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

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 (R(h)) and the number of residues in the polypeptide chain (N) have been established; for native folded proteins R(h) = 4.75N (0.29)A and for highly denatured states R(h) = 2.21N (0.57)A. 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.

Highly Sensitive FRET-FCS Detects Amyloid β-Peptide Oligomers in Solution at Physiological Concentrations

“…Another recent study using FCS reported in contrast a hydrodynamic radius of Aβ1-40 and Aβ1-42 as small as 0.85-0.9 nm 25 . Such a value deviates significantly from the above estimates of R h as well as from other proteins of similar sizes 22,26 , and is only about 50% larger than that of the fluorophore Rhodamine B to which Aβ was coupled (R h =0.57 nm) 25 .…”

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

“…This is put into evidence, for example, by the data on hydrodynamic radii and radii of gyration of chemically denatured proteins. [9][10][11] The random-coil-like behavior of unfolded proteins has been sometimes underappreciated, since much (deserved) attention has been given to the investigation of residual structure. It is this category of proteins, where disorder prevails over order, which is the focus of the present article.…”

Protein folding: Then and now

“…Using intrinsic viscosity measurements for 12 proteins denatured by 5-6 M GuHCl, the authors obtained a scaling exponent ν=0.67±0.09. Wilkins et al [191] showed that the hydrodynamic radii of sets of 8 highly denatured, disulfide-free proteins follow a power law scaling with ν=0.58±0.11. Recently, Kohn et al [192] reassessed the scaling behavior of denatured proteins using small angle x-ray scattering for 17 proteins of lengths varying from 8 to 549 residues.…”