Structure-Free Validation of RDC and PRE Measurements of Disordered Proteins
de, Simone Alfonso
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Newby, F., de, S. A., Yagi-Utsumi, M., Salvatella, X., Dobson, C., & Vendruscolo, M. (2015). Structure-Free Validation of RDC and PRE Measurements of Disordered Proteins. Biochemistry, 54 6876-6886. https://doi.org/10.1021/acs.biochem.5b00670
Residual dipolar couplings (RDCs) and paramagnetic relaxation enhancements (PREs) have emerged as valuable parameters for defining the structures and dynamics of disordered proteins by nuclear magnetic resonance (NMR) spectroscopy. Procedures for their measurement, however, may lead to conformational perturbations because of the presence of the alignment media necessary for recording RDCs, or of the paramagnetic groups that must be introduced for measuring PREs. We discuss here experimental methods to quantify these effects by considering the case of the 40-residue isoform of the amyloid peptide (A40), which is associated with Alzheimer's disease. By carrying out RDC measurements over a range of concentrations of given alignment media, we show that perturbations arising from transient binding of A40 can be identified, enabling appropriate corrections to be made. In addition, by using NMR experiments sensitive to long-range interactions we show that it is possible to identify relatively non-perturbing sites for attaching nitroxide radicals for PRE measurements. Thus, controlling the conformational perturbations introduced by RDC and PRE measurements should facilitate their use for the rigorous determination of the conformational properties of disordered proteins.
External DOI: https://doi.org/10.1021/acs.biochem.5b00670
This record's URL: https://www.repository.cam.ac.uk/handle/1810/252363