A proteomic Ramachandran plot (PRplot) (original) (raw)
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.
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Acknowledgments
This work was in part supported by the BIN-III project of the Austrian GEN-AU initiative.
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Authors and Affiliations
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
Oliviero Carugo - Max F. Perutz Laboratories, Department of Structural and Computational Biology, Vienna University, Campus Vienna Biocenter 5, 1030, Vienna, Austria
Kristina Djinović-Carugo - Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000, Ljubljana, Slovenia
Kristina Djinović-Carugo
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- Oliviero Carugo
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Correspondence toOliviero Carugo or Kristina Djinović-Carugo.
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Carugo, O., Djinović-Carugo, K. A proteomic Ramachandran plot (PRplot).Amino Acids 44, 781–790 (2013). https://doi.org/10.1007/s00726-012-1402-z
- Received: 17 March 2012
- Accepted: 10 September 2012
- Published: 25 September 2012
- Issue Date: February 2013
- DOI: https://doi.org/10.1007/s00726-012-1402-z