Protein folding: is hierarchical versus nonhierarchical a productive issue?

Porcine beta-lactoglobulin chemical unfolding: Identification of a non-native α-helical intermediate

The chemical unfolding behavior of porcine beta-lactoglobulin (PLG) has been followed at pH 2 and 6 in the presence of guanidinium hydrochloride. The PLG unfolding transition, monitored by tryptophan fluorescence, far and near UV circular dichroism and 1D-NMR, can be described by a three-state transition suggesting the presence of at least one intermediate state that appears to display an excess of non-native alpha-helical structures. The thermodynamic parameters, as determined through a global analysis fitting procedure, give estimates of the free energy differences of the transitions connecting the native, the intermediate and the unfolded state: DeltaG(NI) (0) = 2.8 +/- 0.7 kcal mol(-1) (pH 2) and 4.2 +/- 0.5 kcal mol(-1) (pH 6) and DeltaG(NU) (0) = 7.2 +/- 0.6 kcal mol(-1) (pH 2) and 6.9 +/- 0.6 kcal mol(-1) (pH 6). CD unfolding data of the bovine species (BLG) have been collected here under the same experimental conditions of PLG to allow a careful comparison of the two beta-lactoglobulins. Intermediates with different characteristics have been identified for BLG and PLG, and their nature has been discussed on a structural analysis basis. The thermodynamic data reported here for PLG and BLG and the comparative analysis with data reported for equine beta lactoglobulin, show that homologous beta-barrel proteins, belonging to the same family and displaying high sequence identity (52-64%) populate unfolding intermediates to different extents, even though a common tendency to the formation of non-native alpha-helical intermediates, can be envisaged. The present results provide a prerequisite foundation of knowledge for the design and interpretation of future folding kinetic studies.

Proteins with H-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis

We noticed that disease-related amyloidogenic proteins and especially cellular prion proteins have the highest proportion of incompletely desolvated backbone H bonds among soluble proteins. Such bonds are vulnerable to water attack and thus represent structural weaknesses. We have measured the adsorption of proteins onto phospholipid bilayers and found a strong correlation between the extent of underwrapping of backbone H bonds in the native structure of a protein and its extent of deposition on the bilayer: the less the H bond wrapping, the higher the propensity for protein-bilayer binding. These observations support the proposition that soluble proteins with amyloidogenic propensity and membrane proteins share a pervasive building motif: the underwrapped H bonds. Whereas in membrane proteins, this motif does not signal a structural vulnerability, in soluble proteins, it is responsible for their reactivity.

Back to units of protein folding

In response to the criticism by A. Finkelstein (J Biomol Struct Dyn 20, 311-314, 2002) of our Communication (J Biomol Struct Dyn 20, 5-6, 2002) several issues are dealt with. Importance of the notion of elementary folding unit, its size and structure, and the necessity of further characterization of the units for the elucidation of the protein folding in vivo are discussed. The criticism (J Biomol Struct Dyn 20, 311-314, 2002) on the hierarchical protein folding is also briefly addressed.

Cunning simplicity of a hierarchical folding

A hierarchic scheme of protein folding does not solve the Levinthal paradox since it cannot provide a simultaneous explanation for major features observed for protein folding: (i) folding within non-astronomical time, (ii) independence of the native structure on large variations in the folding rates of given protein under different conditions, and (iii) co-existence, in a visible quantity, of only the native and the unfolded molecules during folding of moderate size (single-domain) proteins. On the contrary, a nucleation mechanism can account for all these major features simultaneously and resolves the Levinthal paradox.