Mapping Ramachandran

A careful analysis of conformational energy maps (Ramachandran plots) revealed that both enantiomers of P-tetralin amino acids were compatible with the right handed a-helical conformation.109 This was an important prerequisite for the development of N- and C-caps since the ( -configuration of the P-tetralin amino acid is needed for N-terminal helix induction, whereas the (R)-enantiomer was used in the C-cap series. The fact that both configurations were compatible with a-helical conformations made these amino acids our first choice as building blocks for... 

Figure 58. Energy contour map (Ramachandran plot) for versus of the alanine dipeptide. Solid lines mark the five lowest-energy contours at 1 kcal/mol and the bottom contour is marked with a heavy line dashed lines mark the higher contours at 1-kcal/mol intervals (a) vacuum potential surface (b) solvent-modified potential surface.

Fig. 5. Subdivisions of the phi/psi or Ramachandran map labeled with the range of propensities for the 18 amino acids (glycine and proline are excluded) as they map to each subdivision calculated from a large collection of folded protein structures. The propensity is defined by the probability that amino acid x will be found in a subdivision divided by the probability that an average amino acid will be found in a subregion. Data are taken from Table 1 of Shortle (2002).

The CD spectra of nine proteins in 6 M Gdm-HCl were studied by Cortijo etal. (1973). Those proteins with disulfide bridges were reduced and carboxymethylated. The spectra of individual proteins were not reported, but the range of values at wavelengths from 240 to 210 nm was given. The [0]222 values ranged from —800 to —2400 deg cm2/dmol. From this substantial variation, Cortijo etal. (1973) concluded that the proteins studied are not true random coils in 6 M Gdm-HCl, because random coils should have CD spectra essentially independent of amino acid composition and sequence. The observed variation was attributed to differences in the conformational distribution between allowed regions of the Ramachandran map or to residual interactions between different parts of the chain that are resistant to Gdm-HCl denaturation. 

McAllister, M. A., A. Perczel, P. Csaszar, and I. G. Csizmadia. 1993a. Peptide Models 5. Topological Features of Molecular Mechanics and Ab Initio 4D-Ramachandran Maps. Conformational Data for Ac-L-Ala-L-Ala-NHMe and For-L-Ala-L-Ala-NH2. J. Mol. Struct. (Theochem) 288,181-198. 

McAllister, M. A., Perczel, P. Csaszar, W. Viviani, J.-L. Rivail, and I. G. Csizmadia. 1993b. Peptide Models 4. Topological Features of Molecular Mechanics and Ab Initio 2D-Ramachandran Maps. Conformational Data for For-Gly-NH2, For-L-Ala-NH2, Ac-l-Ala-NHMe and For-L-Val-NH2. J. Mol. Struct. (Theochem) 288, 161-179. Mehrotra, P. K., M. Mezei, and D. L. Beveridge. 1984. Monte Carlo Determination of the Internal Energies of Hydration for the Ala Dipeptide in the C7, C5, aR, and Pn Conformations. Int. J. Quantum Chem. Quantum Biol. Symp. 11, 301-308. 

An example of such a surface is shown in Figure 2, which presents the "Ramachandran map" for the disaccharide segment, cellobiose, of cellulose. In this case, since cellulose is homopolymeric. Figure 2 contains all of the energetic infor-... 

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... 

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