Protein Ramachandran plot

Ramachandran plot (see Figure 1.7a). The a helix has 3.6 residues per turn with hydrogen bonds between C =0 of residue n and NH of residue n + 4 (Figure 2.2). Thus all NH and C O groups are joined with hydrogen bonds except the first NH groups and the last C O groups at the ends of the a helix. As a consequence, the ends of a helices are polar and are almost always at the surface of protein molecules. 

G. N. Ramachandran and his coworkers in Madras, India, first showed that it was convenient to plot (p values against i/t values to show the distribution of allowed values in a protein or in a family of proteins. A typical Ramachandran plot is shown in Figure 6.4. Note the clustering of (p and i/t values in a few regions of the plot. Most combinations of (p and i/t are sterically forbidden, and the corresponding regions of the Ramachandran plot are sparsely populated. The combinations that are sterically allowed represent the subclasses of structure described in the remainder of this section. 

Fig. 8. A Ramachandran plot (37) indicating the overall geometrical quality of the structure of the Fepr protein from D. vulgaris at 1.7 A resolution. Some 94% of the residues lie within the most favored regions, 5.5% in the additional allowed regions, and only one residue, N303 on the border of a disallowed region. The electron density of this residue is very well defined (see text).

Figure 5-1. Ramachandran plot of the main chain phi (< ) and psi (T) angles for approximately 1000 nonglycine residues in eight proteins whose structures were solved at high resolution. The dots represent allowable combinations and the spaces prohibited combinations of phi and psi angles. (Reproduced, with permission, from Richardson JS The anatomy and taxonomy of protein structures. Adv Protein Chem 1981 34 167.)...

A detailed quantitative analysis of the preferences of amino acids in folded proteins for different regions of the Ramachandran plot reveals that the 18 nonglycine, nonproline residues exhibit different preferences (Shortle, 2002). Figure 5 shows the range of relative propensities displayed by these 18 amino acids for a somewhat arbitrary subdivision... 

Fig. 44. Distribution of Ala in the Ramachandran plot when using (A) all secondary structure conformations in the protein database or (B) only those Ala residues in a coil conformation. (From Serrano, 1995. 1995, with permission from Academic Press.)...

The favoured dihedral angles for protein main chains were derived from energy considerations of steric clashes in peptides giving the well known Ramachandran plot (Ramachandran and Sasisekharan, 1968). These phi/psi combinations characterize the elements of secondary structure. Accurate main chain models can be constructed from spare parts, that is short pieces of helices, sheets, turns, and random coils taken from highly refined structures, provided a series of C-alpha positions can be established from the electron density map... 

A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the oi-amino group of one amino acid and the a-carboxyl group of another. The peptide bond has partial double bond character and is nearly always in the trans configuration. The backbone conformation of a polypeptide is specified by the rotation angles about the Ca-N bond phi, (j>) and Ca-C bond psi, amino acid residues. The sterically allowed values of 0 and yr are visualized in a Ramachandran plot. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. 

Ramachandran plots serve to answer the question of why the a-helical or the pleated sheet structures have the properties that they do however, the plots do not serve to predict whether a given polypeptide chain will assume the a-helical, the pleated sheet, or a random conformation. Anfinsen and his colleagues have proposed that it is the amino acid composition and sequence in a given peptide chain that determine the conformation the chain assumes. Ideally, we should be able to look at an amino acid sequence of a protein and then... 

Figure 10.1 Basic polypeptide geometry. The upper panel shows a short peptide sequence of three amino acids joined by two peptide bonds. A relatively rigid planar structure, indicated by dashed lines, is formed by each peptide bond. The relative positions of two adjacent peptide bond planes is determined by the rotational dihedral angles

The average of these converged structures is taken as the protein structure, whose precision can be assessed by the deviations of the individual structures from the average. The quality of the final structure can be described in terms of this root mean square deviation, for both the peptide backbone and side chains, and to some extent by the extent to which it conforms to limitations of dihedral bond angles and interatomic contacts anticipated from thousands of previously known structures (the Ramachandran plot ). By all criteria, NMR structures of proteins that are determined in this way are comparable to structures determined by x-ray crystallography. In addition, NMR methods can be applied to evaluate the... 

Hruby VJ, Nikiforovich GV (1991) The Ramachandran Plot and Beyond Conformational and Topographical Considerations in the Design of Peptides and Proteins. In Molecular Conformation and Biological Interactions (Balaram P and Ramasehan S, eds) pp 429 45. Bangalore Indian Academy of Sciences. 

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