title: A proteomic Ramachandran plot (PRplot).
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 ϕ-ψ 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.
authors.affiliation: Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy. oliviero.carugo@univie.ac.at
authors.forename: Oliviero
authors.initials: O
authors.lastname: Carugo
authors.forename: Kristina
authors.initials: K
authors.lastname: Djinović-Carugo
mesh_terms: D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*
chemical_list: D011506:Proteins