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 (?, ?)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ? 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, ?)-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, ?)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ?)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ?)-plot side-by-side with the R-plot.

SUBMITTER: Zacharias J 

PROVIDER: S-EPMC3831682 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature