Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques

Abstract

The size distribution of molecules within an unfolded state of the N-terminal SH3 domain of drk (drkN SH3) has been studied by small-angle X-ray scattering (SAXS) and pulsed-field-gradient NMR (PFG-NMR) methods. An empirical model to describe this distribution in the unfolded state ensemble has been proposed based on (i) the ensemble-averaged radius of gyration and hydrodynamic radius derived from the SAXS and PFG-NMR data, respectively, and (ii) a histogram of the size distribution of structures obtained from preliminary analyses of structural parameters recorded on the unfolded state. Results show that this unfolded state, U exch, which exists in equilibrium with the folded state, F exch, under non-denaturing conditions, is relatively compact, with the average size of conformers within the unfolded state ensemble only 30–40 % larger than the folded state structure. In addition, the model predicts a significant overlap in the size range of structures comprising the U exch state with those in a denatured state obtained by addition of 2 M guanidinium chloride.