Is There or Isn't There? The Case for (and Against) Residual Structure in Chemically Denatured Proteins

Abstract

First raised some 60 years ago, the question of whether chemically denatured proteins are fully unfolded has, in recent years, seen significantly renewed interest. This increased attention has been spurred, in large part, by new spectroscopic and computational approaches that suggest even the most highly denatured polypeptides contain significant residual structure. In contrast, the most recent scattering results uphold the long-standing view that chemically denatured proteins adopt random coil configurations. Here we review the evidence both for and against residual structure in chemically denatured proteins, and attempt to reconcile these seemingly contradictory observations.

DMSO-Induced Denaturation of Hen Egg White Lysozyme

“…Recent experimental works as well as MD simulations on other protein systems have also provided some evidence for the persistence of secondary structural elements in the denatured state. 51,[56][57][58][59][60] Apparently, the tertiary structure is lost well before all (nonorthodox) secondary structure is lost.…”

The hydrodynamic and conformational properties of denatured proteins in dilute solutions

“…If interpreted alone, the value of qln R G /qln M would indicate a very strong intramolecular excluded volume effect, and that has been the usual interpretation. 1,5 Similarly, if taken alone the values of qln [g]/qln M and qln R H /qln M would each represent a more modest excluded volume effect. As mentioned above the data in the intermolecular thermodynamics given by the dependence of A 2 versus M would suggest a so-called good solvent, consistent with a substantial intramolecular excluded volume for a flexible-coil chain, but irrelevant to such behavior for rodlike or even wormlike chains with a large persistence length â .…”

“…1,[20][21][22] This includes evidence that these sections may be involved in intramolecular association among units far removed along the chain backbone, forming loops that flicker in and out of existence. As observed above, the result that K for the lower molecular weight proteins in aqueous GuHCl solutions is comparable to the behavior seen for the ring-shaped polystyrene, suggesting the presence of ring-shaped molecules or chains with containing loops, at least in that range of M. As with the data on polystyrene, the modestly decreasing value of K noted with the data on the protein solutions in aqueous GuHCl solution may reflect a modest intramolecular excluded volume effect, with the higher value obtained at low M closer to the limit that would be observed under Flory theta solvent conditions.…”

“…1 Since that publication, studies have continued to reveal secondary structure in strongly denatured proteins and polypeptides in dilute solution, mostly based on NMR analysis, with such studies often motivated by interest in the folding of the denatured chain. The aforementioned use of the random flight model, which has dominated most of the interpretations of hydrodynamic behavior of proteins and polypeptides in dilute solution, starting with the seminal studies of Tanford et al, 2 led to the conclusion that the chains may be modeled by an ensemble of random flight chains with excluded volume effects.…”

“…The aforementioned use of the random flight model, which has dominated most of the interpretations of hydrodynamic behavior of proteins and polypeptides in dilute solution, starting with the seminal studies of Tanford et al, 2 led to the conclusion that the chains may be modeled by an ensemble of random flight chains with excluded volume effects. 1,3 One study treated the same data to conclude that the data on the intrinsic viscosity could be represented by a wormlike chain model with the chain having an appreciable persistence length, but negligible excluded volume. 4 In this study, we suggest that taken together the experimental data on intrinsic viscosity, hydrodynamic radii, and the radius of gyration suggest a somewhat compact structure of the denatured proteins and polypeptides studied above, possibly owing to intramolecular association to form transient loops among chain elements widely separated along the chain backbone.…”