RAMPAGE

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In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide planar. The generated figure by RAMPAGE,in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran hard-sphere calculations, full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines. Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For example, the small strip of allowed values along the lower-left edge of the plot area continuation of the large, extended-chain region at upper left. The input needed for RAMPAGE is the PDB (File format) coordinates of the target proteins.


A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein. A second is to show the empirical distribution of data points observed in a single structure in usage for structure validation, or else in a database of many structures. Either case is usually shown against outlines for the theoretically favored regions.


One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot, but the effect of side chains is small. In practice, the major effect seen is that of the presence or absence of the methylene group at Cβ. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH3, CH2, or CH group that starts the side chain of all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine for which the allowable area is considerably larger. In contrast, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows a limited number of possible combinations of ψ and φ. The residue preceding proline ("pre-proline") also has limited combinations compared to the general case.


The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined, although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots.


While the Ramachandran plot has been a textbook resource for explaining the structural behavior of peptide bond, an exhaustive exploration of how a peptide behaves in every region of the Ramachandran plot was only recently published.


The Molecular Biophysics Unit at Indian Institute of Science celebrated 50 years of Ramachandran Map by organizing International Conference on Biomolecular Forms and Functions from 8–11 January 2013.

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