Unfolding four-helix bundles

Abstract

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c 0 and c-b 562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c 0 unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b 562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

Euclidean perspective on the unfolding of azurin: angular correlations

“…We note that the approach used here, and in our previous work [1][2][3][4], used the redox centre in metalloproteins as the origin of the coordinate system. This is an arbitrary choice and the above procedure can be carried out using any point as the origin of the coordinate system.…”

“…Moreover, as elaborated in our earlier studies [2][3][4], the model accounts for experimental evidence on cytochromes c [10], c [11], and cb 562 [12]. However, spatial correlations are only part of the picture.…”

“…Our approach was designed to explore and quantify the role of excluded-volume effects in influencing the early stages in the unfolding of a protein, and has been applied successfully to azurin [1], lysozyme and three cytochromes (c, cb 562 , c ) [2][3][4]. Like others, our model is based on the idea that an investigation of the early stages of protein unfolding is the reverse of investigating protein folding directly [e.g., [5][6][7].…”

“…We have developed a geometrical model to investigate the stability of structural perturbations of a protein in its native state [1][2][3][4]. Our approach was designed to explore and quantify the role of excluded-volume effects in influencing the early stages in the unfolding of a protein, and has been applied successfully to azurin [1], lysozyme and three cytochromes (c, cb 562 , c ) [2][3][4].…”

A Euclidean perspective on the unfolding of azurin: chain motion

“…Our geometrical model presented for azurin [6,7], and elaborated previously for several other proteins [8–10], makes fundamental use of crystallographic data for each protein being studied. From these data, the geometry of n = 3 residues, a central residue and its two nearest-neighbors, is determined for each residue of the polypeptide chain (except the two terminal ones).…”