Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protein backbone dynamics through 13C'-13Calpha cross-relaxation in NMR spectroscopy.

ABSTRACT: Internal dynamics of proteins are usually characterized by the analysis of (15)N relaxation rates that reflect the motions of NH(N) vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C'C(alpha) vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2N(z)() and 2N(z)(). This amounts to "anchoring" the and operators to the N(z)() term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C'C(alpha) vector appear more restricted than those of the NH(N) vector.

SUBMITTER: Ferrage F

PROVIDER: S-EPMC2365922 | biostudies-literature | 2006 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Protein backbone dynamics through 13C'-13Calpha cross-relaxation in NMR spectroscopy.

Ferrage Fabien F Pelupessy Philippe P Cowburn David D Bodenhausen Geoffrey G

Journal of the American Chemical Society 20060801 34

Internal dynamics of proteins are usually characterized by the analysis of (15)N relaxation rates that reflect the motions of NH(N) vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C'C(alpha) vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2N(z)() and 2N(z)(). This amounts to "anchoring" the and oper ...[more]

PMID: 16925424

Similar Datasets

Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.

Project description:Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently developed, metabolically directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2' and C4' sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R(1rho) relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond time scale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3'-endo/C2'-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA.

| S-EPMC2729180 | biostudies-literature

Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label.

Project description:The refolding kinetics of bistable RNA sequences were studied in unperturbed equilibrium via (13)C exchange NMR spectroscopy. For this purpose a straightforward labeling technique was elaborated using a 2'-(13)C-methoxy uridine modification, which was prepared by a two-step synthesis and introduced into RNA using standard protocols. Using (13)C longitudinal exchange NMR spectroscopy the refolding kinetics of a 20 nt bistable RNA were characterized at temperatures between 298 and 310K, yielding the enthalpy and entropy differences between the conformers at equilibrium and the activation energy of the refolding process. The kinetics of a more stable 32 nt bistable RNA could be analyzed by the same approach at elevated temperatures, i.e. at 314 and 316 K. Finally, the dynamics of a multi-stable RNA able to fold into two hairpin- and a pseudo-knotted conformation was studied by (13)C relaxation dispersion NMR spectroscopy.

| S-EPMC3105391 | biostudies-literature

Mapping membrane protein backbone dynamics: a comparison of site-directed spin labeling with NMR 15N-relaxation measurements.

Project description:The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins.

| S-EPMC4190660 | biostudies-literature

Probing local backbone geometries in intrinsically disordered proteins by cross-correlated NMR relaxation.

Project description:An ultra-high-resolution NMR experiment for the measurement of intraresidue (1)H(i)-(15)N(i)-(13)C'(i) dipolar-chemical shift anisotropy relaxation interference is employed to extract information about local backbone geometries in intrinsically disordered proteins. The study of tumor suppressor BASP1 revealed a population shift of β-turn geometries at low pH conditions and a compaction of the BASP1 structural ensemble.

| S-EPMC3659411 | biostudies-literature

Probing Local Backbone Geometries in Intrinsically Disordered Proteins by Cross-Correlated NMR Relaxation.

Project description: Not available

| S-EPMC4373133 | biostudies-literature

Project description:Although collective dynamics of atom groups steer many biologically relevant processes in biomacromolecules, most atomic resolution motional studies focus on isolated bonds. In this study, a new method is introduced to assess correlated dynamics between bond vectors by cross relaxation nuclear magnetic resonance (NMR). Dipole-dipole cross correlated relaxation rates between intra- and inter-residual H(N)-N and H(alpha)-C(alpha) in the 56 residue protein GB3 are measured with high accuracy. It is demonstrated that the assumption of anisotropic molecular tumbling is necessary to evaluate rates accurately and predictions from the static structure using effective bond lengths of 1.041 and 1.117 A for H(N)-N and H(alpha)-C(alpha) are within 3% of both experimental intra- and inter-residual rates. Deviations are matched to models of different degrees of motional correlation. These models are based on previously determined orientations and motional amplitudes from residual dipolar couplings with high accuracy and precision. Clear evidence of correlated motion in the loops comprising residues 10-14, 20-22, and 47-50 and anticorrelated motion in the alpha helix comprising 23-38 is presented. Somewhat weaker correlation is observed in the beta strands 2-4, which have previously been shown to exhibit slow correlated motional modes.

| S-EPMC2750032 | biostudies-literature

Project description:Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns-ms) time scales. The measurement of heteronuclear ((13)C, (15)N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1? relaxation) provides access to such motions, and an increasing number of studies involving R1? relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1? experiments is measurable and that the CCR rate constant depends on ns-ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1? rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.

| S-EPMC5010779 | biostudies-other

Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding.

Project description:An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class?I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.

| S-EPMC4353840 | biostudies-literature

Heteronuclear cross-relaxation effects in the NMR spectroscopy of hyperpolarized targets.

Project description:Dissolution dynamic nuclear polarization (DNP) enables high-sensitivity solution-phase NMR experiments on long-lived nuclear spin species such as (15)N and (13)C. This report explores certain features arising in solution-state (1)H NMR upon polarizing low-γ nuclear species. Following solid-state hyperpolarization of both (13)C and (1)H, solution-phase (1)H NMR experiments on dissolved samples revealed transient effects, whereby peaks arising from protons bonded to the naturally occurring (13)C nuclei appeared larger than the typically dominant (12)C-bonded (1)H resonances. This enhancement of the satellite peaks was examined in detail with respect to a variety of mechanisms that could potentially explain this observation. Both two- and three-spin phenomena active in the solid state could lead to this kind of effect; still, experimental observations revealed that the enhancement originates from (13)C→(1)H polarization-transfer processes active in the liquid state. Kinetic equations based on modified heteronuclear cross-relaxation models were examined, and found to well describe the distinct patterns of growth and decay shown by the (13)C-bound (1)H NMR satellite resonances. The dynamics of these novel cross-relaxation phenomena were determined, and their potential usefulness as tools for investigating hyperpolarized ensembles and for obtaining enhanced-sensitivity (1)H NMR traces was explored.

| S-EPMC5040509 | biostudies-literature

Unique backbone-water interaction detected in sphingomyelin bilayers with 1H/31P and 1H/13C HETCOR MAS NMR spectroscopy.

Project description:Two-dimensional (1)H/(31)P dipolar heteronuclear correlation (HETCOR) magic-angle spinning nuclear magnetic resonance (NMR) is used to investigate the correlation of the lipid headgroup with various intra- and intermolecular proton environments. Cross-polarization NMR techniques involving (31)P have not been previously pursued to a great extent in lipid bilayers due to the long (1)H-(31)P distances and high degree of headgroup mobility that averages the dipolar coupling in the liquid crystalline phase. The results presented herein show that this approach is very promising and yields information not readily available with other experimental methods. Of particular interest is the detection of a unique lipid backbone-water intermolecular interaction in egg sphingomyelin (SM) that is not observed in lipids with glycerol backbones like phosphatidylcholines. This backbone-water interaction in SM is probed when a mixing period allowing magnetization exchange between different (1)H environments via the nuclear Overhauser effect (NOE) is included in the NMR pulse sequence. The molecular information provided by these (1)H/(31)P dipolar HETCOR experiments with NOE mixing differ from those previously obtained by conventional NOE spectroscopy and heteronuclear NOE spectroscopy NMR experiments. In addition, two-dimensional (1)H/(13)C INEPT HETCOR experiments with NOE mixing support the (1)H/(31)P dipolar HETCOR results and confirm the presence of a H(2)O environment that has nonvanishing dipolar interactions with the SM backbone.

| S-EPMC2479603 | 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