Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques

Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations . From these experimental data, empirical relationships between the measure d hydrodynamic radius (R-h) and the number of residues in the polypeptide c hain (N) have been established; for native folded proteins R-h = 4.75N (0.2 9)Angstrom and for highly denatured states R-h, = 2.21N (0.57)Angstrom. Pre dictions from these equations agree well with experimental data from dynami c light scattering and small-angle X-ray or neutron scattering studies repo rted in the literature for proteins ranging in size from 58 to 760 amino ac id residues, The predicted values of the hydrodynamic radii provide a frame work that can be used to analyze the conformational properties of a range o f nonnative states of proteins. Several examples are given here to illustra te this approach including data for partially structured molten globule sta tes and for proteins that are unfolded but biologically active under physio logical conditions. These reveal evidence for significant coupling between local and global features of the conformational ensembles adopted in such s tates. In particular, the effective dimensions of the polypeptide chain are found to depend significantly on the level of persistence of regions of se condary structure or features such as hydrophobic clusters within a conform ational ensemble.