Ramachandran plot, showing

Fig. 3. Ramachandran plot showing the allowed angles for poly-L-alanine (grey regions), a, (p-y/values that produce the right-handed a-helix ji, the antiparallel fi-pleated sheet /3, the parallel (5-pleated sheet C, the collagen helix.

Figure 4.11 Ramachandran plot showing permissible conformational regions. aR and aL indicate positions of the right- and left-handed a helices /3A and /3P indicate the positions of the anti-parallel and parallel pleated sheet structures, respectively. C indicates collagen.

Fig. 2. Left The Penta-alanine peptide in baU-and-stick representation. The ten peptide angles determining the secondary structure are marked by Right Ramachandran plot, showing the energetically preferred regions of a L> [ pair with the associated secondary structures (simplefied plot due to [32])...

Fig. 15.3. a Ramachandran plot showing 0, y/ values of residues i +1 and (+2 in each classic ) -turn type. 

The angle pairs iji and <)/ are usually plotted against each other in a diagram called a Ramachandran plot after the Indian biophysicist G.N. Ramachandran who first made calculations of sterically allowed regions. Figure 1.7 shows the results of such calculations and also a plot for all amino... 

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. 

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... 

Figure 8.6 Ramachandran plot of the crystal I ographi model of ALBP. The main-chain torsional angle (N-C, bond) is plotted versus (C-C, bond). The following symbols are used (.) nonglycine residues (+) glycine residues. The enclosed areas of the plot show sterically allowed angles. Reprinted with permission from Z. Xu et al. (1992) Biochemistry 31, 3484-3492. Copyright 1992 American Chemical Society.

Not all combinations of and <]/ angles are possible, as many lead to clashes between atoms in adjacent residues. For all residues except glycine, the existence of such steric restriction involving side-chain atoms reduces drastically the number of possible conformations. The possible combinations of and ip angles that do not lead to clashes can be plotted on a conformation map (also known as a Ramachandran plot, named after the chemist who did much of the pioneering work in this field). Figure 4-5 shows a Ramachandran plot for the allowed conformations of alanylalanine. The... 

Fig. 4-5 Ramachandran plot for alanylalanine, showing the fully allowed regions (double-hatched) and partially allowed regions (single-hatched) of and ip angles (see Fig. 4-4). The coordinates for the parallel and antiparallel /3 structures (/3p and /3a, respectively) and for the left-handed and right-handed a helices (aL and aR, respectively) are indicated.

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

Sasisekharan, first performed such an analysis. The Ramachandran plot in Figure 12.27 shows peptide torsion angles for D-xylose isomerase. " ... 

The Ramachandran Plot also shows that both right- and left-handed polypeptide helices can be stable, though it turns out that right-handed helices are more stable than left-handed ones, due to the bulkiness of the side chains of the L-amino acids making up biological proteins. 

Fig. 4 Ramachandran plot, (a) Diagram showing regions with high energy due to steric hindrance between specified atoms on neighboring amino acid residues, (b) An example of dihedral angle plotting of for proteins from PDB data. (Reproduced from [37] with pemussion)...

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. 

Ramachandran-type plots in which the t and (p dihedrals of the chromphore within the GFP protein matrix were systematically varied [50] showed that there are two minima for all protonation states, one at z = 60 30° and

protein environment of GFP allows the chromophore some rotational freedom, especially by a HT or in the (p dihedral angle (Fig. 5.7). There is a significant energy barrier for t = 180-270°, therefore a cis-trans photoisomerization cannot occur by a 180° rotation of the (p dihedral angle. The protein exerts some strain on the chromophore when it is planar, and the only reason planar chromophores are found in GFP is due to their delocalized -electrons. These results have been confirmed by molecular dynamics simulations of the chromophore with freely rotating t and cp dihedral... 

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