Journal of Magnetic Resonance Open最新文献

{"title":"Quantum sensing tools to characterize physical, chemical and biological processes with magnetic resonance","authors":"Analia Zwick,&nbsp;Gonzalo A. Álvarez","doi":"10.1016/j.jmro.2023.100113","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100113","url":null,"abstract":"<div><p>Nuclear Magnetic Resonance (NMR) plays a central role in developing quantum information sciences and technologies. Key features such as its non-invasive nature and the ability to process information on nuclear spins by versatile quantum control designs with electromagnetic fields, have made NMR to become a powerful technique for sensing systems from atomic and molecular scales with spectroscopy to millimeters in imaging. This brief overview provides quantum sensing tools with which we are contributing from Latin America, by combining quantum dynamical control and estimation strategies with NMR methods to probe physical, chemical, and biological processes. It introduces the basic and key concepts on how controlled spin-sensors can monitor the correlation dynamics of their environment, and selectively and optimally infer its relevant parameters. Then these concepts are illustrated with state-of-the-art implementations for characterizing (i) biological tissue microstructure with diffusion weighting imaging, (ii) quantum information dynamics and scrambling in out-of-equilibrium systems with solid-state NMR quantum simulations, and (iii) molecular structures by selective estimation of spin–spin couplings and online learning control designs with experimental proposals. We expect these concepts will motivate the development of quantum dynamical control of spin sensors to monitor systems in a variety of fields, and in particular to exploit the non-invasive strength of NMR, e.g. in biomedical diagnosis.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100113"},"PeriodicalIF":2.624,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3451235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RF coil efficacy for efficient spin control in low field magnetic resonance experiments✰","authors":"Michele N. Martin,&nbsp;Anthony B. Kos,&nbsp;Stephen E. Russek,&nbsp;Karl F. Stupic","doi":"10.1016/j.jmro.2023.100110","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100110","url":null,"abstract":"<div><p>At low magnetic fields (&lt;1 T), the low loss of radio frequency (RF) coils can cause RF pulses, in magnetic resonance (MR) experiments, to suffer from long rise and fall times. When severe, long rise and fall times can result in RF pulses with undesirable and/or unexpected shapes, lengths, and amplitudes leading to inadequate spin control during an MR experiment. Experimentally, the lack of spin control becomes evident in the shape of the nutation curve and the inversion efficiency, the degree to which full inversion is accomplished following a 180° pulse. Lowering the quality factor (Q) of tuned coil is shown to reduce the duration of the rise and fall times. The effects of long rise and fall times on the spin behavior during an MR experiment is explored. It is shown that the inversion efficiency can be used to provide a threshold that ensures high fidelity pulses with adequate spin control.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100110"},"PeriodicalIF":2.624,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3138357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High resolution protein in-cell NMR in zebrafish embryos","authors":"Verónica A. Lombardo ,&nbsp;Rubina Armesto ,&nbsp;Idalia Herrera-Estrada ,&nbsp;Andrés Binolfi","doi":"10.1016/j.jmro.2023.100111","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100111","url":null,"abstract":"<div><p>In-cell NMR spectroscopy has emerged as a powerful tool to evaluate protein conformations and dynamics in the native environment of live cells. Here we extend these studies to a multicellular developing vertebrate. Zebrafish (<em>Danio rerio</em>) embryos are complex organisms with dynamic tissue organization and may be well suited for the high resolution NMR analysis of microinjected, isotopically enriched proteins. We used the intrinsically disordered protein Alpha-synuclein (aSyn) as a test model. aSyn has been thoroughly evaluated inside bacterial and mammalian cells, providing good reference points for NMR comparisons and the critical analysis of the advantages and disadvantages of the zebrafish system. High resolution 2D ¹H-¹⁵N NMR showed that aSyn in zebrafish embryos had the same conformational and biological features previously observed in mammalian cells, including conserved interactions with cellular biomolecules and the establishment of physiological protein post-translational modifications. A direct comparative analysis of gamma-synuclein (gSyn), a naturally occurring homolog of aSyn, in bacteria, mammalian cells and zebrafish embryos confirmed these observations. Our results showed that high resolution in-cell NMR is attainable in embryonic cells within the native environment of a live animal. This system provides more physiological cellular environments for high resolution, <em>in situ</em> protein biophysical studies.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100111"},"PeriodicalIF":2.624,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"2623849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved linker length in double dsRBD proteins from plants restricts interdomain motion","authors":"Florencia C. Mascali ,&nbsp;Roberta Crespo ,&nbsp;Leandro C. Tabares ,&nbsp;Rodolfo M. Rasia","doi":"10.1016/j.jmro.2023.100109","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100109","url":null,"abstract":"<div><p>Double stranded RNA binding domains (dsRBDs) are ubiquitous in all kingdoms of life. They can participate both in RNA and protein recognition and are usually present in multiple copies in multidomain proteins. We analyzed the linkers between dsRBDs in different proteins and found that sequences corresponding to plant proteins have a highly conserved linker length. In order to assess the importance of linker length in the conformational freedom of double dsRBD plant proteins, we introduced lanthanide binding tags (LBTs) in different positions of the dsRBD containing protein HYL1 from <em>Arabidopsis thaliana</em>. These constructs were used to obtain conformational restraints from Double electron–electron resonance (DEER) measurements on doubly labeled proteins and from paramagnetic relaxation enhancement (PRE) in single labeled samples. Fitting the experimental datasets to a computational model of the ensemble created by allowing freedom to the linker region we found that the domains tend to explore a particular region of the allowed conformational space. The high conservation in linker length suggests that this restricted conformational sampling is functional, possibly hindering HYL1-dsRBD2 from contacting the substrate dsRNA and allowing it to participate in protein-protein interactions.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100109"},"PeriodicalIF":2.624,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A primer in pulse EPR-based hyperfine spectroscopy for NMR spectroscopists","authors":"Nino Wili","doi":"10.1016/j.jmro.2023.100108","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100108","url":null,"abstract":"<div><p>The theoretical foundations of NMR and EPR are very similar. Nevertheless, the fields differ significantly in practical aspects. This primer is an attempt to bridge some of the gaps between the fields, and at the same time it highlights some applications of pulse EPR. Basic EPR pulse sequences to detect nuclei in the vicinity of unpaired electrons are introduced. An emphasis is placed on explaining the concept to researchers familiar with NMR. The theoretical background as well as examples are given for electron-nuclear double resonance (ENDOR), electron-spin echo envelope modulation (ESEEM), including hyperfine sublevel correlation spectroscopy (HYSCORE), and electron double resonance (ELDOR)-detected NMR.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100108"},"PeriodicalIF":2.624,"publicationDate":"2023-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3138356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant defensins as a model to study the thermostability of surface hydrophobic clusters: The Pisum sativum defensin 2 (Psd2)","authors":"Ramon Pinheiro-Aguiar ,&nbsp;Caroline Corrêa-Almeida ,&nbsp;Eleonora Kurtenbach ,&nbsp;Fabio C.L. Almeida","doi":"10.1016/j.jmro.2023.100106","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100106","url":null,"abstract":"<div><p>Plant defensins (PDs) display a CSαβ-fold that lacks a canonical hydrophobic core. They display almost all hydrophobic residues on the protein surface. The exposed hydrophobic residues form surface clusters stabilized by the vicinity of hydrophilic residues and the hydration shell. Here, we used Psd2 as a model to study the formation and stabilization of these local foldons named surface hydrophobic clusters (SHC). We characterized the temperature dependence of ¹⁵N CPMG relaxation dispersion profiles to describe the complex dynamics of Psd2 and indirectly study the thermodynamics of SHCs in PDs. We show a correlation between residues undergoing conformational exchange and the SHCs. Chemical shift changes between the native ground state and the first thermally accessible excited state enabled us to map the major conformational changes in Psd2 conformational equilibrium. The observation of a cold-driven excited state revealed that SHCs are stabilized by hydrophobic contacts, which are exposed at low temperatures, leading to a favorable decrease in enthalpy compensated by an unfavorable entropy reduction. At higher temperatures, we detected another excited conformer that may play a role in membrane-specific interaction, as previously described for other defensins.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100106"},"PeriodicalIF":2.624,"publicationDate":"2023-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low perturbation limit decoherence analyzed by scaling the Double Quantum Hamiltonian","authors":"C.M. Sánchez,&nbsp;H.M. Pastawski,&nbsp;A.K. Chattah","doi":"10.1016/j.jmro.2023.100104","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100104","url":null,"abstract":"<div><p>By varying the magnitude of the effective interaction between spins in relation to the perturbations, we study the decoherence behavior in a connected proton system. Making use of the Magnus expansion, we introduce a NMR pulse sequence that generates an average Hamiltonian with Double Quantum terms multiplied by a scaling factor, <span><math><mi>δ</mi></math></span>, with the possibility to take positive and negative values. The performance of the pulse sequence for different values of the scaling factors was validated in polycrystalline adamantane, by observing the evolution of the polarization. A time reversal procedure, accessible through the change of sign in the controlled Hamiltonian, was necessary to observe multiple quantum coherences. The spin counting develops a characteristic growth in two species of clusters for the scaled time. The influence of the scaling factor on the reversibility was observed through the behavior of the Loschmidt echoes, which decayed faster as the scaling factor increases. From the analysis of dynamics and its reversibility, we extracted characteristic times for the spin diffusion, <span><math><msubsup><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow><mrow><mi>δ</mi></mrow></msubsup></math></span> and the intrinsic decoherence decay, <span><math><msubsup><mrow><mi>T</mi></mrow><mrow><mn>3</mn></mrow><mrow><mi>δ</mi></mrow></msubsup></math></span> for each scaling factor <span><math><mi>δ</mi></math></span>, and perturbation time scale, <span><math><msub><mrow><mi>T</mi></mrow><mrow><mi>Σ</mi></mrow></msub></math></span>. Observing the dependence of reversibility vs. perturbation rates, both normalized with the spin diffusion rate, we find that in the limit of low perturbations, <span><math><mrow><msubsup><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow><mrow><mi>δ</mi></mrow></msubsup><mo>/</mo><msubsup><mrow><mi>T</mi></mrow><mrow><mn>3</mn></mrow><mrow><mi>δ</mi></mrow></msubsup></mrow></math></span> deviates from the linear dependence on <span><math><mrow><msubsup><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow><mrow><mi>δ</mi></mrow></msubsup><mo>/</mo><msub><mrow><mi>T</mi></mrow><mrow><mi>Σ</mi></mrow></msub></mrow></math></span> that corresponds to strong perturbation. The asymptotic value <span><math><mrow><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>/</mo><msub><mrow><mi>T</mi></mrow><mrow><mn>3</mn></mrow></msub><mo>≈</mo><mn>0</mn><mo>.</mo><mn>15</mn></mrow></math></span> as <span><math><mrow><msubsup><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow><mrow><mi>δ</mi></mrow></msubsup><mo>/</mo><msub><mrow><mi>T</mi></mrow><mrow><mi>Σ</mi></mrow></msub></mrow></math></span> vanishes, gives evidence that the main source of irreversibility is the <em>intrinsic decoherence</em> associated to the chaotic many-body dynamics of the system.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100104"},"PeriodicalIF":2.624,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3451234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring quantum thermodynamics with NMR","authors":"C.H.S. Vieira ,&nbsp;J.L.D. de Oliveira ,&nbsp;J.F.G. Santos ,&nbsp;P.R. Dieguez ,&nbsp;R.M. Serra","doi":"10.1016/j.jmro.2023.100105","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100105","url":null,"abstract":"<div><p>Quantum thermodynamics seeks to extend non-equilibrium stochastic thermodynamics to small quantum systems where non-classical features are essential to its description. Such a research area has recently provided meaningful theoretical and experimental advances by exploring the wealth and the power of quantum features along with informational aspects of a system’s thermodynamics. The relevance of such investigations is related to the fact that quantum technological devices are currently at the forefront of science and engineering applications. This short review article provides an overview of some concepts in quantum thermodynamics highlighting test-of-principles experiments using nuclear magnetic resonance techniques.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100105"},"PeriodicalIF":2.624,"publicationDate":"2023-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1693968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Segmented solenoid RF coils for MRI of ex vivo brain samples at ultra-high field preclinical and clinical scanners","authors":"Daniel Papoti ,&nbsp;Diego Szczupak ,&nbsp;Luiz G.C. Santos ,&nbsp;Khallil T. Chaim ,&nbsp;Maria C.G. Otaduy ,&nbsp;David J. Schaeffer ,&nbsp;Edson L.G. Vidoto ,&nbsp;Alberto Tannús ,&nbsp;Afonso C. Silva","doi":"10.1016/j.jmro.2023.100103","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100103","url":null,"abstract":"<div><p>Magnetic resonance imaging (MRI) is a well-known and widespread imaging modality for neuroscience studies and the clinical diagnoses of neurological disorders, mainly due to its capability to visualize brain microstructures and quantify various metabolites. Additionally, its noninvasive nature makes possible the correlation of high-resolution MRI from ex vivo brain samples with histology, supporting the study of neurodegenerative disorders such as Alzheimer's or Parkinson's disease. However, the quality and resolution of ex vivo MRI highly depend on the availability of specialized radiofrequency coils with maximized filling factors for the different sizes and shapes of the samples to be studied. For instance, small, dedicated radiofrequency (RF) coils are not always commercially available in ultrahigh field whole-body MRI scanners. Even for ultrahigh field preclinical scanners, specific RF coils for <em>ex vivo</em> MRI are expensive and not always available. Here, we describe the design and construction of two RF coils based on the solenoid geometry for <em>ex vivo</em> MRI of human brain tissues in a 7T whole-body scanner and for <em>ex vivo</em> MRI of marmoset brain samples in a 9.4T preclinical scanner. We designed the 7T solenoid RF coil to maximize the filling factor of human brain samples conditioned on cassettes for histology, while the 9.4T solenoid was constructed to accommodate marmoset brain samples conditioned in 50 ml centrifuge tubes. Both solenoid designs operate in transceiver mode. The measured B₁⁺ maps show a high level of homogeneity in the imaging volume of interest, with a high signal-to-noise ratio over the imaging volume. High-resolution (80 µm in plane, 500 µm slice thickness) images of human brain samples were acquired with the 7T solenoid, while marmoset brain samples were acquired with an isotropic resolution of 60 µm using the 9.4T solenoid coil.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100103"},"PeriodicalIF":2.624,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3451233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"17O hyperfine spectroscopy in surface chemistry and catalysis","authors":"Yu-Kai Liao ,&nbsp;Paolo Cleto Bruzzese ,&nbsp;Enrico Salvadori ,&nbsp;Mario Chiesa","doi":"10.1016/j.jmro.2023.100101","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100101","url":null,"abstract":"<div><p>Oxide-based materials are of key technological importance in different areas including advanced functional materials, solid state chemistry and catalysis. Many of the key questions concerning these areas involve understanding the chemical bond between the metal and the oxygen ions in the first or subsequent coordinating shells. The spectroscopic study of oxygen is therefore of fundamental importance to elucidate the complex interfacial coordination chemistry that underlies the development of metal-oxide supported catalysts and other advanced materials. Oxygen atoms at solid surfaces or lining the pores of zeolite frameworks play a vital role in stabilizing and defining the electronic and geometric structure of single metal atoms or clusters that act as catalytically active sites. In the case of paramagnetic species, EPR and its related hyperfine techniques offer a unique opportunity to explore and understand the nature of the chemical bonding in metal-oxide systems through the detection of the ¹⁷O hyperfine interaction. In this perspective we offer an overview of experimental considerations and relevant examples specific to ¹⁷O hyperfine spectroscopy of transition metal ions in zeolites relevant to catalysis. ¹⁷O hyperfine coupling values are obtained, which allow discriminating σ- and π-bonding channels in metal-oxygen bonds involving first-row transition metal ions. An exhaustive collection of ¹⁷O hyperfine and nuclear quadrupole couplings in different systems including molecular and biomolecular chemistry is provided, emphasizing the connection between interfacial and molecular inorganic coordination chemistry.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100101"},"PeriodicalIF":2.624,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3138355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}