Journal of magnetic resonance最新文献

{"title":"Field-domain rapid-scan EPR at 240 GHz for studies of protein functional dynamics at room temperature","authors":"","doi":"10.1016/j.jmr.2024.107744","DOIUrl":"10.1016/j.jmr.2024.107744","url":null,"abstract":"<div><p>We present field-domain rapid-scan (RS) electron paramagnetic resonance (EPR) at 8.6<!--> <!-->T and 240<!--> <!-->GHz. To enable this technique, we upgraded a home-built EPR spectrometer with an FPGA-enabled digitizer and real-time processing software. The software leverages the Hilbert transform to recover the in-phase (<span><math><mi>I</mi></math></span>) and quadrature (<span><math><mi>Q</mi></math></span>) channels, and therefore the raw absorptive and dispersive signals, <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mo>′</mo></mrow></msup></math></span> and <span><math><msup><mrow><mi>χ</mi></mrow><mrow><mo>′</mo><mo>′</mo></mrow></msup></math></span>, from their combined magnitude (<span><math><msqrt><mrow><msup><mrow><mi>I</mi></mrow><mrow><mn>2</mn></mrow></msup><mo>+</mo><msup><mrow><mi>Q</mi></mrow><mrow><mn>2</mn></mrow></msup></mrow></msqrt></math></span>). Averaging a magnitude is simpler than real-time coherent averaging and has the added benefit of permitting long-timescale signal averaging (up to at least <span><math><mrow><mn>2</mn><mo>.</mo><mn>5</mn><mo>×</mo><mn>1</mn><msup><mrow><mn>0</mn></mrow><mrow><mn>6</mn></mrow></msup></mrow></math></span> scans) because it eliminates the effects of source-receiver phase drift. Our rapid-scan (RS) EPR provides a signal-to-noise ratio that is approximately twice that of continuous wave (CW) EPR under the same experimental conditions, after scaling by the square root of acquisition time. We apply our RS EPR as an extension of the recently reported time-resolved Gd-Gd EPR (TiGGER) [Maity et al., 2023], which is able to monitor inter-residue distance changes during the photocycle of a photoresponsive protein through changes in the Gd-Gd dipolar couplings. RS, opposed to CW, returns field-swept spectra as a function of time with 10<!--> <!-->ms time resolution, and thus, adds a second dimension to the static field transients recorded by TiGGER. We were able to use RS TiGGER to track time-dependent and temperature-dependent kinetics of AsLOV2, a light-activated phototropin domain found in oats. The results presented here combine the benefits of RS EPR with the improved spectral resolution and sensitivity of Gd chelates at high magnetic fields. In the future, field-domain RS EPR at high magnetic fields may enable studies of other real-time kinetic processes with time resolutions that are otherwise difficult to access in the solution state.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724001289/pdfft?md5=f06bb2dfd5a7dd417b03580fd438e9ff&pid=1-s2.0-S1090780724001289-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141840568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of Zeeman and hyperfine interactions on the magnetic properties of paramagnetic metal ions: II. Super-hyperfine interactions with surrounding nuclei","authors":"","doi":"10.1016/j.jmr.2024.107732","DOIUrl":"10.1016/j.jmr.2024.107732","url":null,"abstract":"<div><p>The anisotropic Zeeman and strong hyperfine interactions of a Kramers ion can significantly affect its magnetic properties as well as the interactions with the nearby nuclei. The interactions with the local environment are described in the preceding article. In the current work, the change of the spin states of distant nuclei is studied. Analytical expressions describing the depth of the electron spin echo envelope modulation (ESEEM) are obtained for the ions with anisotropic Zeeman and strong hyperfine interactions. Due to the g-tensor anisotropy, the electron Zeeman interaction axis is tilted in respect to the direction of the external magnetic field which makes non-collinear with the Zeeman interaction axes of the ion and the nearby nuclei and significantly modifies the nuclear spin states. Thus, the isotropic hyperfine interaction, and particularly the Fermi contact interaction can directly contribute to the ESEEM. An additional factor, that can significantly modify the ESEEM signal is the mixing of the multiple oscillations arising when several nuclei occur in optimal conditions for the generation of the nuclear coherence. This situation arises when several EPR transitions of the ion covering a wide range of magnetic fields are examined.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141637234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of Zeeman and hyperfine interactions on the magnetic properties of paramagnetic metal Ions: III. Analysis of the local interactions in a single crystal of 173Yb3+ doped Y5SiO5","authors":"Yu.E. Kandrashkin","doi":"10.1016/j.jmr.2024.107731","DOIUrl":"10.1016/j.jmr.2024.107731","url":null,"abstract":"<div><p>The electron spin echo envelope modulation (ESEEM) technique is a direct method to probe the nuclear spin coherences induced by electron spin transitions. Recently, this approach was used to study an isotopically pure Y₂SiO₅ crystal doped with ¹⁷³Yb³⁺ ions, and the presence of the Fermi contact interaction was proposed to explain the frequency comb detected in the two-pulse ESEEM experiment [Solovarov N. K. et al. <em>JETP Letters</em> 115 (6): 362–67]. Here we simulate the Fourier images of the ESEEM data. The numerical analysis shows that the modulation is mainly due to the nuclear spin coherences induced by the dipole–dipole interactions. However, the correlation between the experimental and simulated data is better when the super-hyperfine interactions of the nearby yttrium nuclei have an additional isotropic contribution. The analysis of the rescaled X-band ESEEM spectra shows that for the EPR transitions at magnetic fields &gt; 100 mT, the main contribution to the modulation comes from the oscillations of the individual nuclei and the effect of interference between coherences originating from several nuclei is not strong. Further experiments to distinguish the sources of the echo modulation are discussed.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective correlations between aliphatic 13C nuclei in protein solid-state NMR","authors":"Hang Xiao ,&nbsp;Weijing Zhao ,&nbsp;Yan Zhang ,&nbsp;Huimin Kang ,&nbsp;Zhengfeng Zhang ,&nbsp;Jun Yang","doi":"10.1016/j.jmr.2024.107730","DOIUrl":"10.1016/j.jmr.2024.107730","url":null,"abstract":"<div><p>Solid-state nuclear magnetic resonance (NMR) is a potent tool for studying the structures and dynamics of insoluble proteins. It starts with signal assignment through multi-dimensional correlation experiments, where the aliphatic ¹³Cα-¹³Cβ correlation is indispensable for identifying specific residues. However, developing efficient methods for achieving this correlation is a challenge in solid-state NMR. We present a simple band-selective zero-quantum (ZQ) recoupling method, named POST-C4₁₆¹ (PC4), which enhances ¹³Cα-¹³Cβ correlations under moderate magic-angle spinning (MAS) conditions. PC4 requires minimal ¹³C radio-frequency (RF) field and proton decoupling, exhibits high stability against RF variations, and achieves superior efficiency. Comparative tests on various samples, including the formyl-Met-Leu-Phe (fMLF) tripeptide, microcrystalline β1 immunoglobulin binding domain of protein G (GB1), and membrane protein of mechanosensitive channel of large conductance from <em>Methanosarcina acetivorans</em> (MaMscL), demonstrate that PC4 selectively enhances ¹³Cα-¹³Cβ correlations by up to 50 % while suppressing unwanted correlations, as compared to the popular dipolar-assisted rotational resonance (DARR). It has addressed the long-standing need for selective ¹³C–¹³C correlation methods. We anticipate that this simple but efficient PC4 method will have immediate applications in structural biology by solid-state NMR.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low power supercycled TPPM decoupling","authors":"Rajat Garg ,&nbsp;Barry DeZonia ,&nbsp;Alexander L. Paterson ,&nbsp;Chad M. Rienstra","doi":"10.1016/j.jmr.2024.107726","DOIUrl":"10.1016/j.jmr.2024.107726","url":null,"abstract":"<div><p>Improving the spectral sensitivity and resolution of biological solids is one of the long-standing problems in nuclear magnetic resonance (NMR) spectroscopy. In this report, we introduce low-power supercycled variants of two-pulse phase-modulated (TPPM) sequence for heteronuclear decoupling. The utility of the sequence is shown by improvements in the transverse relaxation time of observed nuclei (with ¹H decoupling) with its application to different samples (uniformly ¹³C, ¹⁵N, ²H-labeled GB1 back-exchanged with 25% H<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>O and 75% D<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>O, uniformly ¹³C, ¹⁵N, ²H-labeled human derived Asyn fibril back-exchanged with 100% H<span><math><msub><mrow></mrow><mrow><mn>2</mn></mrow></msub></math></span>O and uniformly ¹³C, ¹⁵N -labeled human derived Asyn fibril) at fast MAS using low radiofrequency (RF) fields. To understand the effect of spinning speed, the transverse relaxation time is monitored under different spinning frequencies. In comparison to existing heteronuclear decoupling sequences, the supercycled TPPM (sTPPM) sequence significantly improves the spectral sensitivity and resolution and is robust towards <span><math><msub><mrow><mi>B</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span> inhomogeneity and decoupler offset.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-commutative perturbation theory for spin dynamics explains the factorization properties of RIDME background","authors":"","doi":"10.1016/j.jmr.2024.107729","DOIUrl":"10.1016/j.jmr.2024.107729","url":null,"abstract":"<div><p>The intermolecular hyperfine relaxation-induced dipolar modulation enhancement (ih-RIDME) experiment has a promising potential to quantitatively characterize the nuclear environment in the 0.8-3 nm range around an electron spin. Such information about the spatial arrangement of nuclei is of great interest for structural biology as well as for dynamic nuclear polarization (DNP) methods. In order to develop a reliable and sensitive spectroscopic tool, a solid data model needs to be established. Here, we attempt to provide a theoretical explanation for the experimentally observed properties of the ih-RIDME signal. Our main approach uses a perturbation expansion of the Baker–Campbell–Hausdorff formula during the transverse evolution of the electron spin, treating the nuclear dipolar Hamiltonian as a perturbation. We show that a product structure of the ih-RIDME signal follows directly from the statistical independence of the perturbation terms and the multinuclear hyperfine coupling, and that this signal composition is expected when the mixing time exceeds the 95% decay of the Hahn echo.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724001137/pdfft?md5=69c31975fef8deaf55a79d77abbadb2f&pid=1-s2.0-S1090780724001137-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141630878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hyperpolarized nuclear Overhauser enhancement of alanine methyl groups by doubly relayed proton exchange","authors":"Milan Zachrdla ,&nbsp;Ertan Turhan ,&nbsp;Christopher Pötzl ,&nbsp;Aude Sadet ,&nbsp;Paul R. Vasos ,&nbsp;Dennis Kurzbach","doi":"10.1016/j.jmr.2024.107727","DOIUrl":"10.1016/j.jmr.2024.107727","url":null,"abstract":"<div><p>Hyperpolarized water in dissolution dynamic nuclear polarization (dDNP) experiments has emerged as a promising method for enhancing nuclear magnetic resonance (NMR) signals, particularly in studies of proteins and peptides. Herein, we focus on the application of “proton exchange-doubly relayed” nuclear Overhauser effects (NOE) from hyperpolarized water to achieve positive signal enhancement of methyl groups in the side chain of an alanine-glycine peptide. In particular, we show a cascade hyperpolarization transfer. Initial proton exchange between solvent and amide introduces hyperpolarization into the peptide. Subsequently, intermolecular NOE relays the hyperpolarization first to Ala-H^α and then in a second step to the Ala-CH₃ moiety. Both NOEs have negative signs. Hence, the twice-relayed NOE pathway leads to a positive signal enhancement of the methyl group with respect to the thermal equilibrium magnetization. This effect might indicate a way towards hyperpolarized water-based signal enhancement for methyl groups, which are often used for NMR studies of large proteins in solution.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724001113/pdfft?md5=794ed5d93963c4dacc14fabd5dbbbcf8&pid=1-s2.0-S1090780724001113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bayesian analysis of 1D 1H-NMR spectra","authors":"Flavio De Lorenzi ,&nbsp;Tom Weinmann ,&nbsp;Simon Bruderer ,&nbsp;Björn Heitmann ,&nbsp;Andreas Henrici ,&nbsp;Simon Stingelin","doi":"10.1016/j.jmr.2024.107723","DOIUrl":"10.1016/j.jmr.2024.107723","url":null,"abstract":"<div><p>Extracting spin system parameters from 1D high resolution <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H-NMR spectra can be an intricate task requiring sophisticate methods. With a few exceptions methods to perform such a total line shape analysis commonly rely on local optimization techniques which for increasing complexity of the underlying spin system tend to reveal local solutions. In this work we propose a full Bayesian modeling approach based on a quantum mechanical model of the spin system. The Bayesian formalism provides a global optimization strategy which allows to efficiently include prior knowledge about the spin system or to incorporate additional constraints concerning the parameters of interest. The proposed algorithm has been tested on synthetic and real 1D <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H-NMR data for various spin systems with increasing complexity. The results show that the Bayesian algorithm provides accurate estimates even for complex spectra with many overlapping regions, and that it can cope with symmetry induced local minima. By providing an unbiased estimate of the model evidence the proposed algorithm furthermore offers a way to discriminate between different spin system candidates.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724001071/pdfft?md5=4f020270c8b884b725a432b117255c09&pid=1-s2.0-S1090780724001071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141414257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!","authors":"Jeffrey P. Bonin ,&nbsp;James M. Aramini ,&nbsp;Ying Dong ,&nbsp;Hao Wu ,&nbsp;Lewis E. Kay","doi":"10.1016/j.jmr.2024.107725","DOIUrl":"10.1016/j.jmr.2024.107725","url":null,"abstract":"<div><p>The determination of a protein’s structure is often a first step towards the development of a mechanistic understanding of its function. Considerable advances in computational protein structure prediction have been made in recent years, with AlphaFold2 (AF2) emerging as the primary tool used by researchers for this purpose. While AF2 generally predicts accurate structures of folded proteins, we present here a case where AF2 incorrectly predicts the structure of a small, folded and compact protein with high confidence. This protein, pro-interleukin-18 (pro-IL-18), is the precursor of the cytokine IL-18. Interestingly, the structure of pro-IL-18 predicted by AF2 matches that of the mature cytokine, and not the corresponding experimentally determined structure of the pro-form of the protein. Thus, while computational structure prediction holds immense promise for addressing problems in protein biophysics, there is still a need for experimental structure determination, even in the context of small well-folded, globular proteins.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724001095/pdfft?md5=1102169d5b575472beeb169492cb1f71&pid=1-s2.0-S1090780724001095-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and optimization of THz coupling in zirconia MAS rotors for dynamic nuclear polarization NMR","authors":"Guangjiang Li ,&nbsp;Blake Dastrup ,&nbsp;Ravi Shankar Palani ,&nbsp;Michael A. Shapiro ,&nbsp;Sudheer K. Jawla ,&nbsp;Robert G. Griffin ,&nbsp;Keith A. Nelson ,&nbsp;Richard J. Temkin","doi":"10.1016/j.jmr.2024.107722","DOIUrl":"10.1016/j.jmr.2024.107722","url":null,"abstract":"<div><p>We present 3D electromagnetic simulations of the coupling of a 250 GHz beam to the sample in a 380 MHz DNP NMR spectrometer. To obtain accurate results for magic angle spinning (MAS) geometries, we first measured the complex dielectric constants of zirconia, sapphire, and the sample matrix material (DNP juice) from room temperature down to cryogenic temperatures and from 220 to 325 GHz with a VNA and up to 1 THz with a THz TDS system. Simulations of the coupling to the sample were carried out with the ANSYS HFSS code as a function of the rotor wall material (zirconia or sapphire), the rotor wall thickness, and the THz beam focusing (lens or no lens). For a zirconia rotor, the <em>B₁</em> field in the sample was found to be strongly dependent on the rotor wall thickness, which is attributed to the high refractive index of zirconia. The optimum thickness of the wall is likely due to a transmission maximum but is offset from the thickness predicted by a simple calculation for a flat slab of the wall material. The <em>B₁</em> value was found to be larger for a sapphire rotor than for a zirconia rotor for all cases studied. The results found in this work provide new insights into the coupling of THz radiation to the sample and should lead to improved designs of future DNP NMR instrumentation.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S109078072400106X/pdfft?md5=db8b4347b8201c62a1b0d4f9ecebf092&pid=1-s2.0-S109078072400106X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141404789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}