The Ramachandran number: an order parameter for protein geometry

Abstract

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called $\phi$ and $\psi$. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles $\phi$ and $\psi$, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)]. In order to describe such `higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, ${\mathcal{R}}$, which is a structurally meaningful combination of $\phi$ and $\psi$. We show that the potential applications of ${\mathcal{R}}$ are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that ${\mathcal{R}}$ might be used as an order parameter for protein geometry for a wide range of applications.