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Marien J, Prévost C, Sacquin-Mora S. nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat. J Chem Inf Model 2024; 64:6570-6582. [PMID: 39092904 DOI: 10.1021/acs.jcim.4c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Tau is an intrinsically disordered (IDP) microtubule-associated protein (MAP) that plays a key part in microtubule assembly and organization. The function of tau can be regulated by multiple phosphorylation sites. These post-translational modifications are known to decrease the binding affinity of tau for microtubules, and abnormal tau phosphorylation patterns are involved in Alzheimer's disease. Using all-atom molecular dynamics simulations, we compared the conformational landscapes explored by the tau R2 repeat domain (which comprises a strong tubulin binding site) in its native state and with multiple phosphorylations on the S285, S289, and S293 residues, with four different standard force field (FF)/water model combinations. We find that the different parameters used for the phosphate groups (which can be more or less flexible) in these FFs and the specific interactions between bulk cations and water lead to the formation of a specific type of counterion bridge, termed nP-collab (for nphosphate collaboration, with n being an integer), where counterions form stable structures binding with two or three phosphate groups simultaneously. The resulting effect of nP-collabs on the tau-R2 conformational space differs when using sodium or potassium cations and is likely to impact the peptide overall dynamics and how this MAP interacts with tubulins. We also investigated the effect of phosphoresidue spacing and ionic concentration by modeling polyalanine peptides containing two phosphoserines located one-six residues apart. Three new metrics specifically tailored for IDPs (proteic Menger curvature, local curvature, and local flexibility) were introduced, which allow us to fully characterize the impact of nP-collabs on the dynamics of disordered peptides at the residue level.
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Affiliation(s)
- Jules Marien
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, Université Paris-Cité, CNRS, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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2
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Schiavina M, Bracaglia L, Rodella MA, Kümmerle R, Konrat R, Felli IC, Pierattelli R. Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz. Nat Protoc 2024; 19:406-440. [PMID: 38087081 DOI: 10.1038/s41596-023-00921-9] [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: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 02/12/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterizing biomolecules such as proteins and nucleic acids at atomic resolution. Increased magnetic field strengths drive progress in biomolecular NMR applications, leading to improved performance, e.g., higher resolution. A new class of NMR spectrometers with a 28.2 T magnetic field (1.2 GHz 1H frequency) has been commercially available since the end of 2019. The availability of ultra-high-field NMR instrumentation makes it possible to investigate more complex systems using NMR. This is especially true for highly flexible intrinsically disordered proteins (IDPs) and highly flexible regions (IDRs) of complex multidomain proteins. Indeed, the investigation of these proteins is frequently hampered by the crowding of NMR spectra. The advantages, however, are accompanied by challenges that the user must overcome when conducting experiments at such a high field (e.g., large spectral widths, radio frequency bandwidth, performance of decoupling schemes). This protocol presents strategies and tricks for optimising high-field NMR experiments for IDPs/IDRs based on the analysis of the relaxation properties of the investigated protein. The protocol, tested on three IDPs of different molecular weight and structural complexity, focuses on 13C-detected NMR at 1.2 GHz. A set of experiments, including some multiple receiver experiments, and tips to implement versions tailored for IDPs/IDRs are described. However, the general approach and most considerations can also be applied to experiments that acquire 1H or 15N nuclei and to experiments performed at lower field strengths.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Lorenzo Bracaglia
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Maria Anna Rodella
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | | | - Robert Konrat
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Isabella C Felli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
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3
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Schiavina M, Konrat R, Ceccolini I, Mateos B, Konrat R, Felli IC, Pierattelli R. Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107539. [PMID: 37632987 DOI: 10.1016/j.jmr.2023.107539] [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: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Intrinsically disordered proteins (IDPs) are significantly enriched in proline residues, which can populate specific local secondary structural elements called PPII helices, characterized by small packing densities. Proline is often thought to promote disorder, but it can participate in specific π·CH interactions with aromatic side chains resulting in reduced conformational flexibilities of the polypeptide. Differential local motional dynamics are relevant for the stabilization of preformed structural elements and can serve as nucleation sites for the establishment of long-range interactions. NMR experiments to probe the dynamics of proline ring systems would thus be highly desirable. Here we present a pulse scheme based on 13C detection to quantify dipole-dipole cross-correlated relaxation (CCR) rates at methylene CH2 groups in proline residues. Applying 13C-CON detection strategy provides exquisite spectral resolution allowing applications also to high molecular weight IDPs even in conditions approaching the physiological ones. The pulse scheme is illustrated with an application to the 220 amino acids long protein Osteopontin, an extracellular cytokine involved in inflammation and cancer progression, and a construct in which three proline-aromatic sequence patches have been mutated.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ruth Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Irene Ceccolini
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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4
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Schiavina M, Pontoriero L, Tagliaferro G, Pierattelli R, Felli IC. The Role of Disordered Regions in Orchestrating the Properties of Multidomain Proteins: The SARS-CoV-2 Nucleocapsid Protein and Its Interaction with Enoxaparin. Biomolecules 2022; 12:1302. [PMID: 36139141 PMCID: PMC9496478 DOI: 10.3390/biom12091302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Novel and efficient strategies need to be developed to interfere with the SARS-CoV-2 virus. One of the most promising pharmaceutical targets is the nucleocapsid protein (N), responsible for genomic RNA packaging. N is composed of two folded domains and three intrinsically disordered regions (IDRs). The globular RNA binding domain (NTD) and the tethered IDRs are rich in positively charged residues. The study of the interaction of N with polyanions can thus help to elucidate one of the key driving forces responsible for its function, i.e., electrostatics. Heparin, one of the most negatively charged natural polyanions, has been used to contrast serious cases of COVID-19 infection, and we decided to study its interaction with N at the molecular level. We focused on the NTR construct, which comprises the NTD and two flanking IDRs, and on the NTD construct in isolation. We characterized this interaction using different nuclear magnetic resonance approaches and isothermal titration calorimetry. With these tools, we were able to identify an extended surface of NTD involved in the interaction. Moreover, we assessed the importance of the IDRs in increasing the affinity for heparin, highlighting how different tracts of these flexible regions modulate the interaction.
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Affiliation(s)
| | | | | | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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5
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Abstract
Thanks to recent improvements in NMR spectrometer hardware and pulse sequence design, modern 13C NMR has become a useful tool for biomolecular applications. The complete assignment of a protein can be accomplished by using 13C detected multinuclear experiments and it can provide unique information relevant for the study of a variety of different biomolecules including paramagnetic proteins and intrinsically disordered proteins. A wide range of NMR observables can be measured, concurring to the structural and dynamic characterization of a protein in isolation, as part of a larger complex, or even inside a living cell. We present the different properties of 13C with respect to 1H, which provide the rationale for the experiments developed and their application, the technical aspects that need to be faced, and the many experimental variants designed to address different cases. Application areas where these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C. Felli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High‐Resolution FOSY NMR**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
| | - Tammo Diercks
- NMR Platform CiC bioGUNE Bld. 800, Parque Tecnológico de Bizkaia 48160 Derio Spain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and Neurochemistry University of Gothenburg 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
- Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg 40530 Gothenburg Sweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS 117997 Moscow Russia
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology (State University) 141700 Dolgoprudny Russia
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular Biology University of Gothenburg Box 465 40530 Gothenburg Sweden
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7
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Lesovoy DM, Georgoulia PS, Diercks T, Matečko‐Burmann I, Burmann BM, Bocharov EV, Bermel W, Orekhov VY. Unambiguous Tracking of Protein Phosphorylation by Fast High-Resolution FOSY NMR*. Angew Chem Int Ed Engl 2021; 60:23540-23544. [PMID: 34143912 PMCID: PMC8596425 DOI: 10.1002/anie.202102758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/30/2021] [Indexed: 12/12/2022]
Abstract
Dysregulation of post-translational modifications (PTMs) like phosphorylation is often involved in disease. NMR may elucidate exact loci and time courses of PTMs at atomic resolution and near-physiological conditions but requires signal assignment to individual atoms. Conventional NMR methods for this base on tedious global signal assignment that may often fail, as for large intrinsically disordered proteins (IDPs). We present a sensitive, robust alternative to rapidly obtain only the local assignment near affected signals, based on FOcused SpectroscopY (FOSY) experiments using selective polarisation transfer (SPT). We prove its efficiency by identifying two phosphorylation sites of glycogen synthase kinase 3 beta (GSK3β) in human Tau40, an IDP of 441 residues, where the extreme spectral dispersion in FOSY revealed unprimed phosphorylation also of Ser409. FOSY may broadly benefit NMR studies of PTMs and other hotspots in IDPs, including sites involved in molecular interactions.
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Affiliation(s)
- Dmitry M. Lesovoy
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | - Panagiota S. Georgoulia
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
| | - Tammo Diercks
- NMR PlatformCiC bioGUNEBld. 800, Parque Tecnológico de Bizkaia48160DerioSpain
| | - Irena Matečko‐Burmann
- Department of Psychiatry and NeurochemistryUniversity of Gothenburg40530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of Gothenburg40530GothenburgSweden
| | - Eduard V. Bocharov
- Department of Structural Biology, Shemyakin-OvchinnikovInstitute of Bioorganic Chemistry RAS117997MoscowRussia
- Research Center for Molecular Mechanisms of Aging and Age-related DiseasesMoscow Institute of Physics and Technology (State University)141700DolgoprudnyRussia
| | | | - Vladislav Y. Orekhov
- Department of Chemistry and Molecular BiologyUniversity of GothenburgBox 46540530GothenburgSweden
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8
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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9
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- 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
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10
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Dyson HJ, Wright PE. NMR illuminates intrinsic disorder. Curr Opin Struct Biol 2021; 70:44-52. [PMID: 33951592 DOI: 10.1016/j.sbi.2021.03.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Nuclear magnetic resonance (NMR) has long been instrumental in the characterization of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). This method continues to offer rich insights into the nature of IDPs in solution, especially in combination with other biophysical methods such as small-angle scattering, single-molecule fluorescence, electron paramagnetic resonance (EPR), and mass spectrometry. Substantial advances have been made in recent years in studies of proteins containing both ordered and disordered domains and in the characterization of problematic sequences containing repeated tracts of a single or a few amino acids. These sequences are relevant to disease states such as Alzheimer's, Parkinson's, and Huntington's diseases, where disordered proteins misfold into harmful amyloid. Innovative applications of NMR are providing novel insights into mechanisms of protein aggregation and the complexity of IDP interactions with their targets. As a basis for understanding the solution structural ensembles, dynamic behavior, and functional mechanisms of IDPs and IDRs, NMR continues to prove invaluable.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA.
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11
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Pontoriero L, Schiavina M, Murrali MG, Pierattelli R, Felli IC. Monitoring the Interaction of α‐Synuclein with Calcium Ions through Exclusively Heteronuclear Nuclear Magnetic Resonance Experiments. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Letizia Pontoriero
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Marco Schiavina
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Maria Grazia Murrali
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
- Present address: Department of Chemistry and Biochemistry University of California at Los Angeles USA
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
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12
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Pontoriero L, Schiavina M, Murrali MG, Pierattelli R, Felli IC. Monitoring the Interaction of α‐Synuclein with Calcium Ions through Exclusively Heteronuclear Nuclear Magnetic Resonance Experiments. Angew Chem Int Ed Engl 2020; 59:18537-18545. [DOI: 10.1002/anie.202008079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/14/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Letizia Pontoriero
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Marco Schiavina
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Maria Grazia Murrali
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
- Present address: Department of Chemistry and Biochemistry University of California at Los Angeles USA
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
| | - Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff” University of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italy
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13
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Bodor A, Haller JD, Bouguechtouli C, Theillet FX, Nyitray L, Luy B. Power of Pure Shift HαCα Correlations: A Way to Characterize Biomolecules under Physiological Conditions. Anal Chem 2020; 92:12423-12428. [PMID: 32786451 DOI: 10.1021/acs.analchem.0c02182] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute an important class of biomolecules with high flexibility. Atomic-resolution studies for these molecules are essentially limited to NMR spectroscopy, which should be performed under physiological pH and temperature to populate relevant conformational ensembles. In this context, however, fundamental problems arise with established triple resonance NMR experiments: high solvent accessibility of IDPs promotes water exchange, which disfavors classical amide 1H-detection, while 13C-detection suffers from significantly reduced sensitivity. A favorable alternative, the conventional detection of nonexchangeable 1Hα, so far resulted in broad signals with insufficient resolution and sensitivity. To overcome this, we introduce here a selective Hα,Cα-correlating pure shift detection scheme, the selective Hα,Cα-HSQC (SHACA-HSQC), using extensive hetero- and homonuclear decoupling applicable to aqueous samples (≥90% H2O) and tested on small molecules and proteins. SHACA-HSQC spectra acquired on IDPs provide uncompromised resolution and sensitivity (up to fivefold increased S/N compared to the standard 1H,13C-HSQC), as shown for resonance distinction and unambiguous assignment on the disordered transactivation domain of the tumor suppressor p53, α-synuclein, and folded ubiquitin. The detection scheme can be implemented in any 1Hα-detected triple resonance experiment and may also form the basis for the detection of isotope-labeled markers in biological studies or compound libraries.
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Affiliation(s)
- Andrea Bodor
- Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Jens D Haller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4-Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, Karlsruhe 76133, Germany
| | - Chafiaa Bouguechtouli
- Institute of Integrative Biology of the Cell, UMR9198, CNRS/CEA/ University of Paris Saclay, Gif-Sur-Yvette 911991, France
| | - Francois-Xavier Theillet
- Institute of Integrative Biology of the Cell, UMR9198, CNRS/CEA/ University of Paris Saclay, Gif-Sur-Yvette 911991, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest 1117, Hungary
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4-Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, Karlsruhe 76133, Germany
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14
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p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nat Chem Biol 2020; 16:1078-1086. [DOI: 10.1038/s41589-020-0600-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
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