifluoromethoxyphenylalanine (OCF3Phe) at three different sites of H-Ras, i.e., Tyr32 in switch I, Tyr96 interacting with switch II, and Tyr157 on helix α5, allowed the characterization of their conformational states depending on the nucleotide-bound states and an oncogenic mutational state. Exogenously delivered 19F-labeled H-Ras protein containing a C-terminal hypervariable region was assimilated via endogenous membrane-trafficking, enabling proper association with the cell membrane compartments. Despite poor sensitivity of the in-cell NMR spectra of membrane-associated H-Ras, the Bayesian spectral deconvolution identified distinct signal components on three 19F-labeled sites, thus offering the conformational multiplicity of H-Ras on the PM. Our study may be helpful in elucidating the atomic-scale picture of membrane-associated proteins in living cells.
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Affiliation(s)
- Masaomi Ikari
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Hiromasa Yagi
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Takuma Kasai
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- PRESTO/Japan
Science and Technology Agency, Saitama 332-0012, Japan
| | - Kohsuke Inomata
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- PRESTO/Japan
Science and Technology Agency, Saitama 332-0012, Japan
| | - Masahiro Ito
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Kae Higuchi
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Natsuko Matsuda
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
- SI Innovation
Center, Taiyo Nippon Sanso Corporation, Tokyo 206-0001, Japan
| | - Yutaka Ito
- Department
of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Takanori Kigawa
- RIKEN
Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
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36
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Dos Santos K, Bertho G, Caradeuc C, Baud V, Montagne A, Abergel D, Giraud N, Baudin M. A Toolbox for Glutamine Use in Dissolution Dynamic Nuclear Polarization: from Enzymatic Reaction Monitoring to the Study of Cellular Metabolic Pathways and Imaging. Chemphyschem 2023; 24:e202300151. [PMID: 36973178 DOI: 10.1002/cphc.202300151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023]
Abstract
Glutamine is under scrutiny regarding its metabolic deregulation linked to energetic reprogramming in cancer cells. Many analytical techniques have been used to better understand the impact of the metabolism of amino acids on biological processes, however only a few are suited to work with complex samples. Here, we report the use of a general dissolution dynamic nuclear polarization (D-DNP) formulation using an unexpensive radical as a multipurpose tool to study glutamine, with insights from enzymatic modelling to complex metabolic networks and fast imaging. First, hyperpolarized [5-13 C] glutamine is used as molecular probe to study the kinetic action of two enzymes: L-asparaginase that has been used as an anti-metabolic treatment for cancer, and glutaminase. These results are also compared with those acquired with another hyperpolarized amino acid, [1,4-13 C] asparagine. Second, we explored the use of hyperpolarized (HP) substrates to probe metabolic pathways by monitoring metabolic profiles arising from hyperpolarized glutamine in E. coli extracts. Finally, a highly concentrated sample formulation is proposed for the purpose of fast imaging applications. We think that this approach can be extended to formulate other amino acids as well as other metabolites and provide complementary insights into the analysis of metabolic networks.
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Affiliation(s)
- Karen Dos Santos
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Gildas Bertho
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Cédric Caradeuc
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Véronique Baud
- Laboratoire NF-κB, Différenciation et Cancer, Université Paris Cité, 24, Rue du faubourg Saint Jacques, 75014, Paris, France
| | - Aurélie Montagne
- Laboratoire NF-κB, Différenciation et Cancer, Université Paris Cité, 24, Rue du faubourg Saint Jacques, 75014, Paris, France
| | - Daniel Abergel
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université, 45 Rue d'Ulm, 75005, Paris, France
| | - Nicolas Giraud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Mathieu Baudin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université, 45 Rue d'Ulm, 75005, Paris, France
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37
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Bruno F, Fiorucci L, Ravera E. Sensitivity considerations on denoising series of spectra by singular value decomposition. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:373-379. [PMID: 36840610 DOI: 10.1002/mrc.5338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/11/2023]
Abstract
When acquiring series of spectra ( T 1 , T 2 , CP buildup curves, etc.) on samples with poor SNR, we are usually faced with choosing between taking a few points with a large number of scans to maximize the SNR or more points with a smaller number of scans to maximize the information content. In this Letter, we show how low-rank decomposition can be used to denoise a series of spectra, reducing the trade-off between the number of scans and the number of experiments.
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Affiliation(s)
- Francesco Bruno
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Letizia Fiorucci
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
- Florence Data Science, University of Florence, Firenze, 50134, Italy
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38
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Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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39
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Tatman BP, Franks WT, Brown SP, Lewandowski JR. Nuclear spin diffusion under fast magic-angle spinning in solid-state NMR. J Chem Phys 2023; 158:2890210. [PMID: 37171196 DOI: 10.1063/5.0142201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Solid-state nuclear spin diffusion is the coherent and reversible process through which spin order is transferred via dipolar couplings. With the recent increases in magic-angle spinning (MAS) frequencies and magnetic fields becoming routinely applied in solid-state nuclear magnetic resonance, understanding how the increased 1H resolution obtained affects spin diffusion is necessary for interpretation of several common experiments. To investigate the coherent contributions to spin diffusion with fast MAS, we have developed a low-order correlation in Liouville space model based on the work of Dumez et al. (J. Chem. Phys. 33, 224501, 2010). Specifically, we introduce a new method for basis set selection, which accounts for the resonance-offset dependence at fast MAS. Furthermore, we consider the necessity of including chemical shift, both isotropic and anisotropic, in the modeling of spin diffusion. Using this model, we explore how different experimental factors change the nature of spin diffusion. Then, we show case studies to exemplify the issues that arise in using spin diffusion techniques at fast spinning. We show that the efficiency of polarization transfer via spin diffusion occurring within a deuterated and 100% back-exchanged protein sample at 60 kHz MAS is almost entirely dependent on resonance offset. We additionally identify temperature-dependent magnetization transfer in beta-aspartyl L-alanine, which could be explained by the influence of an incoherent relaxation-based nuclear Overhauser effect.
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Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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40
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Guseva S, Schnapka V, Adamski W, Maurin D, Ruigrok RWH, Salvi N, Blackledge M. Liquid-Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins. J Am Chem Soc 2023; 145:10548-10563. [PMID: 37146977 DOI: 10.1021/jacs.2c13647] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation of flexible biomolecules has been identified as a ubiquitous phenomenon underlying the formation of membraneless organelles that harbor a multitude of essential cellular processes. We use nuclear magnetic resonance (NMR) spectroscopy to compare the dynamic properties of an intrinsically disordered protein (measles virus NTAIL) in the dilute and dense phases at atomic resolution. By measuring 15N NMR relaxation at different magnetic field strengths, we are able to characterize the dynamics of the protein in dilute and crowded conditions and to compare the amplitude and timescale of the different motional modes to those present in the membraneless organelle. Although the local backbone conformational sampling appears to be largely retained, dynamics occurring on all detectable timescales, including librational, backbone dihedral angle dynamics and segmental, chainlike motions, are considerably slowed down. Their relative amplitudes are also drastically modified, with slower, chain-like motions dominating the dynamic profile. In order to provide additional mechanistic insight, we performed extensive molecular dynamics simulations of the protein under self-crowding conditions at concentrations comparable to those found in the dense liquid phase. Simulation broadly reproduces the impact of formation of the condensed phase on both the free energy landscape and the kinetic interconversion between states. In particular, the experimentally observed reduction in the amplitude of the fastest component of backbone dynamics correlates with higher levels of intermolecular contacts or entanglement observed in simulations, reducing the conformational space available to this mode under strongly self-crowding conditions.
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Affiliation(s)
- Serafima Guseva
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Vincent Schnapka
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Wiktor Adamski
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Rob W H Ruigrok
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, 71, Avenue des Martyrs, 38000 Grenoble, France
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41
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Pavao A, Girinathan B, Peltier J, Altamirano Silva P, Dupuy B, Muti IH, Malloy C, Cheng LL, Bry L. Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling. Nat Chem Biol 2023; 19:556-564. [PMID: 36894723 PMCID: PMC10154198 DOI: 10.1038/s41589-023-01275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-resolution magic angle spinning nuclear magnetic resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen's genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine's biosynthesis to support efficient energy generation, nitrogen handling and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.
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Affiliation(s)
- Aidan Pavao
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brintha Girinathan
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Ginkgo Bioworks, The Innovation and Design Building, Boston, MA, USA
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), 91198, University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pamela Altamirano Silva
- Centre for Investigations in Tropical Diseases, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Isabella H Muti
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig Malloy
- Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leo L Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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42
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Žic M, Pereverzyev S. Application of self-adapting regularization, machine learning tools and limits in Levenberg–Marquardt algorithm to solve CNLS problem. J Electroanal Chem (Lausanne) 2023. [DOI: 10.1016/j.jelechem.2023.117420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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43
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Azatian SB, Canny MD, Latham MP. Three segment ligation of a 104 kDa multi-domain protein by SrtA and OaAEP1. JOURNAL OF BIOMOLECULAR NMR 2023; 77:25-37. [PMID: 36539644 PMCID: PMC10149453 DOI: 10.1007/s10858-022-00409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/28/2022] [Indexed: 05/03/2023]
Abstract
NMR spectroscopy is an excellent tool for studying protein structure and dynamics which provides a deeper understanding of biological function. As the size of the biomolecule of interest increases, it can become advantageous to dilute the number of observed signals in the NMR spectrum to decrease spectral overlap and increase resolution. One way to limit the number of resonances in the NMR data is by selectively labeling a smaller domain within the larger macromolecule, a process called segmental isotopic labeling. Many examples of segmental isotopic labeling have been described where two segments of a protein are ligated together by chemical or enzymatic means, but there are far fewer descriptions of a three or more segment ligation reaction. Herein, we describe an enzymatic segmental labeling scheme that combines the widely used Sortase A and more recently described OaAEP1 for a two site ligation strategy. In preparation to study proposed long-range allostery in the 104 kDa DNA damage repair protein Rad50, we ligated side-chain methyl group labeled Zn Hook domain between two long segments of otherwise unlabeled P.furiosus Rad50. Enzymatic activity data demonstrated that the scars resulting from the ligation reactions did not affect Rad50 function within the Mre11-Rad50 DNA double strand break repair complex. Finally, methyl-based NMR spectroscopy confirmed the formation of the full-length ligated protein. Our strategy highlights the strengths of OaAEP1 for segmental labeling, namely faster reaction times and a smaller recognition sequence, and provides a straightforward template for using these two enzymes in multisite segmental labeling reactions.
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Affiliation(s)
- Stephan B Azatian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marella D Canny
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael P Latham
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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44
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Arunachalam V, Sharma K, Mote KR, Madhu PK. Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 124:101858. [PMID: 36796278 DOI: 10.1016/j.ssnmr.2023.101858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C521, and its supercycled version SPC521, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC521 sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U-13C-alanine and 1,4-13C-labelled ammonium phthalate which include 13Cα-13Cβ, 13Cα-13Co, and 13Co-13Co spin systems, and adenosine 5'- triphosphate disodium salt trihydrate (ATP⋅3H2O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, 13Co-13Co. Simulations and experiments are shown to corroborate the results.
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Affiliation(s)
- Vaishali Arunachalam
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kshama Sharma
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
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45
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Kaushik Rangadurai A, Toyama Y, Kay LE. Practical considerations for the measurement of near-surface electrostatics based on solvent paramagnetic relaxation enhancements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 349:107400. [PMID: 36796143 DOI: 10.1016/j.jmr.2023.107400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Electrostatic interactions can play important roles in regulating various biological processes. Quantifying surface electrostatics of biomolecules is, therefore, of significant interest. Recent advances in solution NMR spectroscopy have enabled site-specific measurements of de novo near-surface electrostatic potentials (ϕENS) based on a comparison of solvent paramagnetic relaxation enhancements generated from differently charged paramagnetic co-solutes with similar structures. Although the NMR-derived near-surface electrostatic potentials have been shown to agree with theoretical calculations in the context of folded proteins and nucleic acids, such benchmark comparisons may not always be possible, particularly in cases where high-resolution structural models are lacking, such as in the study of intrinsically disordered proteins. Cross-validation of ϕENS potentials can be achieved by comparing values obtained using three pairs of paramagnetic co-solutes, each with a different net charge. Notably we have found cases where agreement of ϕENS potentials between the three pairs is poor and herein we investigate the source of this discrepancy in some detail. We show that for the systems considered here ϕENS potentials obtained from cationic and anionic co-solutes are accurate and that the use of paramagnetic co-solutes with different structures can be a viable option for validation, although the optimal choice of paramagnetic compounds depends on the system of interest.
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Affiliation(s)
- Atul Kaushik Rangadurai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.
| | - Yuki Toyama
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Hospital for Sick Children, Program in Molecular Medicine, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.
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46
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Hestenes J, Sadowski JT, May R, Marbella LE. Transition Metal Dissolution Mechanisms and Impacts on Electronic Conductivity in Composite LiNi 0.5Mn 1.5O 4 Cathode Films. ACS MATERIALS AU 2023; 3:88-101. [PMID: 38089724 PMCID: PMC9999480 DOI: 10.1021/acsmaterialsau.2c00060] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 01/05/2024]
Abstract
The high-voltage LiNi0.5Mn1.5O4 (LNMO) spinel cathode material offers high energy density storage capabilities without the use of costly Co that is prevalent in other Li-ion battery chemistries (e.g., LiNixMnyCozO2 (NMC)). Unfortunately, LNMO-containing batteries suffer from poor cycling performance because of the intrinsically coupled processes of electrolyte oxidation and transition metal dissolution that occurs at high voltage. In this work, we use operando electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopies to demonstrate that transition metal dissolution in LNMO is tightly coupled to HF formation (and thus, electrolyte oxidation reactions as detected with operando and in situ solution NMR), indicative of an acid-driven disproportionation reaction that occurs during delithiation (i.e., battery charging). Leveraging the temporal resolution (s-min) of magnetic resonance, we find that the LNMO particles accelerate the rate of LiPF6 decomposition and subsequent Mn2+ dissolution, possibly due to the acidic nature of terminal Mn-OH groups. X-ray photoemission electron microscopy (XPEEM) provides surface-sensitive and localized X-ray absorption spectroscopy (XAS) measurements, in addition to X-ray photoelectron spectroscopy (XPS), that indicate disproportionation is enabled by surface reconstruction upon charging, which leads to surface Mn3+ sites on the LNMO particle surface that can disproportionate into Mn2+(dissolved) and Mn4+(s). During discharge of the battery, we observe high quantities of metal fluorides (in particular, MnF2) in the cathode electrolyte interphase (CEI) on LNMO as well as the conductive carbon additives in the composite. Electronic conductivity measurements indicate that the MnF2 decreases film conductivity by threefold compared to LiF, suggesting that this CEI component may impede both the ionic and electronic properties of the cathode. Ultimately, to prevent transition metal dissolution and the associated side reactions in spinel-type cathodes (particularly those that operate at high voltages like LNMO), the use of electrolytes that offer improved anodic stability and prevent acid byproducts will likely be necessary.
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Affiliation(s)
- Julia
C. Hestenes
- Program
of Materials Science and Engineering, Department of Applied Physics
and Applied Mathematics, Columbia University, New York, New York10027, United States
| | - Jerzy T. Sadowski
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York11973, United States
| | - Richard May
- Department
of Chemical Engineering, Columbia University, New York, New York10027, United States
| | - Lauren E. Marbella
- Department
of Chemical Engineering, Columbia University, New York, New York10027, United States
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47
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Dregni AJ, McKay MJ, Surya W, Queralt-Martin M, Medeiros-Silva J, Wang HK, Aguilella V, Torres J, Hong M. The Cytoplasmic Domain of the SARS-CoV-2 Envelope Protein Assembles into a β-Sheet Bundle in Lipid Bilayers. J Mol Biol 2023; 435:167966. [PMID: 36682677 PMCID: PMC9851921 DOI: 10.1016/j.jmb.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein forms a pentameric ion channel in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of the infected cell. The cytoplasmic domain of E interacts with host proteins to cause virus pathogenicity and may also mediate virus assembly and budding. To understand the structural basis of these functions, here we investigate the conformation and dynamics of an E protein construct (residues 8-65) that encompasses the transmembrane domain and the majority of the cytoplasmic domain using solid-state NMR. 13C and 15N chemical shifts indicate that the cytoplasmic domain adopts a β-sheet-rich conformation that contains three β-strands separated by turns. The five subunits associate into an umbrella-shaped bundle that is attached to the transmembrane helices by a disordered loop. Water-edited NMR spectra indicate that the third β-strand at the C terminus of the protein is well hydrated, indicating that it is at the surface of the β-bundle. The structure of the cytoplasmic domain cannot be uniquely determined from the inter-residue correlations obtained here due to ambiguities in distinguishing intermolecular and intramolecular contacts for a compact pentameric assembly of this small domain. Instead, we present four structural topologies that are consistent with the measured inter-residue contacts. These data indicate that the cytoplasmic domain of the SARS-CoV-2 E protein has a strong propensity to adopt β-sheet conformations when the protein is present at high concentrations in lipid bilayers. The equilibrium between the β-strand conformation and the previously reported α-helical conformation may underlie the multiple functions of E in the host cell and in the virion.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Maria Queralt-Martin
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Vicente Aguilella
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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48
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Smrt ST, Gonzalez Salguero N, Thomas JK, Zandian M, Poirier MG, Jaroniec CP. Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy. Front Mol Biosci 2023; 9:1106588. [PMID: 36660422 PMCID: PMC9846530 DOI: 10.3389/fmolb.2022.1106588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin, a dynamic protein-DNA complex that regulates eukaryotic genome accessibility and essential functions, is composed of nucleosomes connected by linker DNA with each nucleosome consisting of DNA wrapped around an octamer of histones H2A, H2B, H3 and H4. Magic angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy can yield unique insights into histone structure and dynamics in condensed nucleosomes and nucleosome arrays representative of chromatin at physiological concentrations. Recently we used J-coupling-based solid-state NMR methods to investigate with residue-specific resolution the conformational dynamics of histone H3 N-terminal tails in 16-mer nucleosome arrays containing 15, 30 or 60 bp DNA linkers. Here, we probe the H3 core domain in the 16-mer arrays as a function of DNA linker length via dipolar coupling-based 1H-detected solid-state NMR techniques. Specifically, we established nearly complete assignments of backbone chemical shifts for H3 core residues in arrays with 15-60 bp DNA linkers reconstituted with 2H,13C,15N-labeled H3. Overall, these chemical shifts were similar irrespective of the DNA linker length indicating no major changes in H3 core conformation. Notably, however, multiple residues at the H3-nucleosomal DNA interface in arrays with 15 bp DNA linkers exhibited relatively pronounced differences in chemical shifts and line broadening compared to arrays with 30 and 60 bp linkers. These findings are consistent with increased heterogeneity in nucleosome packing and structural strain within arrays containing short DNA linkers that likely leads to side-chains of these interfacial residues experiencing alternate conformations or shifts in their rotamer populations relative to arrays with the longer DNA linkers.
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Affiliation(s)
- Sean T. Smrt
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Nicole Gonzalez Salguero
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States,*Correspondence: Christopher P. Jaroniec,
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49
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Jahangiri A, Han X, Lesovoy D, Agback T, Agback P, Achour A, Orekhov V. NMR spectrum reconstruction as a pattern recognition problem. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107342. [PMID: 36459916 DOI: 10.1016/j.jmr.2022.107342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern recognition of the corresponding point spread function (PSF) pattern produced by each spectral peak resulting in the highest quality and robust reconstruction of the NUS spectra as demonstrated in simulations and exemplified in this work on 2D 1H-15N correlation spectra of three representative globular proteins with different sizes: Ubiquitin (8.6 kDa), Azurin (14 kDa), and Malt1 (44 kDa). The pattern recognition by WNN is also demonstrated for successful virtual homo-decoupling in a 2D methyl 1H-13C - HMQC spectrum of MALT1. We demonstrate using WNN that prior knowledge about the NUS schedule, which so far was not been fully exploited, can be used for designing new powerful NMR processing techniques that surpass the existing algorithmic methods.
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Affiliation(s)
- Amir Jahangiri
- Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg 40530, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Dmitry Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, Moscow 117997, Russia
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala 75007, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala 75007, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg 40530, Sweden.
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50
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Bolik-Coulon N, Sever AIM, Harkness RW, Aramini JM, Toyama Y, Hansen DF, Kay LE. Less is more: A simple methyl-TROSY based pulse scheme offers improved sensitivity in applications to high molecular weight complexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107326. [PMID: 36508761 DOI: 10.1016/j.jmr.2022.107326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
The HMQC pulse sequence and variants thereof have been exploited in studies of high molecular weight protein complexes, taking advantage of the fact that fast and slow relaxing magnetization components are sequestered along two distinct magnetization transfer pathways. Despite the simplicity of the HMQC scheme an even shorter version can be designed, based on elimination of the terminal refocusing period, as a further means of increasing signal. Here we present such an experiment, and show that significant sensitivity gains, in some cases by factors of two or more, are realized in studies of proteins varying in molecular masses from 100 kDa to 1 MDa.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Robert W Harkness
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - James M Aramini
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yuki Toyama
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
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