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Ghafoori SM, Sethi A, Petersen GF, Tanipour MH, Gooley PR, Forwood JK. RNA Binding Properties of SOX Family Members. Cells 2024; 13:1202. [PMID: 39056784 PMCID: PMC11274882 DOI: 10.3390/cells13141202] [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: 07/25/2023] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
SOX proteins are a family of transcription factors (TFs) that play critical functions in sex determination, neurogenesis, and chondrocyte differentiation, as well as cardiac, vascular, and lymphatic development. There are 20 SOX family members in humans, each sharing a 79-residue L-shaped high mobility group (HMG)-box domain that is responsible for DNA binding. SOX2 was recently shown to interact with long non-coding RNA and large-intergenic non-coding RNA to regulate embryonic stem cell and neuronal differentiation. The RNA binding region was shown to reside within the HMG-box domain; however, the structural details of this binding remain unclear. Here, we show that all SOX family members, except group H, interact with RNA. Our mutational experiments demonstrate that the disordered C-terminal region of the HMG-box domain plays an important role in RNA binding. Further, by determining a high-resolution structure of the HMG-box domain of the group H family member SOX30, we show that despite differences in RNA binding ability, SOX30 shares a very similar secondary structure with other SOX protein HMG-box domains. Together, our study provides insight into the interaction of SOX TFs with RNA.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Ashish Sethi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - Gayle F. Petersen
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Mohammad Hossein Tanipour
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Paul R. Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
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2
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Naudi-Fabra S, Elena-Real CA, Vedel IM, Tengo M, Motzny K, Jiang PL, Schmieder P, Liu F, Milles S. An extended interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis. Nat Commun 2024; 15:5884. [PMID: 39003270 PMCID: PMC11246429 DOI: 10.1038/s41467-024-50212-4] [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] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
The early phases of clathrin mediated endocytosis are organized through a highly complex interaction network mediated by clathrin associated sorting proteins (CLASPs) that comprise long intrinsically disordered regions (IDRs). AP180 is a CLASP exclusively expressed in neurons and comprises a long IDR of around 600 residues, whose function remains partially elusive. Using NMR spectroscopy, we discovered an extended and strong interaction site within AP180 with the major adaptor protein AP2, and describe its binding dynamics at atomic resolution. We find that the 70 residue-long site determines the overall interaction between AP180 and AP2 in a dynamic equilibrium between its bound and unbound states, while weaker binding sites contribute to the overall affinity at much higher concentrations of AP2. Our data suggest that this particular interaction site might play a central role in recruitment of adaptors to the clathrin coated pit, whereas more transient and promiscuous interactions allow reshaping of the interaction network until cargo uptake inside a coated vesicle.
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Affiliation(s)
- Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Carlos A Elena-Real
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Maud Tengo
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Kathrin Motzny
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Pin-Lian Jiang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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3
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Castaing-Cordier T, Crasnier S, Dubois D, Ladroue V, Buleté A, Prudhomme C, Charvoz C, Besacier F, Jacquemin D, Giraudeau P, Farjon J. Non-uniform sampling to enhance the performance of compact NMR for characterizing new psychoactive substances. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:378-385. [PMID: 37994198 DOI: 10.1002/mrc.5416] [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: 08/24/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023]
Abstract
Efficient and robust analytical methods are needed to improve the identification and subsequent regulation of new psychoactive substances (NPS). NMR spectroscopy is a unique method able to determine the structure of small molecules such as NPS even in mixtures. However, high-field NMR analysis is associated with expensive purchase and maintenance costs. For more than a decade, compact NMR spectrometers have changed this paradigm. It was recently shown that a dedicated analytical workflow combining compact NMR and databases could identify the molecular structure of NPS, in spite of the lower spectral dispersion and sensitivity of compact spectrometers. This approach relies on 1H-13C HSQC to both recognize NPS and elucidate the structure of unknown substances. Still, its performance is limited by the need to compromise between resolution and experiment time. Here, we show that this strategy can be significantly improved by implementing non-uniform sampling (NUS) to improve spectral resolution in the 13C dimension of HSQC at no cost in terms of experiment time. Gains in the range of 3 to 4 in resolution are achieved for pure NPS and for a mixture. Finally, 2D HSQC with NUS was applied to improve the identification of NPS with the assistance of databases. The resulting method appears as a useful tool for the characterization of NPS in mixtures, which is essential for forensic laboratories.
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Affiliation(s)
| | | | - Damien Dubois
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Virginie Ladroue
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Audrey Buleté
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Cédric Prudhomme
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Céline Charvoz
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Fabrice Besacier
- Laboratoire de police scientifique de Lyon, Service National de police scientifique, Ecully, France
| | - Denis Jacquemin
- CNRS, CEISAM UMR 6230, Nantes Université, Nantes, France
- Institut Universitaire de France, Paris, France
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4
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Aljedani SS, Aldehaiman A, Sandholu A, Alharbi S, Mak VC, Wu H, Lugari A, Jaremko M, Morelli X, Backer JW, Ladbury JE, Nowakowski M, Cheung LW, Arold ST. Functional selection in SH3-mediated activation of the PI3 kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591319. [PMID: 38746413 PMCID: PMC11092569 DOI: 10.1101/2024.04.30.591319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The phosphoinositide-3 kinase (PI3K), a heterodimeric enzyme, plays a pivotal role in cellular metabolism and survival. Its deregulation is associated with major human diseases, particularly cancer. The p85 regulatory subunit of PI3K binds to the catalytic p110 subunit via its C-terminal domains, stabilising it in an inhibited state. Certain Src homology 3 (SH3) domains can activate p110 by binding to the proline-rich (PR) 1 motif located at the N-terminus of p85. However, the mechanism by which this N-terminal interaction activates the C-terminally bound p110 remains elusive. Moreover, the intrinsically poor ligand selectivity of SH3 domains raises the question of how they can control PI3K. Combining structural, biophysical, and functional methods, we demonstrate that the answers to both these unknown issues are linked: PI3K-activating SH3 domains engage in additional "tertiary" interactions with the C-terminal domains of p85, thereby relieving their inhibition of p110. SH3 domains lacking these tertiary interactions may still bind to p85 but cannot activate PI3K. Thus, p85 uses a functional selection mechanism that precludes nonspecific activation rather than nonspecific binding. This separation of binding and activation may provide a general mechanism for how biological activities can be controlled by promiscuous protein-protein interaction domains.
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Affiliation(s)
- Safia S. Aljedani
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Abdullah Aldehaiman
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Anandsukeerthi Sandholu
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Siba Alharbi
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Victor C.Y. Mak
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Haiyan Wu
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Adrien Lugari
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
| | - Xavier Morelli
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille University, 13009 Marseille, France
| | - Jonathan W. Backer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John E. Ladbury
- School of Molecular and Cellular Biology, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Lydia W.T. Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering Division, Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 2395-56900, Kingdom of Saudi Arabia
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5
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Cuozzo F, Viloria K, Shilleh AH, Nasteska D, Frazer-Morris C, Tong J, Jiao Z, Boufersaoui A, Marzullo B, Rosoff DB, Smith HR, Bonner C, Kerr-Conte J, Pattou F, Nano R, Piemonti L, Johnson PRV, Spiers R, Roberts J, Lavery GG, Clark A, Ceresa CDL, Ray DW, Hodson L, Davies AP, Rutter GA, Oshima M, Scharfmann R, Merrins MJ, Akerman I, Tennant DA, Ludwig C, Hodson DJ. LDHB contributes to the regulation of lactate levels and basal insulin secretion in human pancreatic β cells. Cell Rep 2024; 43:114047. [PMID: 38607916 PMCID: PMC11164428 DOI: 10.1016/j.celrep.2024.114047] [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: 03/16/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Using 13C6 glucose labeling coupled to gas chromatography-mass spectrometry and 2D 1H-13C heteronuclear single quantum coherence NMR spectroscopy, we have obtained a comparative high-resolution map of glucose fate underpinning β cell function. In both mouse and human islets, the contribution of glucose to the tricarboxylic acid (TCA) cycle is similar. Pyruvate fueling of the TCA cycle is primarily mediated by the activity of pyruvate dehydrogenase, with lower flux through pyruvate carboxylase. While the conversion of pyruvate to lactate by lactate dehydrogenase (LDH) can be detected in islets of both species, lactate accumulation is 6-fold higher in human islets. Human islets express LDH, with low-moderate LDHA expression and β cell-specific LDHB expression. LDHB inhibition amplifies LDHA-dependent lactate generation in mouse and human β cells and increases basal insulin release. Lastly, cis-instrument Mendelian randomization shows that low LDHB expression levels correlate with elevated fasting insulin in humans. Thus, LDHB limits lactate generation in β cells to maintain appropriate insulin release.
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Affiliation(s)
- Federica Cuozzo
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Katrina Viloria
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ali H Shilleh
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daniela Nasteska
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Charlotte Frazer-Morris
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jason Tong
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Zicong Jiao
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK; Geneplus-Beijing, Changping District, Beijing 102206, China
| | - Adam Boufersaoui
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Bryan Marzullo
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Daniel B Rosoff
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Oxford Kavli Centre for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hannah R Smith
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Caroline Bonner
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000 Lille, France
| | - Julie Kerr-Conte
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000 Lille, France
| | - Francois Pattou
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000 Lille, France
| | - Rita Nano
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Lorenzo Piemonti
- San Raffaele Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Paul R V Johnson
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rebecca Spiers
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Gareth G Lavery
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK; Centre for Systems Health and Integrated Metabolic Research (SHiMR), Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Anne Clark
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Carlo D L Ceresa
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Oxford Kavli Centre for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Amy P Davies
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; CHUM Research Centre and Faculty of Medicine, University of Montreal, Montreal, QC, Canada; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Masaya Oshima
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Raphaël Scharfmann
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS UMR 8104, 75014 Paris, France
| | - Matthew J Merrins
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Wisconsin-Madison, Madison, WI 53705, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - Christian Ludwig
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK; Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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6
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Sakhaii P, Bohorc B, Schliedermann U, Griesinger C. Efficient Access to Elusive 1D 13C NMR Spectra through Highly Resolved 1H, 13C-Long-Range Correlation Spectroscopy. Anal Chem 2024; 96:5843-5851. [PMID: 38452395 DOI: 10.1021/acs.analchem.3c05277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
A method for obtaining 1D 13C NMR spectra from natural products or metabolites using proton detection is described. The approach delivers singlets for every 13C signal without conducting any broadband 1H decoupling (CPD) and is based on calculating 13C projections from constant-time HMBC and conventional HSQC experiments, recorded at high digital resolution and processed to pure phases. Paramount to the proposed method is the implication of nonuniform sampling and echo processing. The echo processing produces phase-sensitive 2D CT-HMBC spectra with narrow 13C signal line shapes. Two simple HMBC pulse sequences are utilized with the suppression of homo- and heteronuclear couplings. Due to the removal of the 1H multiplet structure in F1 (no tilt at higher digital resolution), 13C singlets arise. An overall increase in 13C signal-to-noise (SINO) for all types of carbon multiplicities is observed, making the proposed technique superior compared to direct 13C excitation. For otherwise difficult-to-measure quaternary carbon atoms, a SINO enhancement of up to 6 and 12 depending on F1 resolution (3 and 6 Hz/point) is reported. Echo/anti-Echo signal detection cleans up the spectrum. Nonuniform sampling (NUS) lays the groundwork to significantly reduce the total acquisition time. Final 1D 13C projections are obtained by combining the 13C projection from CT HMBC and conventional HSQC. This orthogonal concept of combining the 13C projections from different spectra inherently minimizes the risk of missing 13C cross-peaks by inappropriate setting of long-range nJHC coupling delays and the shortcoming of T2 relaxations. The advantages and some limitations of the concept are discussed.
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Affiliation(s)
- Peyman Sakhaii
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Bojan Bohorc
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Uwe Schliedermann
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926 Frankfurt/Main, Germany
| | - Christian Griesinger
- NMR-Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
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7
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Ceccolini I, Kauffmann C, Holzinger J, Konrat R, Zawadzka-Kazimierczuk A. A set of cross-correlated relaxation experiments to probe the correlation time of two different and complementary spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 361:107661. [PMID: 38547550 DOI: 10.1016/j.jmr.2024.107661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024]
Abstract
Intrinsically disordered proteins (IDPs) defy the conventional structure-function paradigm by lacking a well-defined tertiary structure and exhibiting inherent flexibility. This flexibility leads to distinctive spin relaxation modes, reflecting isolated and specific motions within individual peptide planes. In this work, we propose a new pulse sequence to measure the longitudinal 13C' CSA-13C'-13Cα DD CCR rate [Formula: see text] and present a novel 3D version of the transverse [Formula: see text] CCR rate, adopting the symmetrical reconversion approach. We combined these rates with the analogous ΓxyN/NH and ΓzN/NH CCR rates to derive residue-specific correlation times for both spin-pairs within the same peptide plane. The presented approach offers a straightforward and intuitive way to compare the correlation times of two different and complementary spin vectors, anticipated to be a valuable aid to determine IDPs backbone dihedral angles distributions. We performed the proposed experiments on two systems: a folded protein ubiquitin and Coturnix japonica osteopontin, a prototypical IDP. Comparative analyses of the results show that the correlation times of different residues vary more for IDPs than globular proteins, indicating that the dynamics of IDPs is largely heterogeneous and dominated by local fluctuations.
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Affiliation(s)
- Irene Ceccolini
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | | | - Julian Holzinger
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Anna Zawadzka-Kazimierczuk
- University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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8
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Cattin-Ortolá J, Kaufman JGG, Gillingham AK, Wagstaff JL, Peak-Chew SY, Stevens TJ, Boulanger J, Owen DJ, Munro S. Cargo selective vesicle tethering: The structural basis for binding of specific cargo proteins by the Golgi tether component TBC1D23. SCIENCE ADVANCES 2024; 10:eadl0608. [PMID: 38552021 DOI: 10.1126/sciadv.adl0608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024]
Abstract
The Golgi-localized golgins golgin-97 and golgin-245 capture transport vesicles arriving from endosomes via the protein TBC1D23. The amino-terminal domain of TBC1D23 binds to the golgins, and the carboxyl-terminal domain of TBC1D23 captures the vesicles, but how it recognizes specific vesicles was unclear. A search for binding partners of the carboxyl-terminal domain unexpectedly revealed direct binding to carboxypeptidase D and syntaxin-16, known cargo proteins of the captured vesicles. Binding is via a threonine-leucine-tyrosine (TLY) sequence present in both proteins next to an acidic cluster. A crystal structure reveals how this acidic TLY motif binds to TBC1D23. An acidic TLY motif is also present in the tails of other endosome-to-Golgi cargo, and these also bind TBC1D23. Structure-guided mutations in the carboxyl-terminal domain that disrupt motif binding in vitro also block vesicle capture in vivo. Thus, TBC1D23 attached to golgin-97 and golgin-245 captures vesicles by a previously undescribed mechanism: the recognition of a motif shared by cargo proteins carried by the vesicle.
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Affiliation(s)
- Jérôme Cattin-Ortolá
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan G G Kaufman
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alison K Gillingham
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jane L Wagstaff
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sew-Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jérôme Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David J Owen
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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9
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Bashiri G, Bulloch EMM, Bramley WR, Davidson M, Stuteley SM, Young PG, Harris PWR, Naqvi MSH, Middleditch MJ, Schmitz M, Chang WC, Baker EN, Squire CJ. Poly-γ-glutamylation of biomolecules. Nat Commun 2024; 15:1310. [PMID: 38346985 PMCID: PMC10861534 DOI: 10.1038/s41467-024-45632-1] [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: 06/15/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Poly-γ-glutamate tails are a distinctive feature of archaeal, bacterial, and eukaryotic cofactors, including the folates and F420. Despite decades of research, key mechanistic questions remain as to how enzymes successively add glutamates to poly-γ-glutamate chains while maintaining cofactor specificity. Here, we show how poly-γ-glutamylation of folate and F420 by folylpolyglutamate synthases and γ-glutamyl ligases, non-homologous enzymes, occurs via processive addition of L-glutamate onto growing γ-glutamyl chain termini. We further reveal structural snapshots of the archaeal γ-glutamyl ligase (CofE) in action, crucially including a bulged-chain product that shows how the cofactor is retained while successive glutamates are added to the chain terminus. This bulging substrate model of processive poly-γ-glutamylation by terminal extension is arguably ubiquitous in such biopolymerisation reactions, including addition to folates, and demonstrates convergent evolution in diverse species from archaea to humans.
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Affiliation(s)
- Ghader Bashiri
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Esther M M Bulloch
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - William R Bramley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Madison Davidson
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Stephanie M Stuteley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Paul G Young
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Muhammad S H Naqvi
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Martin J Middleditch
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Michael Schmitz
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Edward N Baker
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- Maurice Wilkins Center for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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10
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Zhan H, Liu J, Fang Q, Chen X, Hu L. Accelerated Pure Shift NMR Spectroscopy with Deep Learning. Anal Chem 2024; 96:1515-1521. [PMID: 38232235 DOI: 10.1021/acs.analchem.3c04007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Pure shift nuclear magnetic resonance (NMR) spectroscopy presents a promising solution to provide sufficient spectral resolution and has been increasingly applied in various branches of chemistry, but the optimal resolution is generally accompanied by long experimental times. We present a proof of concept of deep learning for fast, high-quality, and reliable pure shift NMR reconstruction. The deep learning (DL) protocol allows one to eliminate undersampling artifacts, distinguish peaks with close chemical shifts, and reconstruct high-resolution pure shift NMR spectroscopy along with accelerated acquisition. More meaningfully, the lightweight neural network delivers satisfactory reconstruction performance on personal computers by several hundred simulated data learning, which somewhat lifts the prohibiting demand for a large volume of real training samples and advanced computing hardware generally required in DL projects. Additionally, an M-to-S strategy applicable to common DL cases is further exploited to boost the network generalization capability. As a result, this study takes a meaningful step toward deep learning protocols for broad chemical applications.
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Affiliation(s)
- Haolin Zhan
- Department of Biomedical Engineering, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Jiawei Liu
- Department of Biomedical Engineering, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qiyuan Fang
- Department of Biomedical Engineering, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xinyu Chen
- Department of Biomedical Engineering, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
| | - Liangliang Hu
- Department of Biomedical Engineering, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Optoelectronics Engineering, Hefei University of Technology, Hefei 230009, China
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11
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Lövestam S, Li D, Wagstaff JL, Kotecha A, Kimanius D, McLaughlin SH, Murzin AG, Freund SMV, Goedert M, Scheres SHW. Disease-specific tau filaments assemble via polymorphic intermediates. Nature 2024; 625:119-125. [PMID: 38030728 PMCID: PMC10764278 DOI: 10.1038/s41586-023-06788-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Intermediate species in the assembly of amyloid filaments are believed to play a central role in neurodegenerative diseases and may constitute important targets for therapeutic intervention1,2. However, structural information about intermediate species has been scarce and the molecular mechanisms by which amyloids assemble remain largely unknown. Here we use time-resolved cryogenic electron microscopy to study the in vitro assembly of recombinant truncated tau (amino acid residues 297-391) into paired helical filaments of Alzheimer's disease or into filaments of chronic traumatic encephalopathy3. We report the formation of a shared first intermediate amyloid filament, with an ordered core comprising residues 302-316. Nuclear magnetic resonance indicates that the same residues adopt rigid, β-strand-like conformations in monomeric tau. At later time points, the first intermediate amyloid disappears and we observe many different intermediate amyloid filaments, with structures that depend on the reaction conditions. At the end of both assembly reactions, most intermediate amyloids disappear and filaments with the same ordered cores as those from human brains remain. Our results provide structural insights into the processes of primary and secondary nucleation of amyloid assembly, with implications for the design of new therapies.
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Affiliation(s)
| | - David Li
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Abhay Kotecha
- Thermo Fisher Scientific, Eindhoven, The Netherlands
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12
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Bazzoni M, Mishra R, Dumez JN. Single-Scan Ultraselective NMR Experiments with Preserved Sensitivity. Angew Chem Int Ed Engl 2023; 62:e202314598. [PMID: 37878397 DOI: 10.1002/anie.202314598] [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: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
Selective NMR experiments provide rapid access to important structural information, and are essential to tackle the analysis of large molecules and complex mixtures. Single-scan ultraselective experiments are particularly useful, as they can rapidly select signals that overlap with other signals. Here, we describe a novel type of single-scan ultraselective NMR experiments that is robust against the effects of translational molecular diffusion, and thus make it possible to improve significantly the sensitivity of the experiment. This will largely broaden the applicability of this powerful class of experiments.
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Affiliation(s)
| | - Rituraj Mishra
- Nantes Université, CNRS, CEISAM UMR6230, 44000, Nantes, France
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13
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Agback T, Lesovoy D, Han X, Lomzov A, Sun R, Sandalova T, Orekhov VY, Achour A, Agback P. Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro. Commun Biol 2023; 6:1193. [PMID: 38001280 PMCID: PMC10673835 DOI: 10.1038/s42003-023-05584-6] [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: 06/16/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.
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Affiliation(s)
- Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
| | - Dmitry Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Alexander Lomzov
- Laboratory of Structural Biology, Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090, Novosibirsk, Russia
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Vladislav Yu Orekhov
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
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14
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Koscielniak J, Li J, Sail D, Swenson R, Anklin C, Rozovsky S, Byrd RA. Exploring Sulfur Sites in Proteins via Triple-Resonance 1H-Detected 77Se NMR. J Am Chem Soc 2023; 145. [PMID: 37906952 PMCID: PMC10655107 DOI: 10.1021/jacs.3c07225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023]
Abstract
NMR spectroscopy has been applied to virtually all sites within proteins and biomolecules; however, the observation of sulfur sites remains very challenging. Recent studies have examined 77Se as a replacement for sulfur and applied 77Se NMR in both the solution and solid states. As a spin-1/2 nuclide, 77Se is attractive as a probe of sulfur sites, and it has a very large chemical shift range (due to a large chemical shift anisotropy), which makes it potentially very sensitive to structural and/or binding interactions as well as dynamics. Despite being a spin-1/2 nuclide, there have been rather limited studies of 77Se, and the ability to use 1H-indirect detection has been sparse. Some examples exist, but in the absence of a directly bonded, nonexchangeable 1H, these have been largely limited to smaller molecules. We develop and illustrate approaches using double-labeling of 13C and 77Se in proteins that enable more sensitive triple-resonance schemes via multistep coherence transfers and 1H-detection. These methods require specialized hardware and decoupling schemes, which we developed and will be discussed.
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Affiliation(s)
- Janusz Koscielniak
- Leidos
Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Jess Li
- Center
for Structural Biology, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Deepak Sail
- Chemistry
and Synthesis Center, National Heart Lung
and Blood Institute, Bethesda, Maryland 20814, United States
| | - Rolf Swenson
- Chemistry
and Synthesis Center, National Heart Lung
and Blood Institute, Bethesda, Maryland 20814, United States
| | - Clemens Anklin
- Bruker
BioSpin Corp., Billerica, Massachusetts 01821, United States
| | - Sharon Rozovsky
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - R. Andrew Byrd
- Center
for Structural Biology, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
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15
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Leth JM, Newcombe EA, Grønnemose AL, Jørgensen JT, Qvist K, Clausen AS, Knudsen LBS, Kjaer A, Kragelund BB, Jørgensen TJD, Ploug M. Targeted imaging of uPAR expression in vivo with cyclic AE105 variants. Sci Rep 2023; 13:17248. [PMID: 37821532 PMCID: PMC10567728 DOI: 10.1038/s41598-023-43934-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: 08/17/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
A comprehensive literature reports on the correlation between elevated levels of urokinase-type plasminogen activator receptor (uPAR) and the severity of diseases with chronic inflammation including solid cancers. Molecular imaging is widely used as a non-invasive method to locate disease dissemination via full body scans and to stratify patients for targeted treatment. To date, the only imaging probe targeting uPAR that has reached clinical phase-II testing relies on a high-affinity 9-mer peptide (AE105), and several studies by positron emission tomography (PET) scanning or near-infra red (NIR) fluorescence imaging have validated its utility and specificity in vivo. While our previous studies focused on applying various reporter groups, the current study aims to improve uPAR-targeting properties of AE105. We successfully stabilized the small uPAR-targeting core of AE105 by constraining its conformational landscape by disulfide-mediated cyclization. Importantly, this modification mitigated the penalty on uPAR-affinity typically observed after conjugation to macrocyclic chelators. Cyclization did not impair tumor targeting efficiency of AE105 in vivo as assessed by PET imaging and a trend towards increased tracer uptake was observed. In future studies, we predict that this knowledge will aid development of new fluorescent AE105 derivatives with a view to optical imaging of uPAR to assist precision guided cancer surgery.
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Affiliation(s)
- Julie Maja Leth
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Estella Anne Newcombe
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anne Louise Grønnemose
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine Qvist
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Anne Skovsbo Clausen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Line Bruhn Schneider Knudsen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe Brandt Kragelund
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Michael Ploug
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark.
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16
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Vemulapalli SPB, Griesinger C, Dittmar T. Expanding the Limits of Structural Characterization of Marine Dissolved Organic Matter Using Nonuniform Sampling Frequency-Reversed Edited HSQC NMR. Anal Chem 2023; 95:14770-14776. [PMID: 37725656 PMCID: PMC10551856 DOI: 10.1021/acs.analchem.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
The multiplicity-edited heteronuclear single quantum correlation (ME-HSQC) NMR method is widely used for the structural characterization of marine dissolved organic matter (DOM), which is a complex molecular mixture comprising millions of individual compounds. However, the standard ME-HSQC suffers from significant signal cancellation and subsequent loss of crucial structural information due to the overlap between CH3/CH (positive) and CH2 (negative) cross-peaks in overcrowded regions. This study introduces nonuniform sampling in frequency-reversed ME-HSQC (NUS FR-ME-HSQC), highlighting its remarkable potential for the comprehensive structural characterization of marine DOM. By reversing the frequency of CH2 cross-peaks into an empty region, the FR-ME-HSQC method effectively simplifies the spectra and eliminates signal cancellation. We demonstrate that nonuniform sampling enables the acquisition of comparable spectra in half the time or significantly enhances the sensitivity in time-equivalent spectra. Comparative analysis also identifies vulnerable CH2 cross-peaks in the standard ME-HSQC that coincide with CH3 and CH cross-peaks, resulting in the loss of critical structural details. In contrast, the NUS FR-ME-HSQC retains these missing correlations, enabling in-depth characterization of marine DOM. These findings highlight the potential of NUS FR-ME-HSQC as an advanced NMR technique that effectively addresses challenges such as signal overcrowding and prolonged experimental times, enabling the thorough investigation of complex mixtures with implications in several fields, including chemistry, metabolomics, and environmental sciences. The advantages of NUS FR-ME-HSQC are experimentally demonstrated on two solid-phase-extracted DOM (SPE-DOM) samples from the surface and deep ocean. With this new technology, differences in the composition of DOM from various aquatic environments can be assigned to individual molecules.
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Affiliation(s)
- Sahithya Phani Babu Vemulapalli
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
| | - Christian Griesinger
- Department
of NMR Based Structural Biology, Max Planck
Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thorsten Dittmar
- Research
Group for Marine Geochemistry, Institute for Chemistry and Biology
of the Marine Environment (ICBM), University
of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz
Institute for Functional Marine Biodiversity at the University of
Oldenburg (HIFMB), 26129 Oldenburg, Germany
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17
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Wang Z, Guo D, Tu Z, Huang Y, Zhou Y, Wang J, Feng L, Lin D, You Y, Agback T, Orekhov V, Qu X. A Sparse Model-Inspired Deep Thresholding Network for Exponential Signal Reconstruction-Application in Fast Biological Spectroscopy. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:7578-7592. [PMID: 35120010 DOI: 10.1109/tnnls.2022.3144580] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nonuniform sampling (NUS) is a powerful approach to enable fast acquisition but requires sophisticated reconstruction algorithms. Faithful reconstruction from partially sampled exponentials is highly expected in general signal processing and many applications. Deep learning (DL) has shown astonishing potential in this field, but many existing problems, such as lack of robustness and explainability, greatly limit its applications. In this work, by combining the merits of the sparse model-based optimization method and data-driven DL, we propose a DL architecture for spectra reconstruction from undersampled data, called MoDern. It follows the iterative reconstruction in solving a sparse model to build the neural network, and we elaborately design a learnable soft-thresholding to adaptively eliminate the spectrum artifacts introduced by undersampling. Extensive results on both synthetic and biological data show that MoDern enables more robust, high-fidelity, and ultrafast reconstruction than the state-of-the-art methods. Remarkably, MoDern has a small number of network parameters and is trained on solely synthetic data while generalizing well to biological data in various scenarios. Furthermore, we extend it to an open-access and easy-to-use cloud computing platform (XCloud-MoDern), contributing a promising strategy for further development of biological applications.
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18
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Bhandari V, Reichheld SE, Houliston S, Lemak A, Arrowsmith CH, Sharpe S, Houry WA. The RavA-ViaA chaperone complex modulates bacterial persistence through its association with the fumarate reductase enzyme. J Biol Chem 2023; 299:105199. [PMID: 37660904 PMCID: PMC10585395 DOI: 10.1016/j.jbc.2023.105199] [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: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
Regulatory ATPase variant A (RavA) is a MoxR AAA+ protein that functions together with a partner protein termed von Willebrand factor type A interacting with AAA+ ATPase (ViaA). RavA-ViaA are functionally associated with anaerobic respiration in Escherichia coli through interactions with the fumarate reductase (Frd) electron transport complex. Through this association, RavA and ViaA modulate the activity of the Frd complex and, hence, are proposed to have chaperone-like activity. However, the functional role of RavA-ViaA in the cell is not yet well established. We had demonstrated that RavA-ViaA can sensitize E. coli cells to sublethal concentrations of the aminoglycoside class of antibiotics. Since Frd has been associated with bacterial persistence against antibiotics, the relationship of RavA-ViaA and Frd was explored within this context. Experiments performed here reveal a function of RavA-ViaA in bacterial persistence upon treatment with antibiotics through the association of the chaperone complex with Frd. As part of this work, the NMR structure of the N-terminal domain of ViaA was solved. The structure reveals a novel alpha helical fold, which we name the VAN fold, that has not been observed before. We show that this domain is required for the function of the chaperone complex. We propose that modulating the levels of RavA-ViaA could enhance the susceptibility of Gram-negative bacteria to antibiotics.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sean E Reichheld
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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19
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Szatkowska R, Furmanek E, Kierzek AM, Ludwig C, Adamczyk M. Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis. Int J Mol Sci 2023; 24:14763. [PMID: 37834211 PMCID: PMC10572830 DOI: 10.3390/ijms241914763] [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: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.
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Affiliation(s)
- Roza Szatkowska
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Emil Furmanek
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Andrzej M. Kierzek
- Certara UK Limited, Sheffield S1 2BJ, UK;
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
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20
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Huang Y, Zhao J, Wang Z, Orekhov V, Guo D, Qu X. Exponential Signal Reconstruction With Deep Hankel Matrix Factorization. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:6214-6226. [PMID: 34941531 DOI: 10.1109/tnnls.2021.3134717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Exponential function is a basic form of temporal signals, and how to fast acquire this signal is one of the fundamental problems and frontiers in signal processing. To achieve this goal, partial data may be acquired but result in severe artifacts in its spectrum, which is the Fourier transform of exponentials. Thus, reliable spectrum reconstruction is highly expected in the fast data acquisition in many applications, such as chemistry, biology, and medical imaging. In this work, we propose a deep learning method whose neural network structure is designed by imitating the iterative process in the model-based state-of-the-art exponentials' reconstruction method with the low-rank Hankel matrix factorization. With the experiments on synthetic data and realistic biological magnetic resonance signals, we demonstrate that the new method yields much lower reconstruction errors and preserves the low-intensity signals much better than compared methods.
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21
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Shchukina A, Schwarz TC, Nowakowski M, Konrat R, Kazimierczuk K. Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes. JOURNAL OF BIOMOLECULAR NMR 2023; 77:149-163. [PMID: 37237169 PMCID: PMC10406685 DOI: 10.1007/s10858-023-00418-3] [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: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
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22
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Bohg C, Öster C, Türkaydin B, Lisurek M, Sanchez-Carranza P, Lange S, Utesch T, Sun H, Lange A. The opening dynamics of the lateral gate regulates the activity of rhomboid proteases. SCIENCE ADVANCES 2023; 9:eadh3858. [PMID: 37467320 PMCID: PMC10355837 DOI: 10.1126/sciadv.adh3858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Rhomboid proteases hydrolyze substrate helices within the lipid bilayer to release soluble domains from the membrane. Here, we investigate the mechanism of activity regulation for this unique but wide-spread protein family. In the model rhomboid GlpG, a lateral gate formed by transmembrane helices TM2 and TM5 was previously proposed to allow access of the hydrophobic substrate to the shielded hydrophilic active site. In our study, we modified the gate region and either immobilized the gate by introducing a maleimide-maleimide (M2M) crosslink or weakened the TM2/TM5 interaction network through mutations. We used solid-state nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations, and molecular docking to investigate the resulting effects on structure and dynamics on the atomic level. We find that variants with increased dynamics at TM5 also exhibit enhanced activity, whereas introduction of a crosslink close to the active site strongly reduces activity. Our study therefore establishes a strong link between the opening dynamics of the lateral gate in rhomboid proteases and their enzymatic activity.
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Affiliation(s)
- Claudia Bohg
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Carl Öster
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Berke Türkaydin
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Michael Lisurek
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Pascal Sanchez-Carranza
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Tillmann Utesch
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Han Sun
- Research Unit Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institute of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
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23
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Walder BJ, McBrayer JD, Harrison KL, Fritzsching KJ. Multipurpose Broadband NMR Inversion Sequences. J Phys Chem A 2023. [PMID: 37318142 DOI: 10.1021/acs.jpca.3c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Solution-state 2D correlation experiments increase signal-to-noise, provide improved resolution, and inform about molecular connectivity. NMR experiments are compromised when the nuclei have broad chemical shift ranges that exceed the bandwidth of the experiment. Spectra acquired under these conditions are unphasable and artifact-prone, and peaks may disappear from the spectrum altogether. Existing remedies provide usable spectra only in specific experimental contexts. Here, we introduce a general broadband strategy that leads to a library of high performing NMR experiments. We achieve arbitrary and independent evolution of NMR interactions by only changing delays in our pulse block, letting the block replace inversion elements in any NMR experiment. The experiments improve the experimental bandwidth for both nuclei by an order of magnitude over conventional sequences, covering chemical shift ranges of most molecules, even at ultrahigh field. This library enables robust spectroscopy of molecules such as perfluorinated oils (19F{13C}) and fluorophosphorous compounds in battery electrolytes (19F{31P}).
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Affiliation(s)
- Brennan J Walder
- Sandia National Laboratories, 1611 Innovation Pkwy SE, Albuquerque, New Mexico 87123, United States
| | - Josefine D McBrayer
- Sandia National Laboratories, 1611 Innovation Pkwy SE, Albuquerque, New Mexico 87123, United States
| | - Katharine L Harrison
- Sandia National Laboratories, 1611 Innovation Pkwy SE, Albuquerque, New Mexico 87123, United States
| | - Keith J Fritzsching
- Sandia National Laboratories, 1611 Innovation Pkwy SE, Albuquerque, New Mexico 87123, United States
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24
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Bumbak F, Bower JB, Zemmer SC, Inoue A, Pons M, Paniagua JC, Yan F, Ford J, Wu H, Robson SA, Bathgate RAD, Scott DJ, Gooley PR, Ziarek JJ. Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314. Nat Commun 2023; 14:3328. [PMID: 37286565 PMCID: PMC10247727 DOI: 10.1038/s41467-023-38894-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13CεH3-methionine NMR spectroscopy to show that binding of phosphatidylinositol-4,5-bisphosphate (PIP2) to the receptor's intracellular surface allosterically tunes the timescale of motions at the orthosteric pocket and conserved activation motifs - without dramatically altering the structural ensemble. β-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on exchange rates. A β-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.
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Affiliation(s)
- Fabian Bumbak
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins and Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - James B Bower
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Skylar C Zemmer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Miquel Pons
- Biomolecular NMR laboratory, Department of Inorganic and Organic Chemistry, Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Juan Carlos Paniagua
- Department of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB), Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Fei Yan
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James Ford
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Scott A Robson
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health and Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- The Florey Institute of Neuroscience and Mental Health and Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
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25
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Lyukmanova EN, Mironov PA, Kulbatskii DS, Shulepko MA, Paramonov AS, Chernaya EM, Logashina YA, Andreev YA, Kirpichnikov MP, Shenkarev ZO. Recombinant Production, NMR Solution Structure, and Membrane Interaction of the Phα1β Toxin, a TRPA1 Modulator from the Brazilian Armed Spider Phoneutria nigriventer. Toxins (Basel) 2023; 15:378. [PMID: 37368679 DOI: 10.3390/toxins15060378] [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: 03/24/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Phα1β (PnTx3-6) is a neurotoxin from the spider Phoneutria nigriventer venom, originally identified as an antagonist of two ion channels involved in nociception: N-type voltage-gated calcium channel (CaV2.2) and TRPA1. In animal models, Phα1β administration reduces both acute and chronic pain. Here, we report the efficient bacterial expression system for the recombinant production of Phα1β and its 15N-labeled analogue. Spatial structure and dynamics of Phα1β were determined via NMR spectroscopy. The N-terminal domain (Ala1-Ala40) contains the inhibitor cystine knot (ICK or knottin) motif, which is common to spider neurotoxins. The C-terminal α-helix (Asn41-Cys52) stapled to ICK by two disulfides exhibits the µs-ms time-scale fluctuations. The Phα1β structure with the disulfide bond patterns Cys1-5, Cys2-7, Cys3-12, Cys4-10, Cys6-11, Cys8-9 is the first spider knottin with six disulfide bridges in one ICK domain, and is a good reference to other toxins from the ctenitoxin family. Phα1β has a large hydrophobic region on its surface and demonstrates a moderate affinity for partially anionic lipid vesicles at low salt conditions. Surprisingly, 10 µM Phα1β significantly increases the amplitude of diclofenac-evoked currents and does not affect the allyl isothiocyanate (AITC)-evoked currents through the rat TRPA1 channel expressed in Xenopus oocytes. Targeting several unrelated ion channels, membrane binding, and the modulation of TRPA1 channel activity allow for considering Phα1β as a gating modifier toxin, probably interacting with S1-S4 gating domains from a membrane-bound state.
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Affiliation(s)
- Ekaterina N Lyukmanova
- Department of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel A Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Dmitrii S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Mikhail A Shulepko
- Department of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
| | - Alexander S Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
| | - Elizaveta M Chernaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Yulia A Logashina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Yaroslav A Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Interdisciplinary Scientific and Educational School of Moscow University "Molecular Technologies of the Living Systems and Synthetic Biology", Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 119997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia
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26
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Lin Q, Meng C, Liu J, Liu F, Zhou Q, Liu J, Peng C, Xiong L. An Optimized Two-Dimensional Quantitative Nuclear Magnetic Resonance Strategy for the Rapid Quantitation of Diester-Type C 19-Diterpenoid Alkaloids from Aconitum carmichaelii. Anal Chem 2023. [PMID: 37209123 DOI: 10.1021/acs.analchem.2c05109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
With the development of nuclear magnetic resonance (NMR) spectrometers and probes, two-dimensional quantitative nuclear magnetic resonance (2D qNMR) technology with a high signal resolution and great application potential has become increasingly accessible for the quantitation of complex mixtures. However, the requirement that the relaxation recovery time be equal to at least five times T1 (longitudinal relaxation time) makes it difficult for 2D qNMR to simultaneously achieve high quantitative accuracy and high data acquisition efficiency. By comprehensively using relaxation optimization and nonuniform sampling, we successfully established an optimized 2D qNMR strategy for HSQC experiments at the half-hour level and then accurately quantified the diester-type C19-diterpenoid alkaloids in Aconitum carmichaelii. The optimized strategy had the advantages of high efficiency, high accuracy, good reproducibility, and low cost and thus could serve as a reference to optimize 2D qNMR experiments for quantitative analysis of natural products, metabolites, and other complex mixtures.
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Affiliation(s)
- Qiao Lin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chunwang Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jie Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Fei Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qinmei Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Juan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Liang Xiong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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27
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. Wellcome Open Res 2023; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.2] [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] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D- 1H, 13C-HSQC NMR spectra arising from 13C - 13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D- 1H, 13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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28
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Chhabra Y, Seiffert P, Gormal RS, Vullings M, Lee CMM, Wallis TP, Dehkhoda F, Indrakumar S, Jacobsen NL, Lindorff-Larsen K, Durisic N, Waters MJ, Meunier FA, Kragelund BB, Brooks AJ. Tyrosine kinases compete for growth hormone receptor binding and regulate receptor mobility and degradation. Cell Rep 2023; 42:112490. [PMID: 37163374 DOI: 10.1016/j.celrep.2023.112490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
Growth hormone (GH) acts via JAK2 and LYN to regulate growth, metabolism, and neural function. However, the relationship between these tyrosine kinases remains enigmatic. Through an interdisciplinary approach combining cell biology, structural biology, computation, and single-particle tracking on live cells, we find overlapping LYN and JAK2 Box1-Box2-binding regions in GH receptor (GHR). Our data implicate direct competition between JAK2 and LYN for GHR binding and imply divergent signaling profiles. We show that GHR exhibits distinct mobility states within the cell membrane and that activation of LYN by GH mediates GHR immobilization, thereby initiating its nanoclustering in the membrane. Importantly, we observe that LYN mediates cytokine receptor degradation, thereby controlling receptor turnover and activity, and this applies to related cytokine receptors. Our study offers insight into the molecular interactions of LYN with GHR and highlights important functions for LYN in regulating GHR nanoclustering, signaling, and degradation, traits broadly relevant to many cytokine receptors.
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Affiliation(s)
- Yash Chhabra
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21204, USA.
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rachel S Gormal
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Manon Vullings
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | | | - Tristan P Wallis
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Farhad Dehkhoda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sowmya Indrakumar
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nina L Jacobsen
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nela Durisic
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J Waters
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | - Frédéric A Meunier
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Andrew J Brooks
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia.
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29
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Ferreras-Gutiérrez M, Chaves-Arquero B, González-Magaña A, Merino N, Amusategui-Mateu I, Huecas S, Medrano FJ, Blanco FJ. Structural analysis of ING3 protein and histone H3 binding. Int J Biol Macromol 2023; 242:124724. [PMID: 37148949 DOI: 10.1016/j.ijbiomac.2023.124724] [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: 03/06/2023] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023]
Abstract
Proteins belonging to the ING family regulate the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at Lysine 4 (H3K4me3). This modification is recognized by the Plant HomeoDomain (PHD) present at the C-terminal region of the five ING proteins. ING3 facilitates acetylation of histones H2A and H4 by the NuA4-Tip60 MYST histone acetyl transferase complex, and it has been proposed to be an oncoprotein. The crystal structure of the N-terminal domain of ING3 shows that it forms homodimers with an antiparallel coiled-coil fold. The crystal structure of the PHD is similar to those of its four homologs. These structures explain the possible deleterious effects of ING3 mutations detected in tumors. The PHD binds histone H3K4me3 with low-micromolar, and binds the non-methylated histone with a 54-fold reduced affinity. Our structure explains the impact of site directed mutagenesis experiments on histone recognition. These structural features could not be confirmed for the full-length protein as solubility was insufficient for structural studies, but the structure of its folded domains suggest a conserved structural organization for the ING proteins as homodimers and bivalent readers of the histone H3K4me3 mark.
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Affiliation(s)
| | - Belén Chaves-Arquero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Amaia González-Magaña
- Instituto Biofisika and Departamento de Bioquímica y Biología Molecular (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Francisco J Medrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Francisco J Blanco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain.
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30
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Qiu T, Jahangiri A, Han X, Lesovoy D, Agback T, Agback P, Achour A, Qu X, Orekhov V. Resolution enhancement of NMR by decoupling with the low-rank Hankel model. Chem Commun (Camb) 2023; 59:5475-5478. [PMID: 37070867 PMCID: PMC10152455 DOI: 10.1039/d2cc06682c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/13/2023] [Indexed: 04/19/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although J-coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem. In this work, we introduce a new approach that uses a specific coupling value as prior knowledge, and the Hankel property of the exponential NMR signal to achieve broadband heteronuclear decoupling using the low-rank method. Our results on synthetic and realistic HMQC spectra demonstrate that the proposed method not only effectively enhances resolution by decoupling, but also maintains sensitivity and suppresses spectral artefacts. The approach can be combined with non-uniform sampling, which means that the resolution can be further improved without any extra acquisition time.
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Affiliation(s)
- Tianyu Qiu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Biomedical Intelligent Cloud Research and Development Centre, Xiamen University, Xiamen, 361005, China.
- Department of Chemistry and Molecular Biology, and Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden.
| | - Amir Jahangiri
- Department of Chemistry and Molecular Biology, and 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
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Biomedical Intelligent Cloud Research and Development Centre, Xiamen University, Xiamen, 361005, China.
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, and Swedish NMR Centre, University of Gothenburg, Box 465, Gothenburg, 40530, Sweden.
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31
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Vedel IM, Prestel A, Zhang Z, Skawinska NT, Stark H, Harris P, Kragelund BB, Peters GHJ. Structural characterization of human tryptophan hydroxylase 2 reveals that L-Phe is superior to L-Trp as the regulatory domain ligand. Structure 2023:S0969-2126(23)00127-2. [PMID: 37119821 DOI: 10.1016/j.str.2023.04.004] [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: 12/17/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in serotonin biosynthesis in the brain. Consequently, regulation of TPH2 is relevant for serotonin-related diseases, yet the regulatory mechanism of TPH2 is poorly understood and structural and dynamical insights are missing. We use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared with the natural substrate, L-Trp. Using cryo-EM, we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM two-dimensional (2D) class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2's regulatory mechanism.
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Affiliation(s)
- Ida M Vedel
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Zhenwei Zhang
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Natalia T Skawinska
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Pernille Harris
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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32
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Nixon-Abell J, Ruggeri FS, Qamar S, Herling TW, Czekalska MA, Shen Y, Wang G, King C, Fernandopulle MS, Sneideris T, Watson JL, Pillai VVS, Meadows W, Henderson JW, Chambers JE, Wagstaff JL, Williams SH, Coyle H, Lu Y, Zhang S, Marciniak SJ, Freund SMV, Derivery E, Ward ME, Vendruscolo M, Knowles TPJ, St George-Hyslop P. ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533832. [PMID: 36993242 PMCID: PMC10055329 DOI: 10.1101/2023.03.22.533832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Phase transitions of cellular proteins and lipids play a key role in governing the organisation and coordination of intracellular biology. The frequent juxtaposition of proteinaceous biomolecular condensates to cellular membranes raises the intriguing prospect that phase transitions in proteins and lipids could be co-regulated. Here we investigate this possibility in the ribonucleoprotein (RNP) granule-ANXA11-lysosome ensemble, where ANXA11 tethers RNP granule condensates to lysosomal membranes to enable their co-trafficking. We show that changes to the protein phase state within this system, driven by the low complexity ANXA11 N-terminus, induce a coupled phase state change in the lipids of the underlying membrane. We identify the ANXA11 interacting proteins ALG2 and CALC as potent regulators of ANXA11-based phase coupling and demonstrate their influence on the nanomechanical properties of the ANXA11-lysosome ensemble and its capacity to engage RNP granules. The phenomenon of protein-lipid phase coupling we observe within this system offers an important template to understand the numerous other examples across the cell whereby biomolecular condensates closely juxtapose cell membranes. GRAPHICAL ABSTRACT
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33
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Kathpalia A, Nagaraj N. Granger causality for compressively sensed sparse signals. Phys Rev E 2023; 107:034308. [PMID: 37072975 DOI: 10.1103/physreve.107.034308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/26/2023] [Indexed: 04/20/2023]
Abstract
Compressed sensing is a scheme that allows for sparse signals to be acquired, transmitted, and stored using far fewer measurements than done by conventional means employing the Nyquist sampling theorem. Since many naturally occurring signals are sparse (in some domain), compressed sensing has rapidly seen popularity in a number of applied physics and engineering applications, particularly in designing signal and image acquisition strategies, e.g., magnetic resonance imaging, quantum state tomography, scanning tunneling microscopy, and analog to digital conversion technologies. Contemporaneously, causal inference has become an important tool for the analysis and understanding of processes and their interactions in many disciplines of science, especially those dealing with complex systems. Direct causal analysis for compressively sensed data is required to avoid the task of reconstructing the compressed data. Also, for some sparse signals, such as for sparse temporal data, it may be difficult to discover causal relations directly using available data-driven or model-free causality estimation techniques. In this work, we provide a mathematical proof that structured compressed sensing matrices, specifically circulant and Toeplitz, preserve causal relationships in the compressed signal domain, as measured by Granger causality (GC). We then verify this theorem on a number of bivariate and multivariate coupled sparse signal simulations which are compressed using these matrices. We also demonstrate a real world application of network causal connectivity estimation from sparse neural spike train recordings from rat prefrontal cortex. In addition to demonstrating the effectiveness of structured matrices for GC estimation from sparse signals, we also show a computational time advantage of the proposed strategy for causal inference from compressed signals of both sparse and regular autoregressive processes as compared to standard GC estimation from original signals.
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Affiliation(s)
- Aditi Kathpalia
- Department of Complex Systems, Institute of Computer Science of the Czech Academy of Sciences, Prague 18200, Czech Republic
| | - Nithin Nagaraj
- Consciousness Studies Programme, National Institute of Advanced Studies, Bengaluru 560012, India
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34
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Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris. Int J Mol Sci 2023; 24:ijms24043973. [PMID: 36835381 PMCID: PMC9961634 DOI: 10.3390/ijms24043973] [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: 11/30/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (2H, 13C and 15N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the 1H-15N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.
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35
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Foo ACY, Nesbit JB, Gipson SAY, DeRose EF, Cheng H, Hurlburt BK, Kulis MD, Kim EH, Dreskin SC, Mustafa S, Maleki SJ, Mueller GA. Structure and IgE Cross-Reactivity among Cashew, Pistachio, Walnut, and Peanut Vicilin-Buried Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2990-2998. [PMID: 36728846 PMCID: PMC10402694 DOI: 10.1021/acs.jafc.2c07061] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Peanut and tree-nut allergies are frequently comorbid for reasons not completely understood. Vicilin-buried peptides (VBPs) are an emerging family of food allergens whose conserved structural fold could mediate peanut/tree-nut co-allergy. Peptide microarrays were used to identify immunoglobulin E (IgE) epitopes from the N-terminus of the vicilin allergens Ara h 1, Ana o 1, Jug r 2, and Pis v 3 using serum from three patient diagnosis groups: monoallergic to either peanuts or cashew/pistachio, or dual allergic. IgE binding peptides were highly prevalent in the VBP domains AH1.1, AO1.1, JR2.1, and PV3.1, but not in AO1.2, JR2.2, JR2.3, and PV3.2 nor the unstructured regions. The IgE profiles did not correlate with diagnosis group. The structure of the VBPs from cashew and pistachio was solved using solution-NMR. Comparisons of structural features suggest that the VBP scaffold from peanuts and tree-nuts can support cross-reactivity. This may help understand comorbidity and cross-reactivity despite a distant evolutionary origin.
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Affiliation(s)
- Alexander C Y Foo
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD-MR01, Durham, North Carolina 27709, United States
| | - Jacqueline B Nesbit
- Agricultural Research Service, United States Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, Louisiana 70124, United States
| | - Stephen A Y Gipson
- Agricultural Research Service, United States Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, Louisiana 70124, United States
| | - Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD-MR01, Durham, North Carolina 27709, United States
| | - Hsiaopo Cheng
- Agricultural Research Service, United States Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, Louisiana 70124, United States
| | - Barry K Hurlburt
- Agricultural Research Service, United States Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, Louisiana 70124, United States
| | - Michael D Kulis
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7220, United States
| | - Edwin H Kim
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7220, United States
| | - Stephen C Dreskin
- Division of Allergy and Clinical Immunology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045-2560, United States
| | - Shahzad Mustafa
- Rochester Regional Health, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Soheila J Maleki
- Agricultural Research Service, United States Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, Louisiana 70124, United States
| | - Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD-MR01, Durham, North Carolina 27709, United States
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36
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Ligands selectively tune the local and global motions of neurotensin receptor 1 (NTS 1). Cell Rep 2023; 42:112015. [PMID: 36680775 PMCID: PMC9930568 DOI: 10.1016/j.celrep.2023.112015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/05/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use 13Cε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS1). We establish that the NTS1 solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.
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37
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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38
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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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39
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Dumez JN. NMR methods for the analysis of mixtures. Chem Commun (Camb) 2022; 58:13855-13872. [PMID: 36458684 PMCID: PMC9753098 DOI: 10.1039/d2cc05053f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/19/2022] [Indexed: 07/31/2023]
Abstract
NMR spectroscopy is a powerful approach for the analysis of mixtures. Its usefulness arises in large part from the vast landscape of methods, and corresponding pulse sequences, that have been and are being designed to tackle the specific properties of mixtures of small molecules. This feature article describes a selection of methods that aim to address the complexity, the low concentrations, and the changing nature that mixtures can display. These notably include pure-shift and diffusion NMR methods, hyperpolarisation methods, and fast 2D NMR methods such as ultrafast 2D NMR and non-uniform sampling. Examples or applications are also described, in fields such as reaction monitoring and metabolomics, to illustrate the relevance and limitations of different methods.
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40
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Structural and functional insights into CST tethering in Tetrahymena thermophila telomerase. Structure 2022; 30:1565-1572.e4. [DOI: 10.1016/j.str.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/11/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022]
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41
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Timári I, Bagi P, Keglevich G, E. Kövér K. Ultrahigh-Resolution Homo- and Heterodecoupled 1H and TOCSY NMR Experiments. ACS OMEGA 2022; 7:43283-43289. [PMID: 36467931 PMCID: PMC9713892 DOI: 10.1021/acsomega.2c06102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
The original homonuclear decoupled (pure shift) experiments provide ultrahigh-resolution 1H spectra of compounds containing NMR-active heteronuclei of low natural isotopic abundance (e.g., 13C or 15N). In contrast, molecules containing highly abundant heteronuclei (like 31P or 19F) give doublets or a multiple of doublets in their homonuclear decoupled spectra, depending on the number of heteronuclear coupling partners and the magnitude of the respective coupling constants. In these cases, the complex and frequently overlapping signals may hamper the unambiguous assignment of resonances. Here, we present new heteronuclear decoupled (HD) PSYCHE 1H and TOCSY experiments, which result in simplified spectra with significantly increased resolution, allowing the reliable assessment of individual resonances. The utility of the experiments has been demonstrated on a challenging stereoisomeric mixture of a platinum-phosphine complex, where ultrahigh resolution of the obtained HD PSYCHE spectra made the structure elucidation of the chiral products feasible. HD PSYCHE methods can be potentially applied to other important 31P- or 19F-containing compounds in medicinal chemistry and metabolomics.
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Affiliation(s)
- István Timári
- Department
of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Péter Bagi
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - György Keglevich
- Department
of Organic Chemistry and Technology, Budapest
University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Katalin E. Kövér
- Department
of Inorganic and Analytical Chemistry, University
of Debrecen, Egyetem
tér 1, H-4032 Debrecen, Hungary
- ELKH-DE
Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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42
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Li C, Cong Y, Deng W. Identifying molecular functional groups of organic compounds by deep learning of NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1061-1069. [PMID: 35674984 DOI: 10.1002/mrc.5292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
We preprocess the raw nuclear magnetic resonance (NMR) spectrum and extract key features by using two different methodologies, called equidistant sampling and peak sampling for subsequent substructure pattern recognition. We also provide a strategy to address the imbalance issue frequently encountered in statistical modeling of NMR data set and establish two conventional support vector machine (SVM) and K-nearest neighbor (KNN) models to assess the capability of two feature selections, respectively. Our results in this study show that the models using the selected features of peak sampling outperform those using equidistant sampling. Then we build the recurrent neural network (RNN) model trained by data collected from peak sampling. Furthermore, we illustrate the easier optimization of hyperparameters and the better generalization ability of the RNN deep learning model by detailed comparison with traditional machine learning SVM and KNN models.
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Affiliation(s)
- Chongcan Li
- School of Mathematics and Statistics, Gansu Key Laboratory of Applied Mathematics and Complex Systems, Lanzhou University, Lanzhou, China
| | - Yong Cong
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization, Lanzhou University, Lanzhou, China
| | - Weihua Deng
- School of Mathematics and Statistics, Gansu Key Laboratory of Applied Mathematics and Complex Systems, Lanzhou University, Lanzhou, China
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43
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D-1H,13C-HSQC NMR spectra. Wellcome Open Res 2022; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D-1H,13C-HSQC NMR spectra arising from 13C -13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D-1H,13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D-1H,13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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44
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Romero JA, Putko P, Urbańczyk M, Kazimierczuk K, Zawadzka-Kazimierczuk A. Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins. PLoS Comput Biol 2022; 18:e1010258. [PMID: 36201530 PMCID: PMC9578625 DOI: 10.1371/journal.pcbi.1010258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/18/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
NMR spectroscopy is key in the study of intrinsically disordered proteins (IDPs). Yet, even the first step in such an analysis-the assignment of observed resonances to particular nuclei-is often problematic due to low peak dispersion in the spectra of IDPs. We show that the assignment process can be aided by finding "hidden" chemical shift patterns specific to the amino acid residue types. We find such patterns in the training data from the Biological Magnetic Resonance Bank using linear discriminant analysis, and then use them to classify spin systems in an α-synuclein sample prepared by us. We describe two situations in which the procedure can greatly facilitate the analysis of NMR spectra. The first involves the mapping of spin systems chains onto the protein sequence, which is part of the assignment procedure-a prerequisite for any NMR-based protein analysis. In the second, the method supports assignment transfer between similar samples. We conducted experiments to demonstrate these cases, and both times the majority of spin systems could be unambiguously assigned to the correct residue types.
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Affiliation(s)
- Javier A. Romero
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Paulina Putko
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Mateusz Urbańczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- * E-mail: (KK); (AZK)
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45
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Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E. De novo design of immunoglobulin-like domains. Nat Commun 2022; 13:5661. [PMID: 36192397 PMCID: PMC9530121 DOI: 10.1038/s41467-022-33004-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding loops and constitute the largest growing class of drugs. Current engineering strategies for this class of compounds rely on naturally existing Ig frameworks, which can be hard to modify and have limitations in manufacturability, designability and range of action. Here, we develop design rules for the central feature of the Ig fold architecture—the non-local cross-β structure connecting the two β-sheets—and use these to design highly stable Ig domains de novo, confirm their structures through X-ray crystallography, and show they can correctly scaffold functional loops. Our approach opens the door to the design of antibody-like scaffolds with tailored structures and superior biophysical properties. The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to scaffold functional loops.
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Affiliation(s)
- Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.,Novartis Institutes for BioMedical Research Inc., San Diego, CA, 92121, USA
| | - Soraia R Mendes
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jason C Klima
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Encodia, Inc., San Diego, CA, 92121, USA
| | - Marta Nadal
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jorge Roel-Touris
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Hugh K Haddox
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Adam Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
| | - Enrique Marcos
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
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46
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Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F. Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:237-246. [PMID: 35474152 PMCID: PMC9510119 DOI: 10.1007/s12104-022-10086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein.
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Affiliation(s)
- Christoph Wiedemann
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Biostructural Interactions, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
| | - Kingsley Benjamin Obika
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Sandra Liebscher
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Jirschitzka
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Frank Bordusa
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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47
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Han X, Levkovets M, Lesovoy D, Sun R, Wallerstein J, Sandalova T, Agback T, Achour A, Agback P, Orekhov VY. Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL 3 domain in solution. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:363-371. [PMID: 36094731 PMCID: PMC9510110 DOI: 10.1007/s12104-022-10105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-κB signalling pathway. Herein, we present the partial 1H, 13C Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL3 domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).
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Affiliation(s)
- Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Maria Levkovets
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Dmitry Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry RAS, Moscow, Russia, 117997
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Johan Wallerstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and, Division of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07, Uppsala, Sweden.
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden.
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden.
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48
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Karschin N, Becker S, Griesinger C. Interdomain Dynamics via Paramagnetic NMR on the Highly Flexible Complex Calmodulin/Munc13-1. J Am Chem Soc 2022; 144:17041-17053. [PMID: 36082939 PMCID: PMC9501808 DOI: 10.1021/jacs.2c06611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paramagnetic NMR constraints are very useful to study protein interdomain motion, but their interpretation is not always straightforward. On the example of the particularly flexible complex Calmodulin/Munc13-1, we present a new approach to characterize this motion with pseudocontact shifts and residual dipolar couplings. Using molecular mechanics, we sampled the conformational space of the complex and used a genetic algorithm to find ensembles that are in agreement with the data. We used the Bayesian information criterion to determine the ideal ensemble size. This way, we were able to make an accurate, unambiguous, reproducible model of the interdomain motion of Calmodulin/Munc13-1 without prior knowledge about the domain orientation from crystallography.
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Affiliation(s)
- Niels Karschin
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany
| | - Stefan Becker
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany
| | - Christian Griesinger
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen D-37075, Germany
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49
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Sekar G, Singh G, Qin X, Guibao CD, Schwam B, Inde Z, Grace CR, Zhang W, Slavish PJ, Lin W, Chen T, Lee RE, Rankovic Z, Sarosiek K, Moldoveanu T. Small molecule SJ572946 activates BAK to initiate apoptosis. iScience 2022; 25:105064. [PMID: 36147946 PMCID: PMC9485059 DOI: 10.1016/j.isci.2022.105064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023] Open
Abstract
Poration of the outer mitochondrial membrane by the effector BCL-2 proteins BAK and BAX initiates apoptosis. BH3-only initiators BID and BIM trigger conformational changes in BAK and BAX transforming them from globular dormant proteins to oligomers of the apoptotic pores. Small molecules that can directly activate effectors are being sought for applications in cancer treatment. Here, we describe the small molecule SJ572946, discovered in a fragment-based screen that binds to the activation groove of BAK and selectively triggers BAK activation over that of BAX in liposome and mitochondrial permeabilization assays. SJ572946 independently kills BAK-expressing BCL2allKO HCT116 cells revealing on target cellular activity. In combination with apoptotic inducers and BH3 mimetics, SJ572946 kills experimental cancer cell lines. SJ572946 also cooperates with the endogenous BAK activator BID in activating a misfolded BAK mutant substantially impaired in activation. SJ572946 is a proof-of-concept tool for probing BAK-mediated apoptosis in preclinical cancer research.
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Affiliation(s)
- Giridhar Sekar
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Geetika Singh
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Children’s GMP, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xingping Qin
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Cristina D. Guibao
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brittany Schwam
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zintis Inde
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Weixing Zhang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - P. Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristopher Sarosiek
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Roeck, AR 72205, USA,Corresponding author
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50
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Sethi A, Horne CR, Fitzgibbon C, Wilde K, Davies KA, Garnish SE, Jacobsen AV, Samson AL, Hildebrand JM, Wardak A, Czabotar PE, Petrie EJ, Gooley PR, Murphy JM. Membrane permeabilization is mediated by distinct epitopes in mouse and human orthologs of the necroptosis effector, MLKL. Cell Death Differ 2022; 29:1804-1815. [PMID: 35264780 PMCID: PMC9433430 DOI: 10.1038/s41418-022-00965-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
Necroptosis is a lytic programmed cell death pathway with origins in innate immunity that is frequently dysregulated in inflammatory diseases. The terminal effector of the pathway, MLKL, is licensed to kill following phosphorylation of its pseudokinase domain by the upstream regulator, RIPK3 kinase. Phosphorylation provokes the unleashing of MLKL's N-terminal four-helix bundle (4HB or HeLo) domain, which binds and permeabilizes the plasma membrane to cause cell death. The precise mechanism by which the 4HB domain permeabilizes membranes, and how the mechanism differs between species, remains unclear. Here, we identify the membrane binding epitope of mouse MLKL using NMR spectroscopy. Using liposome permeabilization and cell death assays, we validate K69 in the α3 helix, W108 in the α4 helix, and R137/Q138 in the first brace helix as crucial residues for necroptotic signaling. This epitope differs from the phospholipid binding site reported for human MLKL, which comprises basic residues primarily located in the α1 and α2 helices. In further contrast to human and plant MLKL orthologs, in which the α3-α4 loop forms a helix, this loop is unstructured in mouse MLKL in solution. Together, these findings illustrate the versatility of the 4HB domain fold, whose lytic function can be mediated by distinct epitopes in different orthologs.
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Affiliation(s)
- Ashish Sethi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Karyn Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, NSW, 2234, Australia
| | - Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - André L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ahmad Wardak
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma J Petrie
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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