Factors affecting the amplitude of the s angle in proteins: a revisitation

The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the tau (N-C-alpha-C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported. The data clearly indicate that the local backbone conformation has a prominent impact on the modulation of the tau angle. Therefore, a proper assessment of the impact of the other potential factors can only be appropriately evaluated when small (phi, psi) regions are considered. Here, it is shown that when the contribution of the backbone conformation is removed by considering small (phi, psi) areas, an impact of secondary structure, as defined by DSSP, and/or the residue type on tau is still detectable, although to a limited extent. Indeed, distinct tau-value distributions are detected for Pro/Gly and beta-branched (Ile/Val) residues. The key role of the local backbone conformation highlighted here supports the use of variable local backbone geometry in protein refinement protocols.