Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

Abstract

Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970-2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins. Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary structure in disordered proteins.

The Role of Hydration in Protein Stability: Comparison of the Cold and Heat Unfolded States of Yfh1

“…The most sensitive way to exploit this information uses a combination of them as in the calculation of the secondary structure propensity (SSP) score that makes the results more robust against spectrum referencing problems. 17 The SSP plot and secondary chemical shifts along the sequence calculated assuming random-coil values obtained from model peptides 14,18 at − 1°C and at 50°C are qualitatively similar, although with interesting local differences (Fig. 2b).…”

“…14 It is customary to identify secondary structural elements by calculating a chemical shift index. 15 However, it has been correctly pointed out that, in unfolded proteins, the use of the chemical shift index could be inappropriate because it might be too rough a parameter to reflect only transiently formed residual secondary structure.…”

“…15 However, it has been correctly pointed out that, in unfolded proteins, the use of the chemical shift index could be inappropriate because it might be too rough a parameter to reflect only transiently formed residual secondary structure. 14 It is preferable to evaluate elements of secondary structure by secondary chemical shifts 16 that represent the deviation of the chemical shifts at a given temperature from random-coil chemical shift values at 25°C. The most sensitive way to exploit this information uses a combination of them as in the calculation of the secondary structure propensity (SSP) score that makes the results more robust against spectrum referencing problems.…”

“…14 We also compared the plot calculated for CyaY, the bacterial frataxin orthologue, a whole compact globular protein with the same secondary structure as Yfh1 (except for the Nterminal tail that is absent in CyaY) but very different stability. We observe a clear separation between the slopes of folded proteins and randomcoil states with the latter being steeper (Fig.…”

Use of 1H and 31P HRMAS to evaluate the relationship between quantitative alterations in metabolite concentrations and tissue features in human brain tumour biopsies

“…The study of the pH in tissues in vivo or ex vivo has been usually relied upon 31 Histidine has shown changes in the chemical shift of H4 and H2 [41,42] that occur in the interval of pH observed in the samples here studied, but unfortunately, Histidine has not been detected among the metabolites here assigned. Several studies have dealt with the pH and 1 H spectra, either from the point of view of assessment of the pH [41] or with the objective of searching the pH in which the chemical shifts of the metabolites may be invariant [43].…”