Ramachandran Plot as a Tool for Peptide and Protein Structures’ Quality Determination
- structural – structural proteins are responsible for the cell and tissue shape. Collagen and histones are good examples of such proteins;
- transport – e.g. hemoglobin which is responsible for oxygen and carbon dioxide transport between lungs and tissues;
- protective – immune system protects the organism from pathogens and foreign substances. It’s key compound is immunoglobulin G;
- regulatory – in the biochemical chain proteins play both signal and receptor functions. E.g. complex of somatotropin and its receptor activates cytoplasmic domain and leads to transduction of the cell;
- catalytic – enzymes are the biggest group of proteins (approximately 2000 known biomolecules);
- mobile – e.g. interactions between actin and myosin are responsible for muscle contraction and cellular movements;
- storage – plants contain special proteins, which are important to human because of dietary reasons, e.g. kasein or ferritin.
Figure 1. Dihedral angles describing the orientation of two peptide bonds linked at the same Cα atom
Figure 2. Ramachandran plot with the most favoured (dark green) and additional allowed (light green) regions
Figure 3. Ramachandran plot with marked secondary structure elements and example of steric distortion
Figure 4. Ramachandran plot generated in ProCheck software. The plot area is divided into four following regions: most favoured (red), additional allowed (yellow), generously allowed (light yellow) and disallowed (white)
Figure 5. Myoglobin [1mbn] and its Ramachandran plot
Figure 6. Structure of bovine rhodopsin [1gzm] and its Ramachandran plot
Figure 7. Model of VAPB protein [4cv7] and its Ramachandran plot
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 C. Geerds, J. Wohlmann, A. Haas, H.H. Niemann, Structure of Rhodococcus Equi Virulence-Associated Protein B (VAPB) Reveals an Eight-Stranded Antiparallel [Beta]-Barrel Consisting of Two Greek-Key Motifs, Acta Crystallogr., Sect. F, 70, 866 (2014).