Journal of Magnetic Resonance Open最新文献

{"title":"Conformational dynamics and kinetics of protein interactions by nuclear magnetic resonance","authors":"Adolfo H. Moraes ,&nbsp;Ana Paula Valente","doi":"10.1016/j.jmro.2023.100093","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100093","url":null,"abstract":"<div><p>Structural information of protein complexes is fundamental for the rational drug design and improvement of vaccines and biosensors. Also, protein misassembly can have severe biological consequences. Here we discuss the challenges of studying protein complexes and show examples of systems characterized using NMR.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"14 ","pages":"Article 100093"},"PeriodicalIF":2.624,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826376","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":"Conducting a three-pulse DEER experiment without dead time: A review","authors":"Sergei A. Dzuba","doi":"10.1016/j.jmro.2023.100100","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100100","url":null,"abstract":"<div><p>Double electron-electron resonance spectroscopy (DEER, also known as PELDOR) is used to study spin-spin dipolar interactions between spin labels, at the nanoscale range of distances. The DEER effect is obtained as a signal generated by echo-forming microwave (mw) pulses with an additional mw pump pulse applied at a different frequency. It is important to carry out measurements without artefacts induced by overlap of the pulses in the time scale. Such an experiment without the dead-time effect is achieved using the 4-pulse (4p) DEER method. The analysis of the literature performed here shows however that the 3-pulse (3p) DEER can also be free of the dead time problem, for which there are two possibilities. The first occurs using a specially designed bimodal resonator, for which the two frequencies are completely decoupled. The second possibility, which can be implemented for any commercial spectrometer, involves the signal correction based on an additional “blank” measurement with the pump pulse applied outside the EPR resonance. A detailed comparison of the 3p and 4p DEER data obtained previously by Milov et al. [Appl. Magn. Reson. 41 (2011) 59–67] shows that 3p and 4p approaches give similar results. The advantages of the 3p DEER techniques are discussed.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"14 ","pages":"Article 100100"},"PeriodicalIF":2.624,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826378","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 broadband pulse EPR spectrometer for high-throughput measurements in the X-band","authors":"Nikolay P. Isaev ,&nbsp;Anatoly R. Melnikov ,&nbsp;Konstantin A. Lomanovich ,&nbsp;Mikhail V. Dugin ,&nbsp;Mikhail Yu. Ivanov ,&nbsp;Dmitriy N. Polovyanenko ,&nbsp;Sergey L. Veber ,&nbsp;Michael K. Bowman ,&nbsp;Elena G. Bagryanskaya","doi":"10.1016/j.jmro.2022.100092","DOIUrl":"https://doi.org/10.1016/j.jmro.2022.100092","url":null,"abstract":"<div><p>We present an X-band pulse EPR spectrometer with high throughput and excellent sensitivity in the 8.5-11.5GHz range. It is designed for high stability and low noise Fourier Transform measurements for applications in pulse dipolar spectroscopy, pulse hyperfine spectroscopy, and spin relaxation from cryogenic temperatures to room temperature. An arbitrary waveform generator is used to generate pulses of any frequency and shape for multiple resonance experiments or for uniform broadband excitation with bandwidths exceeding 350 MHz. We illustrate the capabilities and performance of the spectrometer by measurements on free radicals and biradicals in solids and liquids. Relaxation times of radicals in liquid solution are measured for fewer than 30,000,000 spins (less than 3 nanomoles per liter). Non-uniform acquisition provides higher throughput for mixtures of radicals with quite different relaxation rates. Conventional DEER measurements on a rigid biradical have good modulation depth. Broadband SIFTER with chirped adiabatic WURST pulses demonstrates versatility for the latest broadband pulse schemes. A broadband ESEEM measurement correlates ESEEM and EPR frequencies which characterize the conformation of a nitroxide radical. The entire EPR spectrum with a width approaching 300 MHz was excited and detected throughout the measurement. The spectrometer supports the operator in tuning, setting up experiments and monitoring their progress so that even novice users consistently can obtain optimal results.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"14 ","pages":"Article 100092"},"PeriodicalIF":2.624,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3451239","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":"Inductively coupled, transmit-receive coils for proton MRI and X-nucleus MRI/MRS in small animals","authors":"Atsushi M. Takahashi ,&nbsp;Jitendra Sharma ,&nbsp;David O. Guarin ,&nbsp;Julie Miller ,&nbsp;Hiroaki Wakimoto ,&nbsp;Daniel P. Cahill ,&nbsp;Yi-Fen Yen","doi":"10.1016/j.jmro.2023.100123","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100123","url":null,"abstract":"<div><p>We report several inductively coupled RF coil designs that are very easy to construct, produce high signal-to-noise ratio (SNR) and high spatial resolution while accommodating life support, anesthesia and monitoring in small animals. Inductively coupled surface coils were designed for hyperpolarized ¹³ C MR spectroscopic imaging (MRSI) of mouse brain, with emphases on the simplicity of the circuit design, ease of use, whole-brain coverage, and high SNR. The simplest form was a resonant loop designed to crown the mouse head for a snug fit to achieve full coverage of the brain with high sensitivity when inductively coupled to a broadband pick-up coil. Here, we demonstrated the coil's performance in hyperpolarized ¹³ C MRSI of a normal mouse and a glioblastoma mouse model at 4.7 T. High SNR exceeding 70:1 was obtained in the brain with good spatial resolution (1.53 mm x 1.53 mm). Similar inductively coupled loop for other X-nuclei can be made very easily in a few minutes and achieve high performance, as demonstrated in ³¹ P spectroscopy. Similar design concept was expanded to splitable, inductively coupled volume coils for high-resolution proton MRI of marmoset at 3T and 9.4T, to easily accommodate head restraint, vital-sign monitoring, and anesthesia delivery.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100123"},"PeriodicalIF":2.624,"publicationDate":"2023-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3135445","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":"Optimal control derived sensitivity-enhanced CA-CO mixing sequences for MAS solid-state NMR – Applications in sequential protein backbone assignments","authors":"Jan Blahut ,&nbsp;Matthias J. Brandl ,&nbsp;Riddhiman Sarkar ,&nbsp;Bernd Reif ,&nbsp;Zdeněk Tošner","doi":"10.1016/j.jmro.2023.100122","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100122","url":null,"abstract":"<div><p>We have recently introduced optimal-control derived pulse sequences for sensitivity-enhanced heteronuclear correlation NMR experiments of solid proteins. Preservation of equivalent coherence transfer pathways using transverse-mixing pulses (TROP) in multidimensional pulse schemes allows to increase the sensitivity of the experiments by more than a factor of <span><math><msqrt><mn>2</mn></msqrt></math></span> per each indirect dimension. In this article, we present homonuclear CA-CO transverse-mixing elements (homoTROP) that are based on dipolar interactions and achieve similar gains as the heteronuclear TROP pulses described previously. Both transfer elements were subsequently implemented in 3D se-hCAcoNH and se-hCOcaNH, that together with the previously introduced 3D se-hCANH and se-hCONH experiments yield a complete set of sensitivity-enhanced protein backbone assignment experiments. In contrast to the J-coupling based methods that are used at fast (60 kHz) and ultrafast MAS (&gt;100 kHz), the homoTROP experiments employ about 10-times shorter mixing times making use of the larger magnitude of the dipolar coupling in comparison to the J couplings. The experiments are demonstrated using a microcrystalline, perdeuterated sample of the chicken alpha-spectrin SH3 domain in which all exchangeable sites are fully back-substituted with protons. We evaluated the gains in efficiency in all experiments site-specifically observing that the se-hCAcoNH and se-hCOcaNH experiments yield an increase in sensitivity by a factor of 1.36±0.09 and at least a factor of 1.8 with respect to the conventional hcoCAcoNH and hCOcaNH J-based experiments.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100122"},"PeriodicalIF":2.624,"publicationDate":"2023-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3451237","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":"Solid state nuclear magnetic resonance of polymers","authors":"Gustavo Alberto Monti ,&nbsp;Rodolfo Héctor Acosta ,&nbsp;Ana Karina Chattah ,&nbsp;Yamila Garro Linck","doi":"10.1016/j.jmro.2023.100119","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100119","url":null,"abstract":"<div><p>The development of Solid-State Nuclear Magnetic Resonance (SSNMR) in Argentina took a great buster at the beginning of the 1990s along with the acquisition of many “state-of-the-art” high-field NMR spectrometers, two of them multipurpose solid-liquid spectrometers. From then to nowadays, the study of solid samples, including polymers, has been a current topic at the NMR group of the Facultad de Matemática, Astronomía, Física y Computación of Universidad Nacional de Córdoba, in Argentina. In this work, we propose a review approach of several research works on solid polymers performed in our group, covering low-field relaxation studies and high-resolution SSNMR.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100119"},"PeriodicalIF":2.624,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826465","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":"The application of solution NMR spectroscopy to study dynamics of two-domain calcium-binding proteins","authors":"Roberto Kopke Salinas","doi":"10.1016/j.jmro.2023.100120","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100120","url":null,"abstract":"<div><p>Protein dynamics due to flexible linkers connecting otherwise rigid domains may be critical for the functioning of a variety of biological systems, ranging from membrane transporters to calcium-signaling and the formation of intercellular junctions. Considering that NMR spectroscopy is extremely powerful to characterize dynamics at various time scales, this manuscript brings an overview of the main strategies that have been employed to characterize inter-domain dynamics in relevant biological systems. Emphasis was given to the calcium binding proteins: calmodulin, cadherin, and the Na⁺/Ca²⁺ exchanger calcium-sensor domain. The introduction of paramagnetic centers in diamagnetic proteins is seen as key to obtaining unambiguous information about inter-domain dynamics. This is because the self-alignment of one of the domains in multi-domain proteins avoids the problem of dealing with alignment tensor fluctuations in dynamic systems. The combination of residual dipolar couplings (RDCs) and pseudocontact shifts (PCSs) with computational strategies aiming to provide an ensemble description of protein dynamics is seen as the most powerful strategy to gain detailed atomistic information on inter-domain motions. It is noteworthy that the cadherin ectodomains and the Na⁺/Ca²⁺ exchanger calcium sensor respond in the same way upon calcium-binding: in the absence of calcium the two domains are flexibly linked to one another and may preferentially sample kinked inter-domain arrangements, while calcium binding stabilizes a rigid and extended inter-domain arrangement. It is thus remarkable that nature chose the same molecular mechanism to promote two very different biological functions that are triggered by calcium signaling: intercellular adhesion by the formation of cadherin dimers and the allosteric regulation of a membrane transporter in the case of the Na⁺/Ca²⁺ exchanger.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100120"},"PeriodicalIF":2.624,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3266170","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 3D method called mdMRS for post-processing Magnetic Resonance Spectroscopy data","authors":"Dale H. Mugler ,&nbsp;Dorothea D. Jenkins","doi":"10.1016/j.jmro.2023.100116","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100116","url":null,"abstract":"<div><p>The data obtained from a scanner for Magnetic Resonance Spectroscopy (MRS) is three-dimensional (3D) since the FID data from the scanner has spectrum values which are 2D complex numbers and 1D time values. This paper describes an MRS frequency-based post-processing method that has the advantage that it quickly determines the values needed for metabolite intensities and concentrations, even for most overlapping spectral terms.</p><p>The method of this paper does not depend on area under a curve or a user-chosen basis set. As few as three valid points corresponding to a peak on the spectral curve are all that is needed, other than similar information on a reference metabolite, for concentration determination of the associated metabolite. All four of the key values of peak location, amplitude, phase angle, and damping constant are determined simultaneously with high accuracy, dependent upon noise, and with computational simplicity from only three complex-valued constants. The theory behind <em>mdMRS</em> uses the knowledge that the projection of the 3D spectrum to the complex plane is a simple circle. Several concepts from complex variables theory are important, such as the Linear Fractional Transformation (LFT) that maps the frequency axis to that circle. The duality linking an LFT with a 2 <span><math><mo>×</mo></math></span> 2 Moebius matrix enables a fast iteration process that sharpens the four key value estimates on each iteration. The iteration removes all other terms when considering one of them. Applied to initial estimates, this leads to increasingly accurate output.</p><p>To be useful to clinicians and to researchers developing treatments based on metabolite concentrations, the goal for post-processing of the data include both fast and accurate computations, with speed sufficient to provide results “on console” and output provided as concentrations. Besides the number of protons associated with a metabolite, concentrations are determined using both amplitude and damping constant values. Since the methods of <em>mdMRS</em> provide both of those characteristics simultaneously, the time from data collection to metabolite concentration output is minimized. The name of this new post-processing method was chosen since the attributes of the method help bring that goal closer to reality for <u>M</u>edical <u>D</u>octors.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100116"},"PeriodicalIF":2.624,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3135444","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":"X-nuclear MRS and MRI on a standard clinical proton-only MRI scanner","authors":"Yi-Fen Yen ,&nbsp;Atsushi M. Takahashi ,&nbsp;Jerome L. Ackerman","doi":"10.1016/j.jmro.2023.100118","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100118","url":null,"abstract":"<div><p>In light of the growing interest <em>in-vivo</em> deuterium metabolic imaging, hyperpolarized ¹³C, ¹⁵N, ³He, and ¹²⁹Xe imaging, as well as ³¹P spectroscopy and imaging in large animals on clinical MR scanners, we demonstrate the use of a (radio)frequency converter system to allow X-nuclear MR spectroscopy (MRS) and MR imaging (MRI) on standard clinical MRI scanners without multinuclear capability. This is not only an economical alternative to the multinuclear system (MNS) provided by the scanner vendors, but also overcomes the frequency bandwidth problem of some vendor-provided MNSs that prohibit users from applications with X-nuclei of low magnetogyric ratio, such as deuterium (6.536 MHz/Tesla) and ¹⁵N (-4.316 MHz/Tesla). Here we illustrate the design of the frequency converter system and demonstrate its feasibility for ³¹P (17.235 MHz/Tesla), ¹³C (10.708 MHz/Tesla), and ¹⁵N MRS and MRI on a clinical MRI scanner without vendor-provided multinuclear hardware.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100118"},"PeriodicalIF":2.624,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3138358","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":"Continuous-wave electron paramagnetic resonance (CW-EPR) for studying structure-function relationships in a Cu-containing nitrite reductase and a Mo-containing aldehyde oxidoreductase","authors":"Pablo J. González,&nbsp;María G. Rivas,&nbsp;Ana L. Pérez,&nbsp;Carlos D. Brondino","doi":"10.1016/j.jmro.2023.100117","DOIUrl":"https://doi.org/10.1016/j.jmro.2023.100117","url":null,"abstract":"<div><p>Transition metal ion-containing oxidoreductases, which carry out long-distance electron transfer reactions, are a large family of metalloproteins that are widely distributed in nature. The metal ions are either present as mononuclear centers or are organized in clusters. One of the metal cofactors is the active site of the enzyme where the substrate is converted to a product, while the others serve as electron transfer centers. Metal cofactors are paramagnetic in certain protein redox states and may additionally exhibit different relaxation rates and weak superexchange interactions transferred via intraprotein electron transfer pathways. Cu-containing nitrite reductase and Mo-containing aldehyde oxidoreductase are two representative examples of oxidoreductases in which these phenomena occur, making them interesting systems to study using electron magnetic resonance techniques. We summarize here several X-band Continuous-Wave Electron Paramagnetic Resonance (CW-EPR) studies that have allowed insights into structural and functional aspects of these two proteins and may help characterize closely related systems.</p></div>","PeriodicalId":365,"journal":{"name":"Journal of Magnetic Resonance Open","volume":"16 ","pages":"Article 100117"},"PeriodicalIF":2.624,"publicationDate":"2023-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1826463","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}