Original Article

Amino Acids

, Volume 44, Issue 2, pp 781-790

A proteomic Ramachandran plot (PRplot)

  • Oliviero CarugoAffiliated withDepartment of Chemistry, University of Pavia Email author 
  • , Kristina Djinović-CarugoAffiliated withMax F. Perutz Laboratories, Department of Structural and Computational Biology, Vienna UniversityDepartment of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana Email author 

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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 conformation Protein fold Protein structure Proteome Ramachandran plot Structural bioinformatics