Conformational plot

Zheng, J., Knighton, D. R., Xuong, N.-H., Taylor, S. S., Sowadski, J. M., and Ten Eyck, L. F. (1993). Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Plot. Sci. 2, 1559-1573. 

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 2.13. Conformational plot for glycine-aspartic acid. The allowable conformations are only slightly reduced compared to the plot in Figure 2.12 because the side chain length is increased in going from alanine to aspartic acid.

Figure 2.14. Conformational plot for glycine-proline. Addition of proline to a dipeptide further reduces the number of allowable conformations when compared to Figures 2.12 and 2.13.

Figure 2.15. Conformational plot showing location of a helix, (3 sheet, and collagen triple helix. The plot shows the locahzation of the predominant chain structures found in proteins, including the a helix (a), (3 sheet ((3), and collagen triple helix (C).The it stands for a helix that does not occur in nature.

Figure 2.33. Conformational plot of p (1—>3) and p (1—>4) linkages in hyaluronic acid plots of fully allowed (—) and partially allowed (—) conformations of (p and )/ for (a) D-glucuronic acid which is linked P (1—>4) to N-acetyl glucosamine and (b) N-acetyl glucosamine which is finked P (1—>3) to D-glucuronic acid. Allowed conformations center around (0°, 0°) and indicate that stereochemically the backbone of hyaluronan has some flexibility.

Figure 1 presents the conformation plot for log(r ) versus log(M) as obtained from a MALS measurement for the polystyrene broad linear standard NIST706 in toluene. Superimposed thereon is a plot of the calculated log [17] as a function of log(M) for the same sample. From the latter plot, the MHS coefficients may be deduced by inspection of the slope and intercept to yield a = 0.77 and K 0.008. 

Fig. (Jl). Conformation plot, Rg = /(M), from a SEC-MALS system, obtained from the superimposition of the data of four high molar mass HA samples...

Fig. 3 shows the MALS-derived molar mass and RMS radius as a function of elution volume for a broad polystyrene sample. Measurements were made in toluene at 690 nm.The value of dn/dc chosen was 0.11. From Fig. 3, it should be noted that the radius data begins to deteriorate around 10 nm, whereas the mass data extends to its detection limits. From the mass and radius data of Fig. 3, a conformation plot is easily generated with a slope of about 0.57 (i.e., corresponding to a random coil). These same data can also be used immediately to calculate the mass and size moments of the sample as well as its poly-dispersity as shown in the next section. 

In a comparative study, linear HDPE has been analyzed by HT-SEC and HT-AE4. The samples had been of low molar mass to minimize shear degradation in HT-SEC. Consequently, both methods provided similar results as can be seen from the conformation plot presented in Eig. 36. 

Fig. 35 Comparison of the conformation plots of HDPE and LDPE (a) separation with HT- AE4 and (b) separation with HT-SEC. (Reprinted from [86] with permission of Elsevier Limited)...

Fig. 38 MMD from HT-AF4 and HT-SEC separation overlaid with eraresponding conformation plots obtained by IR-MALS (a) LDPE 1, (b) LDPE 2. (Adapted from [201] of Elsevier Limited)...

Figure 38 shows the differential MMDs and the conformation plots of both LDPE samples obtained by HT-SEC-IR-MALS as well as HT-AF4-IR-MALS. 

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. 

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