Dataset Information

Protein conformational dynamics studied by 15N and 1H R1? relaxation dispersion: Application to wild-type and G53A ubiquitin crystals.

ABSTRACT: Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45-60kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a ?-turn region in the wild-type protein. We use 15N R1? relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1? relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility.

SUBMITTER: Gauto DF

PROVIDER: S-EPMC5531261 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Protein conformational dynamics studied by 15N and 1H R1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals.

Gauto Diego F DF Hessel Audrey A Rovó Petra P Kurauskas Vilius V Linser Rasmus R Schanda Paul P

Solid state nuclear magnetic resonance 20170414

Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45-60kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. ...[more]

PMID: 28438365

Similar Datasets

Project description:BackgroundR1ρ (or spin-lock) imaging is prone to artifacts arising from field inhomogeneities that may impact the R1ρ quantification. Previous research has proposed two types of method to manage the artifacts in continuous-wave constant amplitude spin-lock, one is based on the composite block pulses to compensate for the field imperfections, another category uses adiabatic pulses in the R1ρ pre-pulse to excite and reverse the magnetization (named adiabatic prepared approach). Although both methods have proved their efficiency in alleviating artifacts, we observed that the adiabatic pulse approach could produce much lower R1ρ dispersion in human knee cartilage than the block pulse method (characterized by the R1ρ difference ∆R1ρ =11.4 Hz (from spin-lock field 50 to 500 Hz) for the block pulse method vs. ∆R1ρ =4.5 Hz for the adiabatic pulse approach). Prompted by this observation, the purpose of this study was to investigate the underlying factors that may affect the R1ρ dispersion through numerical simulations based on the two-pool exchanging Bloch-McConnell equations.MethodsThe effects of free water pool size Pa (from 0.80 to 0.95), chemical exchange rate kb (from the bound to free water pool, ranged from 500 to 3,000 Hz), adiabatic pulse duration Tp (from 5.0 to 25 ms), and the chemical shift of the bound pool ppmb (from 1.0 to 5.0 ppm) were examined on the degree of the R1ρ dispersion for the two R1ρ imaging methods.ResultsIn general, the greater the ppmb, kb, Tp, and the smaller Pa, the more significant difference in R1ρ dispersion between the block and adiabatic approaches, with the dispersion curve of the adiabatic method becoming flatter.ConclusionsThe adiabatic prepared approach may compromise the R1ρ dispersion, the effect is determined by the combination of the tissue and radiofrequency (RF) pulse properties. It is suggested that care should be taken when using the adiabatically prepared approach to study R1ρ dispersion.

Project description:BackgroundFast and accurate T1ρ mapping in myocardium is still a major challenge, particularly in small animal models. The complex sequence design owing to electrocardiogram and respiratory gating leads to quantification errors in in vivo experiments, due to variations of the T1ρ relaxation pathway. In this study, we present an improved quantification method for T1ρ using a newly derived formalism of a T1ρ* relaxation pathway.MethodsThe new signal equation was derived by solving a recursion problem for spin-lock prepared fast gradient echo readouts. Based on Bloch simulations, we compared quantification errors using the common monoexponential model and our corrected model. The method was validated in phantom experiments and tested in vivo for myocardial T1ρ mapping in mice. Here, the impact of the breath dependent spin recovery time Trec on the quantification results was examined in detail.ResultsSimulations indicate that a correction is necessary, since systematically underestimated values are measured under in vivo conditions. In the phantom study, the mean quantification error could be reduced from - 7.4% to - 0.97%. In vivo, a correlation of uncorrected T1ρ with the respiratory cycle was observed. Using the newly derived correction method, this correlation was significantly reduced from r = 0.708 (p < 0.001) to r = 0.204 and the standard deviation of left ventricular T1ρ values in different animals was reduced by at least 39%.ConclusionThe suggested quantification formalism enables fast and precise myocardial T1ρ quantification for small animals during free breathing and can improve the comparability of study results. Our new technique offers a reasonable tool for assessing myocardial diseases, since pathologies that cause a change in heart or breathing rates do not lead to systematic misinterpretations. Besides, the derived signal equation can be used for sequence optimization or for subsequent correction of prior study results.

Dataset Information

Protein conformational dynamics studied by 15N and 1H R1? relaxation dispersion: Application to wild-type and G53A ubiquitin crystals.

Publications

Protein conformational dynamics studied by <sup>15</sup>N and <sup>1</sup>H R<sub>1ρ</sub> relaxation dispersion: Application to wild-type and G53A ubiquitin crystals.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets