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Title of Journal: J Biomol NMR

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Abbravation: Journal of Biomolecular NMR

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Springer Netherlands

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DOI

10.1007/s11858-008-0136-6

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1573-5001

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Detection of nanosecond time scale sidechain jump

Authors: Jun Xu Yi Xue Nikolai R Skrynnikov
Publish Date: 2009/07/07
Volume: 45, Issue: 1-2, Pages: 57-72
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Abstract

In solution the correlation time of the overall protein tumbling τ R plays a role of a natural dynamics cutoff—internal motions with correlation times on the order of τ R or longer cannot be reliably identified on the basis of spin relaxation data It has been proposed some time ago that the ‘observation window’ of solution experiments can be expanded by changing the viscosity of solvent to raise the value of τ R To further explore this concept we prepared a series of samples of αspectrin SH3 domain in solvent with increasing concentration of glycerol In addition to the conventional 15N labeling the protein was labeled in the Val Leu methyl positions 13CHD2 on a deuterated background The collected relaxation data were used in asymmetric fashion backbone 15N relaxation rates were used to determine τ R across the series of samples while methyl 13C data were used to probe local dynamics sidechain motions In interpreting the results it has been initially suggested that addition of glycerol leads only to increases in τ R whereas local motional parameters remain unchanged Thus the data from multiple samples can be analyzed jointly with τ R playing the role of experimentally controlled variable Based on this concept the extended modelfree model was constructed with the intent to capture the effect of ns timescale rotameric jumps in valine and leucine side chains Using this model we made a positive identification of nanosecond dynamics in Val23 where ns motions were already observed earlier In several other cases however only tentative identification was possible The lack of definitive results was due to the approximate character of the model—contrary to what has been assumed addition of glycerol led to a gradual ‘stiffening’ of the protein This and other observations also shed light on the interaction of the protein with glycerol which is one of the naturally occurring osmoprotectants In particular it has been found that the overall protein tumbling is controlled by the bulk solvent and not by a thin solvation layer which contains a higher proportion of water


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  2. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK
  3. HNHC: a triple resonance experiment for correlating the H2, N1(N3) and C2 resonances in adenine nucleobases of 13 C-, 15 N-labeled RNA oligonucleotides
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  5. Insights into furanose solution conformations: beyond the two-state model
  6. Selective 1 H- 13 C NMR spectroscopy of methyl groups in residually protonated samples of large proteins
  7. Fast methionine-based solution structure determination of calcium-calmodulin complexes
  8. A procedure to validate and correct the 13 C chemical shift calibration of RNA datasets
  9. Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding
  10. NMR solution structure of the acylphosphatase from Escherichia coli
  11. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data
  12. S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments
  13. Improved NMR experiments with 13 C-isotropic mixing for assignment of aromatic and aliphatic side chains in labeled proteins
  14. Out-and-back 13 C– 13 C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS
  15. Perspectives for sensitivity enhancement in proton-detected solid-state NMR of highly deuterated proteins by preserving water magnetization
  16. A probe to monitor performance of 15 N longitudinal relaxation experiments for proteins in solution
  17. Optimization of NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids
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  22. Erratum to: 13 C α CEST experiment on uniformly 13 C-labeled proteins
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