Journal of Magnetic Resonance Open最新文献

Staphylococcus aureus CzrA is a paradigmatic member of the ArsR family of transcriptional metalloregulators, which are critical for the bacterial response to stress. Zinc binding to CzrA, which induces DNA derepression, is entropically driven, as shown by calorimetry. A detailed equilibrium dynamics study of different allosteric states of CzrA revealed that zinc induces an entropy redistribution that controls for DNA binding regulation; however, this change in conformational entropy only accounts for a small net contribution to the total entropy. This difference between the change in conformational entropy vs. total entropy of zinc binding implies a significant contribution of solvent molecule rearrangements to this equilibrium. However, the absence of major structural changes suggests that solvent rearrangements occur mainly on the protein surface and/or from zinc desolvation, concomitant with a dynamical redistribution of conformational entropy. Previous results also suggest that zinc binding not only leads to a redistribution of protein internal dynamics, but also release of water molecules from the protein surface. In turn, these water molecules may make a significant contribution to the allosteric response that results in dissociation from the DNA.

Quantifying the differential hydration of two conformational states that share very similar crystal structures and then correlating this with the protein's solvent entropy change constitutes an unresolved problem, even when thermodynamics suggest a significant contribution of solvent entropy. Here, we present different avenues to dissect hydration dynamics in a metal-binding transcriptional regulator that provide different insights into this complex problem. We explore primary solution NMR tools for probing protein–water interactions: the laboratory frame nuclear Overhauser effect (NOE) and its rotating frame counterpart (ROE) between long-lived water molecules and the protein residues. The wNOE/wROE ratio is a promising tool for the detection of hydration dynamics near the surface of a protein in a site-specific manner, minimizing contamination from bulk solvent. Molecular dynamics simulations and computational methods designed to provide a spatially resolved picture of solvent thermodynamics were also employed to provide a more complete panorama of solvent redistribution.

This Primer critically reviews the possibilities and limitations of probing the short-range structure of an oxide-based glass by routine magic-angle spinning (MAS) or triple-quantum MAS (3QMAS) nuclear magnetic resonance (NMR) experiments. We briefly outline the structural features of oxide-based glasses and the basics of solid-state NMR. Besides suggesting guidelines for selecting favorable experimental conditions and important considerations for recording high-quality MAS NMR spectra amenable for subsequent analysis, we review options for extracting NMR observables and their distributions from spins-1/2 as well as half-integer spin quadrupolar nuclei. Considering that the isotropic chemical shift remains the primary probe of local structure by MAS NMR, we thoroughly review its dependence on the short-range oxide-based glass parameters from the viewpoint of a very simple and intuitive but qualitative model. The utility of deconvolutions of notably ²⁹Si and ³¹P MAS NMR spectra are discussed critically. We also suggest alternative yet qualitative analysis options that are available whenever MAS NMR spectral deconvolutions are not warranted without additional information, which incidentally applies to a majority of modern multicomponent glasses.

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.

At low magnetic fields (<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.

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 (Danio rerio) 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, in situ protein biophysical studies.

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 Arabidopsis thaliana. 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.

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.

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.

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, $\delta$, 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, $T_2^{\delta }$ and the intrinsic decoherence decay, $T_3^{\delta }$ for each scaling factor $\delta$, and perturbation time scale, $T_{\Sigma }$. Observing the dependence of reversibility vs. perturbation rates, both normalized with the spin diffusion rate, we find that in the limit of low perturbations, $T_2^{\delta }/T_3^{\delta }$ deviates from the linear dependence on $T_2^{\delta }/T_{\Sigma }$ that corresponds to strong perturbation. The asymptotic value $T_2/T_3\approx 0.15$ as $T_2^{\delta }/T_{\Sigma }$ vanishes, gives evidence that the main source of irreversibility is the intrinsic decoherence associated to the chaotic many-body dynamics of the system.

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.