Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanism of dilute-spin-exchange in solid-state NMR.

ABSTRACT: In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, (1)H-(1)H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of (15)N-(15)N spin-exchange mediated by (1)H-(1)H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the (1)H to an off-resonance frequency so that it is at the "magic angle" during the spin-exchange interval in the experiment, since the "magic angle" irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in (15)N-(15)N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the "forbidden" spin-exchange condition under "magic angle" irradiation results in (15)N-(15)N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.

SUBMITTER: Lu GJ

PROVIDER: S-EPMC3971823 | biostudies-other | 2014 Mar

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Tunable exchange bias in dilute magnetic alloys - chiral spin glasses.

Project description:A unidirectional anisotropy appears in field cooled samples of dilute magnetic alloys at temperatures well below the cusp temperature of the zero field cooled magnetization curve. Magnetization measurements on a Cu(13.5 at% Mn) sample show that this anisotropy is essentially temperature independent and acts on a temperature dependent excess magnetization, ?M. The anisotropy can be partially or fully transferred from being locked to the direction of the cooling field at lower fields to becoming locked to the direction of ?M at larger fields, thus instead appearing as a uniaxial anisotropy. This introduces a deceiving division of the anisotropy into a superposition of a unidirectional and a uniaxial part. This two faced nature of the anisotropy has been empirically scrutinized and concluded to originate from one and the same exchange mechanism: the Dzyaloshinsky-Moriya interaction.

| S-EPMC4730205 | biostudies-literature

Spying on the boron-boron triple bond using spin-spin coupling measured from 11B solid-state NMR spectroscopy.

Project description:There is currently tremendous interest in the previously documented example of a stable species exhibiting a boron-boron triple bond (Science, 2012, 336, 1420). Notably, it has recently been stated using arguments based on force constants that this diboryne may not, in reality, feature a boron-boron triple bond. Here, we use advanced solid-state NMR and computational methodology in order to directly probe the orbitals involved in multiple boron-boron bonds experimentally via analysis of 11B-11B spin-spin (J) coupling constants. Computationally, the mechanism responsible for the boron-boron spin-spin coupling in these species is found to be analogous to that for the case of multiply-bonded carbon atoms. The trend in reduced J coupling constants for diborenes and a diboryne, measured experimentally, is in agreement with that known for alkenes and alkynes. This experimental probe of the electronic structure of the boron-boron multiple bond provides strong evidence supporting the originally proposed nature of the bonds in the diboryne and diborenes, and demonstrates that the orbitals involved in boron-boron bonding are equivalent to those well known to construct the multiple bonds between other second-row elements such as carbon and nitrogen.

| S-EPMC5657093 | biostudies-literature

Solid-state NMR spectroscopy.

Project description:Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.

| S-EPMC8341432 | biostudies-literature

Symmetry-amplified J splittings for quadrupolar spin pairs: a solid-state NMR probe of homoatomic covalent bonds.

Project description:Chemically informative J couplings between pairs of quadrupolar nuclei in dimetallic and dimetalloid coordination motifs are measured using J-resolved solid-state NMR experiments. It is shown that the application of a double-quantum filter is necessary to observe the J splittings and that, under these conditions, only a simple doublet is expected. Interestingly, the splitting is amplified if the spins are magnetically equivalent, making it possible to measure highly precise J couplings and unambiguously probe the symmetry of the molecule. This is demonstrated experimentally by chemically breaking the symmetry about a pair of boron spins by reaction with an N-heterocyclic carbene to form a ?-borylation reagent. The results show that the J coupling is a sensitive probe of bonding in diboron compounds and that the J values quantify the weakening of the B-B bond which occurs when forming an sp(2)-sp(3) diboron compound, which is relevant to their reactivity. Due to the prevalence of quadrupolar nuclei among transition metals, this work also provides a new approach to probe metal-metal bonding; results for Mn2(CO)10 are provided as an example.

| S-EPMC3762131 | biostudies-literature

Multiple acquisitions via sequential transfer of orphan spin polarization (MAeSTOSO): How far can we push residual spin polarization in solid-state NMR?

Project description:Conventional multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) experiments detect the signal arising from the decay of a single coherence transfer pathway (FID), resulting in one spectrum per acquisition time. Recently, we introduced two new strategies, namely DUMAS (DUal acquisition Magic Angle Spinning) and MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), that enable the simultaneous acquisitions of multidimensional ssNMR experiments using multiple coherence transfer pathways. Here, we combined the main elements of DUMAS and MEIOSIS to harness both orphan spin operators and residual polarization and increase the number of simultaneous acquisitions. We show that it is possible to acquire up to eight two-dimensional experiments using four acquisition periods per each scan. This new suite of pulse sequences, called MAeSTOSO for Multiple Acquisitions via Sequential Transfer of Orphan Spin pOlarization, relies on residual polarization of both (13)C and (15)N pathways and combines low- and high-sensitivity experiments into a single pulse sequence using one receiver and commercial ssNMR probes. The acquisition of multiple experiments does not affect the sensitivity of the main experiment; rather it recovers the lost coherences that are discarded, resulting in a significant gain in experimental time. Both merits and limitations of this approach are discussed.

| S-EPMC4862926 | biostudies-literature

Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR.

Project description:Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of membrane proteins in liposomes at the atomic level and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we report our study on the fluoride channel Fluc-Ec1 in phospholipid bilayers based on ssNMR and molecular dynamics simulations. Previously unidentified fluoride binding sites in the aqueous vestibules were experimentally verified by 19F-detected ssNMR. One of the two fluoride binding sites in the polar track was identified as a water molecule by 1H-detected ssNMR. Meanwhile, a dynamic hotspot at loop 1 was observed by comparing the spectra of wild-type Fluc-Ec1 in variant buffer conditions or with its mutants. Therefore, we propose that fluoride conduction in the Fluc channel occurs via a "water-mediated knock-on" permeation mechanism and that loop 1 is a key molecular determinant for channel gating.

| S-EPMC10446490 | biostudies-literature

Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy.

Project description:We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.

| S-EPMC3557925 | biostudies-literature

Slow exchange model of nonrigid rotational motion in RNA for combined solid-state and solution NMR studies.

Project description:Functional RNA molecules are conformationally dynamic and sample a multitude of dynamic modes over a wide range of frequencies. Thus, a comprehensive description of RNA dynamics requires the inclusion of a broad range of motions across multiple dynamic rates which must be derived from multiple spectroscopies. Here we describe a slow conformational exchange theoretical approach to combining the description of local motions in RNA that occur in the nanosecond to microsecond window and are detected by solid-state NMR with nonrigid rotational motion of the HIV-1 transactivation response element (TAR) RNA in solution as observed by solution NMR. This theoretical model unifies the experimental results generated by solution and solid-state NMR and provides a comprehensive view of the dynamics of HIV-1 TAR RNA, a well-known paradigm of an RNA where function requires extensive conformational rearrangements. This methodology provides a quantitative atomic level view of the amplitudes and rates of the local and collective displacements of the TAR RNA molecule and provides directly motional parameters for the conformational capture hypothesis of this classical RNA-ligand interaction.

| S-EPMC3246393 | biostudies-literature

Zero-Field NMR of Urea: Spin-Topology Engineering by Chemical Exchange.

Project description:Well-resolved and information-rich J-spectra are the foundation for chemical detection in zero-field NMR. However, even for relatively small molecules, spectra exhibit complexity, hindering the analysis. To address this problem, we investigate an example biomolecule with a complex J-coupling network─urea, a key metabolite in protein catabolism─and demonstrate ways of simplifying its zero-field spectra by modifying spin topology. This goal is achieved by controlling pH-dependent chemical exchange rates of 1H nuclei and varying the composition of the D2O/H2O mixture used as a solvent. Specifically, we demonstrate that by increasing the proton exchange rate in the [13C,15N2]-urea solution, the spin system simplifies, manifesting through a single narrow spectral peak. Additionally, we show that the spectra of 1H/D isotopologues of [15N2]-urea can be understood easily by analyzing isolated spin subsystems. This study paves the way for zero-field NMR detection of complex biomolecules, particularly in biofluids with a high concentration of water.

| S-EPMC8573776 | biostudies-literature

Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations.

Project description:Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural dynamics. Deuterium back-exchange at labile sites of the perdeuterated, fully proton back-exchanged pili was conducted to investigate hydrogen/deuterium (H/D) exchange patterns of backbone amide protons in pre-assembled pili. We found distinct H/D exchange patterns in lateral and axial intermolecular interfaces in pili. Amide protons protected from H/D exchange in pili are mainly located in the core region of the monomeric subunit and in the lateral intermolecular interface, whereas the axial intermolecular interface and the exterior region of pili are highly exposed to H/D exchange. Additionally, we performed molecular dynamics simulations of the type 1 pilus rod and estimated the probability of H/D exchange based on hydrogen bond dynamics. The comparison of the experimental observables and simulation data provides insights into stability and mechanical properties of pili.

| S-EPMC6692446 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data