Denatured States of Proteins

Abstract

The denatured "state" of a protein is a distribution of many different molecular conformations, the averages of which are measured by experiments. The properties of this ensemble depend sensitively on the solution conditions. There is now considerable evidence that even in strong denaturants such as 6M GuHC1 and 9M urea, some structure may remain in protein chains. Under milder or physiological conditions, the denatured states of most proteins appear to be highly compact with extensive secondary structure. Both theoretical and experimental studies suggest that hydrophobic interactions, chain conformational entropies, and electrostatic forces are dominant in determining this structure. The denaturation reaction of many proteins in GuHC1 or urea can be most simply modelled as a two-state transition between the native structure and a relatively compact denatured state, which then undergoes a gradual increase in radius on further addition of denaturant. However, when a protein acquires a large net charge in acids or bases, it can have two stable denatured populations, one compact and the other more highly unfolded. The prediction and elucidation of the structural details of the non-native states of proteins may ultimately prove to be as difficult as predicting the native structures, particularly for D0, the denatured state under physiological conditions. Just as with the native state, the structure of this biologically important denatured state appears to depend on the amino acid sequence. The development of synthetic, peptide and protein fragment models of the denatured state and the recent progress in NMR spectroscopy provide bases for optimism that new insights will be gained into this poorly understood realm of protein biochemistry.

Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra

“…One of the most plausible mechanisms to stabilize the MG conformer by sorbitol is the preferential hydration effect, which is the same mechanism as that which stabilizes the N conformer of proteins (Timasheff, 1992(Timasheff, , 1993. The effects of sorbitol support the view that an equilibrium between D and MG conformers of cyt c is determined by the electrostatic repulsive force in balance with the hydrophobic attractive force strengthened by the preferential hydration (Dill & Shortle, 1991;Goto & Nishikiori, 1991;Dill et al, 1995). Another typical example of the SVD analysis is shown in Figure 7 for TFE-induced denaturation at pH 3.2.…”

“…To support this view experimentally, a comprehensive description on the structure of protein in a full range of the conformational space is necessary. The D, MG, and H conformers and their variants of various proteins have been characterized extensively by many experimental methods (Roder et al, 1988;Hughson et al, 1990;Dill & Shortle, 1991;Jeng & Englander, 1991;Sosnick & Trewhella, 1992;Fan et al, 1993;Alexandrescu et al, 1994;Konno et al, 1995). However, limited sensitivity and resolution of any experimental methods make this problem still largely unsolved.…”

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.…”

Specific neurotrophin binding to leucine‐rich motif peptides of TrkA and TrkB

“…in terms of the underlying highly specific biochemical mechanism, the observed binding phenomena apparently can not quantitatively account for the binding affinity observed in vivo [3,22,25,34] or using recombinant receptor proteins [39]. It must therefore be assumed that the capacity of the columns was aggravated by the fact that a large percentage of the peptides was either coupled to the matrix in a way that abolished binding affinity or was simply folded in an incorrect fashion [4,10,20]. Some peptides only exhibit a weak tendency to adopt a defined tertiary structure so that in a steady state balance only a small number of peptides exists in an active form at a given time point [10].…”