Peptides conformational plot, figure

What Figure 2.11 tells us is that a conformational map for a dipeptide of glycine (the side chain in glycine is very small, just a hydrogen) has mostly allowed or partially allowed conformations and therefore polyglycine is flexible. One question that you might ask is how do we know that the conformational plot for a polypeptide is the same as for a dipeptide The answer is that because the side chain points away from the backbone for most conformations the atoms in the side chains are separated by more than the sum of the van der Waals radii. However, below we discuss several highly observed conformations of proteins in which the conformational map is an overestimation of the flexibility because of interactions between atoms more than two peptide units apart in space. 

Figure 2.12. Conformational plot for glycine-alanine. Plot of allowable angles for peptides containing a repeat unit of glycine and alanine showing totally (outer solid lines) and partially (inner solid lines) allowed conformations determined from normal and minimum interatomic distances.

FIGURE 13.1 MALDI ion mobility MS analysis of a grade II human astrocytoma tissue section, (a) The 2D conformation plot with predicted phospholipid and peptide trend-lines are indicated hy dashed lines. Ion mohility MS signal intensity is indicated hy false coloring (scale displayed), (h) Signals from the phospholipid and peptide trend-lines were exported separately and plotted as m/z to intensity. 

T. P. Creamer (unpublished results). A plot of estimated (ASA) against %PPII content is given in Figure 5. At first glance, it would appear that there is little correlation between the two properties. However, three residues—proline, glycine, and glutamine—can be considered outliers, each for a specific reason. Proline has a high %PPII content in the polyproline-based host peptide used by Kelly et al. (2001) as a result of its unique properties as an imine. As discussed above, a proline that is followed in sequence by a second proline is restricted to the PPII conformation by steric interactions. 

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 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

For /1-peptide secondary structures, cooperative formation has been investigated in various ways. One test of cooperativity involves examining the onset of conformational order as a function of chain length. The earliest study of this sort for discrete /1-peptide oligomer appears to date back to 1979 on poly(S-/lAspOiBu).198 However, at that time the structure of the ordered conformation was not understood. Clues about cooperativity in forming the 14-helix with /1-peptides can be found from CD studies. Figure 37 shows a plot of CD intensity (normalized per... 

The plot of In fcgt vs. the number, n, of Pro residues (Figure 1) demonstrates that for longer hnear peptides (n = 3-5), the rate of electron transfer decreases exponentially with growing n. However, the k t data for shorter (n = 0-2) hnear peptides fall off considerably from the plot extrapolated to lower n values. This indicates that the rate of LRET in short-bridged peptides is faster than would be expected on the assumption of a common mechanism of electron transfer in the whole group of peptides. In order to rationahze these findings in terms of the theory of the distance dependence of LRET kinetics (33, 34), the separation distances and spatial disposition of the aromatic side chains in the hnear peptides studied had to be evaluated from their conformational preferences and conformational dynamics. 

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