Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein
- 489 Downloads
Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise 2H isotope shift measurements for 13Cα, 13Cβ, 13C′, 15N, and 1HN have been obtained by using a mixed sample of protonated and uniformly perdeuterated α-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil 2H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.
KeywordsChemical shift IDP IUP Protein NMR 2H Random coil Triple resonance NMR
We thank James L. Baber for experimental support. This work was funded by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH) and the Intramural AIDS-Targeted Antiviral Program of the Office of the Director, NIH.
- Goddard TD, Kneller DG (2008) Sparky 3. University of California, San FranciscoGoogle Scholar
- Jameson CJ (1996) Isotope effects on chemical shifts and coupling constants. In: Grant DM, Harris RK (eds) Encyclopedia of nuclear magnetic resonance, vol 4. Wiley, New York, pp 2638–2655Google Scholar
- Nietlispach D, Clowes RT, Broadhurst RW, Ito Y, Keeler J, Kelly M, Ashurst J, Oschkinat H, Domaille PJ, Laue ED (1996) An approach to the structure determination of larger proteins using triple resonance NMR experiments in conjunction with random fractional deuteration. J Am Chem Soc 118:407–415CrossRefGoogle Scholar
- Ozenne V, Bauer F, Salmon L, Huang J-r, Jensen MR, Segard S, Bernado P, Charavay C, Blackledge M (2012) Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables. Bioinformatics 28:1463–1470CrossRefGoogle Scholar
- Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685–4690ADSCrossRefGoogle Scholar
- Uversky VN, Dunker AK (2010) Understanding protein non-folding. BBA-Proteins. Proteomics 1804:1231–1264Google Scholar