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Whipham JW, Sabba M, Dagys L, Moustafa G, Bengs C, Levitt MH. Cross-correlated relaxation in the NMR of near-equivalent spin pairs: Longitudinal relaxation and long-lived singlet order. J Chem Phys 2024; 161:014112. [PMID: 38953443 DOI: 10.1063/5.0213997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
The evolution of nuclear spin state populations is investigated for the case of a 13C2-labeled triyne in solution, for which the near-equivalent coupled pairs of 13C nuclei experience cross-correlated relaxation mechanisms. Inversion-recovery experiments reveal different recovery curves for the main peak amplitudes, especially when the conversion of population imbalances to observable coherences is induced by a radio frequency pulse with a small flip angle. Measurements are performed over a range of magnetic fields by using a sample shuttle apparatus. In some cases, the time constant TS for decay of nuclear singlet order is more than 100 times larger than the time constant T1 for the equilibration of longitudinal magnetization. The results are interpreted by a theoretical model incorporating cross-correlated relaxation mechanisms, anisotropic rotational diffusion, and an external random magnetic field. A Lindbladian formalism is used to describe the dissipative dynamics of the spin system in an environment of finite temperature. Good agreement is achieved between theory and experiment.
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Affiliation(s)
- James W Whipham
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
| | - Mohamed Sabba
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
| | - Laurynas Dagys
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
- Institute of Chemical Physics, Vilnius University, Vilnius LT-10257, Lithuania
| | - Gamal Moustafa
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
| | - Christian Bengs
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Malcolm H Levitt
- School of Chemistry, Southampton University, Southampton SO17 1BJ, United Kingdom
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Sicoli G, Sieme D, Overkamp K, Khalil M, Backer R, Griesinger C, Willbold D, Rezaei-Ghaleh N. Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins. Nat Commun 2024; 15:1610. [PMID: 38383529 PMCID: PMC10881997 DOI: 10.1038/s41467-024-45788-w] [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: 03/31/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
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Affiliation(s)
- Giuseppe Sicoli
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Kerstin Overkamp
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Mahdi Khalil
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Robin Backer
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Dieter Willbold
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany.
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Razanahoera A, Sonnefeld A, Bodenhausen G, Sheberstov K. Paramagnetic relaxivity of delocalized long-lived states of protons in chains of CH 2 groups. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:47-56. [PMID: 37904798 PMCID: PMC10583270 DOI: 10.5194/mr-4-47-2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/23/2023] [Indexed: 11/01/2023]
Abstract
Long-lived states (LLSs) have lifetimes T LLS that can be much longer than longitudinal relaxation times T 1 . In molecules containing several geminal pairs of protons in neighboring CH2 groups, it has been shown that delocalized LLSs can be excited by converting magnetization into imbalances between the populations of singlet and triplet states of each pair. Since the empirical yield of the conversion and reconversion of observable magnetization into LLSs and back is on the order of 10 % if one uses spin-lock induced crossing (SLIC), it would be desirable to boost the sensitivity by dissolution dynamic nuclear polarization (d-DNP). To enhance the magnetization of nuclear spins by d-DNP, the analytes must be mixed with radicals such as 4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPOL). After dissolution, these radicals lead to an undesirable paramagnetic relaxation enhancement (PRE) which shortens not only the longitudinal relaxation times T 1 but also the lifetimes T LLS of LLSs. It is shown in this work that PRE by TEMPOL is less deleterious for LLSs than for longitudinal magnetization for four different molecules: 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), homotaurine, taurine, and acetylcholine. The relaxivities r LLS (i.e., the slopes of the relaxation rate constants R LLS as a function of the radical concentration) are 3 to 5 times smaller than the relaxivities r 1 of longitudinal magnetization. Partial delocalization of the LLSs across neighboring CH2 groups may decrease this advantage, but in practice, this effect was observed to be small, for example, when comparing taurine containing two CH2 groups and homotaurine with three CH2 groups. Regardless of whether the LLSs are delocalized or not, it is shown that PRE should not be a major problem for experiments combining d-DNP and LLSs, provided the concentration of paramagnetic species after dissolution does not exceed 1 mM, a condition that is readily fulfilled in typical d-DNP experiments. In bullet d-DNP experiments however, it may be necessary to decrease the concentration of TEMPOL or to add ascorbate for chemical reduction.
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Affiliation(s)
- Aiky Razanahoera
- Department of Chemistry, École Normale Supérieure, PSL University,
75005 Paris, France
| | - Anna Sonnefeld
- Department of Chemistry, École Normale Supérieure, PSL University,
75005 Paris, France
| | - Geoffrey Bodenhausen
- Department of Chemistry, École Normale Supérieure, PSL University,
75005 Paris, France
| | - Kirill Sheberstov
- Department of Chemistry, École Normale Supérieure, PSL University,
75005 Paris, France
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Gangwar U, Singh B, Kurur ND. Long-Lived States Provide Insights from NMR into the β-Cyclodextrin Drug Assemblies. J Phys Chem A 2023; 127:1158-1167. [PMID: 36705632 DOI: 10.1021/acs.jpca.2c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the last two decades, extending spin memory in NMR has been used for several purposes. Long-lived states (LLS) or singlet states are one of the first spin memory enhancement techniques used. LLS have the potential to extract structural information and intra- and intermolecular interactions of complex systems other than studying slow phenomenon. The motional regime of β-cyclodextrin (β-CD) drug inclusion complexes generally lies in the intermediate region, where ωτc ≈ 1, and the standard methods of studying these interactions, i.e., NOE and chemical shift monitoring, suffer from insufficient output information. The sensitivity of LLS toward the environmental changes is utilized here to gain insights into the drug assemblies formed by β-CD. One can use change in relaxation of LLS to study the structural changes during complexation. The examples of β-CD with the drugs indomethacin, paracetamol, gliclazide, and CI-933 (a precursor 4-methoxybenzamide) were studied. Indomethacin, paracetamol, and 4-methoxybenzamide show strong interaction through the para-substituted benzene ring, unlike gliclazide. Relaxation of LLS in β-CD-drug complexes is modeled using standard Redfield Relaxation Theory. Computational studies performed support the experimental observations. Docking and molecular dynamics simulation provided the explanation of the relaxation properties of these drug molecules.
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Affiliation(s)
- Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi110016, India
| | - Balvinder Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi110016, India
| | - Narayanan D Kurur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi110016, India
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Korenchan DE, Lu J, Sabba M, Dagys L, Brown LJ, Levitt MH, Jerschow A. 31P spin-lattice and singlet order relaxation mechanisms in pyrophosphate studied by isotopic substitution, field shuttling NMR, and molecular dynamics simulation. Phys Chem Chem Phys 2022; 24:24238-24245. [PMID: 36168981 DOI: 10.1039/d2cp03801c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nuclear spin relaxation mechanisms are often difficult to isolate and identify, especially in molecules with internal flexibility. Here we combine experimental work with computation in order to determine the major mechanisms responsible for 31P spin-lattice and singlet order (SO) relaxation in pyrophosphate, a physiologically relevant molecule. Using field-shuttling relaxation measurements (from 2 μT to 9.4 T) and rates calculated from molecular dynamics (MD) trajectories, we identified chemical shift anisotropy (CSA) and spin-rotation as the major mechanisms, with minor contributions from intra- and intermolecular coupling. The significant spin-rotation interaction is a consequence of the relatively rapid rotation of the -PO32- entities around the bridging P-O bonds, and is treated by a combination of MD simulations and quantum chemistry calculations. Spin-lattice relaxation was predicted well without adjustable parameters, and for SO relaxation one parameter was extracted from the comparison between experiment and computation (a correlation coefficient between the rotational motion of the groups).
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Affiliation(s)
- David E Korenchan
- Department of Chemistry, New York University, 100 Washington Square E, New York, NY 10003, USA.
| | - Jiaqi Lu
- Department of Chemistry, New York University, 100 Washington Square E, New York, NY 10003, USA.
| | - Mohamed Sabba
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Laurynas Dagys
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Lynda J Brown
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Malcolm H Levitt
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Alexej Jerschow
- Department of Chemistry, New York University, 100 Washington Square E, New York, NY 10003, USA.
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