Geometry motivated alternative view on local protein backbone structures

Abstract

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, Ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ν and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ν)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains-the latter can yield a better separation of different local secondary structure motives-and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ν)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ν)-plot for protein structures we provide a web application (http:==agknapp.chemie.fu-berlin.de=secsass), which shows the (d, ν)-plot side-by-side with the R-plot. © 2013 The Protein Society.