Amino Acids

, Volume 44, Issue 2, pp 781–790

A proteomic Ramachandran plot (PRplot)

Original Article

DOI: 10.1007/s00726-012-1402-z

Cite this article as:
Carugo, O. & Djinović-Carugo, K. Amino Acids (2013) 44: 781. doi:10.1007/s00726-012-1402-z

Abstract

Each protein structure can be characterized by the average values of the main chain torsion angles ϕ and ψ and, as a consequence, be plotted on a bidimensional diagram, which resembles the Ramachandran plot. Here, we describe a proteomic ϕψ plot (PRplot) where each protein structure is associated with one point, allowing in this way to represent the entire protein structure universe. It was verified that the PRplot is a robust tool since it does not depend on the dimension of the proteins, on the crystallographic resolution of the structures, nor on the biological source; moreover, it is little affected by disordered and structurally uncharacterized residues. The proteins mapped on the PRplot tend to cluster in three regions that correspond to the structures rich in alpha-helices, in beta-strands, and in both helices and strands, and are distributed along a sigmoidal curve that connect these three highly populated regions. PRplots are a unique instrument to project all protein structures on a single bidimensional plane where the entire structural complexity is reduced to a striking simplicity, with the sigmoid curve clearly delineating the space fraction accessible to a stable protein.

Keywords

Protein backbone conformationProtein foldProtein structureProteomeRamachandran plotStructural bioinformatics

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of PaviaPaviaItaly
  2. 2.Max F. Perutz Laboratories, Department of Structural and Computational BiologyVienna UniversityViennaAustria
  3. 3.Department of Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia