Hydrodynamic Radii of Native and Denatured Proteins Measured by Pulse Field Gradient NMR Techniques

TLDR

Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations. The predicted hydrodynamic radii provide a framework for analyzing the conformational properties of various nonnative protein states. Several examples illustrate this approach, including data for partially structured molten globule states and for proteins that are unfolded yet biologically active under physiological conditions. Empirical equations Rh = 4.75 N^0.29 Å for native and Rh = 2.21 N^0.57 Å for denatured proteins, validated against DLS, SAXS, and SANS data for 58–760 residues, show that effective dimensions depend on the persistence of secondary structure or hydrophobic clusters, indicating strong coupling between local and global conformational features.

Abstract

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 measured hydrodynamic radius (Rh) and the number of residues in the polypeptide chain (N) have been established; for native folded proteins Rh = 4.75N 0.29Å and for highly denatured states Rh = 2.21N 0.57Å. Predictions from these equations agree well with experimental data from dynamic light scattering and small-angle X-ray or neutron scattering studies reported in the literature for proteins ranging in size from 58 to 760 amino acid residues. The predicted values of the hydrodynamic radii provide a framework that can be used to analyze the conformational properties of a range of nonnative states of proteins. Several examples are given here to illustrate this approach including data for partially structured molten globule states and for proteins that are unfolded but biologically active under physiological conditions. These reveal evidence for significant coupling between local and global features of the conformational ensembles adopted in such states. In particular, the effective dimensions of the polypeptide chain are found to depend significantly on the level of persistence of regions of secondary structure or features such as hydrophobic clusters within a conformational ensemble.