Ramachandran maps

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-... 

Figure 18. Ramachandran map indicating the predominant torsional angles for P-turns (see Table 5).

In vacuo most peptides are constrained to quasi-planar conformations (, i/i 0°, 180°), while Polarizable Continuum Model (PCM) calculations show that in aqueous solution another stable structure appears for 4> -60°, tft -60° this is noteworthy because such angles are typical of a-helix conformations of polypeptides, which is particularly favoured by the solvent [2], This feature is illustrated in Figure 3.2, where Ramachandran maps (i.e. plots of the energy versus 4> and tft) are reported both in vacuo and in aqueous solution. 

Figure 3.2 Ramachandran maps for TDA (a) in vacuo and (b) in aqueous solution.

The impact of solvation on conformation becomes stronger as the size of the flexible system increases and is specially great for biological molecules as seen in Figure 4.7, which represents the Ramachandran map in the gas phase and water of an alanine dipeptide as determined by LMP2/6-31G/(d) and MST/6-31G(d) calculations. Because of the polymeric nature of proteins the marked effect of solvation in the [Pg.505]

Since the Ramachandran map contains about ten energy minima (i.e., stable conformations of two peptide bonds), a hundred amino acid protein (proteins may have several hundreds of amino acids) corresponds to an astronomic number of possible backbone conformations (of about 10100). This number has to be additionally multiplied by a number of possible conformations of side chains (some of... 

The conformational angles derived in this study are unusual values in the Ramachandran map because these maps are based on conformational energy calculations for molecules as N-acetyl-alanine-N -methyl amide, which do not incorporate charged groups and thus will reproduce an uncharged peptide fragment better than an aqueous solution of a zwitterionic peptide. 

Figure 7. (a) Ramachandran map of tyrosine peptide analogue calculated by the AMBER force field in vacuo (a) and in aqueous solution (b). 

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