Euclidean perspective on the unfolding of azurin: angular correlations

Abstract

The geometrical model introduced previously by the authors has been extended quantitatively to document changes in angular correlations between and among residues as azurin unfolds. In the early stages of denaturation, these changes are found to be more pronounced than changes in the spatial displacement of residues, a result that is also found for residues acting in concert, viz., α-helices, β-sheet residues and residues in 'turning regions.' Our analysis leads to a picture of the large-scale motion of the polypeptide chain as azurin denatures. Flanking a central 'ribbon' of residues whose orientation remains essentially invariant, we find that in the early stages of unfolding, left-and right-hand 'wings' adjacent to this stationary scaffolding pivot counterclockwise, while smaller regions on opposing ends of the β-barrel pivot clockwise. As spatial constraints characterising the native state are further relaxed, our calculations show that some regions reverse their orientational motion, reflecting the enhanced flexibility of the polypeptide chain in the denatured state.

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).…”

“…At each stage of unfolding, the length of the sides and the defining angles of the triangle formed by connecting the left-most and right-most residue in a segment to the Cu 2+ are determined (see [6,7] for full details). The distances and angles characterizing, for example, the triangle Ser34-Cu-Asn38, are specified with respect to the coordinates of the Cu and the calculated coordinates of the α-carbon of Ser34 and Asn38.…”

“…We focused on Pseudomonas aeruginosa azurin (Figure 1) and documented changes in the spatial coordinates of each residue with respect to the Cu 2+ ion [6]. We then extended our model to quantify the associated changes in the angular configuration of neighboring residues as the protein unfolds [7]. In the present study, we further develop our geometrical approach to track the motion of distinct regions of the polypeptide chain as azurin denatures; we consider α-helical regions, β-strand residues, and regions in which secondary structure is absent.…”

Relaxation of structural constraints during Amicyanin unfolding

“…Our geometrical model has been elaborated in earlier publications [11][12][13][14][15][16][17]. We emphasize that we have now extended our approach to account for the native structure of amicyanin (as well as those of other BCPs), as this structure features several beta sheets [See Fig.…”

“…By choosing this configuration for all proteins in a given family, or for proteins of different families with very different physiological functions (e.g., the cytochromes [11], or microbial proteins [14]), unfolding processes can be systematically compared (as the reference state is fixed).…”