To-Helix

An example is shown in Figure 7 for the case of the coil-to-helix transition. The endpoints of the calculation are an unstructured coil Tr and helix rp. Intermediate peptide structures correspond to transition intermediates defining the pathway l(r). 

This method has been applied to derive a multitude of paths for the coil-to-helix transition in polyalanine using a continuum solvation model [36]. 

Lesk and Chothia did find, however, that there is a striking preferential conservation of the hydrophobic character of the amino acids at the 59 buried positions, but that no such conservation occurs at positions exposed on the surface of the molecule. With a few exceptions on the surface, hydrophobic residues have replaced hydrophilic ones and vice versa. However, the case of sickle-cell hemoglobin, which is described below, shows that a charge balance must be preserved to avoid hydrophobic patches on the surface. In summary, the evolutionary divergence of these nine globins has been constrained primarily by an almost absolute conservation of the hydro-phobicity of the residues buried in the helix-to-helix and helix-to-heme contacts. 

Chothia, C., Lesk, A.M. Helix movements in proteins. Trends Biochem. Sci. 13 116-118, 1985. hothia, C., Levitt, M., Richardson, D. Helix-to-helix packing in proteins. /. Mol. Biol. 145 215-250, 1981. 

Tetracycline has a secondary binding site in the H27 switch region that may also be fimctionally significant. The dtug binds at the interface of the three domains of 16S rRNA, close to helix 44 and between helices 11 and 27. As with the primary binding site, contacts are made from the hydrophilic face of the dtug to the backbone of 16S rRNA. In this binding site, tetracycline may function to stabilize the ram state. 

The time needed for the coil-to-helix transition is relatively long, whereas it is much shorter for the inverse reaction. As the time needed for reaching the equilibrium in the... 

Table 8. Thermodynamic parameters of the coil-to-helix transition of collagen-model peptides, covalently linked with 1,2,3-propanetricarboxylic acid (PTC) and Lys-Lys, respectively. Solvent 1% aqueous acetic arid (pH 3.0)...

Fig. 3. Model for the two-dimensional arrangement of the human erythrocyte glucose transporter in the membrane. Amino acid residues are identified by their single letter code. Solid bars indicate the location of introns in the transporter gene. The regions coloured black are released from the membrane upon tryptic digestion. Shaded segments indicate the probable regions photolabelled by ATB-BMPA (helix 8) and by cytochalasin B (helix 11 and the loop connecting it to helix 10). The circles with heavy outlines indicate the region labelled by lAPS-forskolin (helix 10).

Fig. 13 Schematic diagram showing the change of chain conformation, i.e., coil to helix, during the induction period of crystallization for sPS and iPS...

Figure 3.44 Calculated structure of complex 23ao-(S)-41a. (a) View perpendicular to helix axis and (b) expanded region of same stmcture model as viewed along helix axis. (Reprinted with permission from Ref. 209. Copyright 1996 by the American Chemical Society.)...

Figure 3.47 Calculated structures of 23a aggregates as viewed perpendicular to helix axis.

Chothia C, Levitt M, Richardson D. Helix to helix packing in proteins. J Mol Biol 1981 145 215-250. 

FIGURE1.1 The architecture of myoglohin. 8 a-helices (A-H) accommodate a heme group, which is attached to the protein via the proximal His93. CO is hound to the iron (Fe) on the distal side of the heme. Here the L29W mutant (Nienhaus et al., 2005) is depicted with the bulky Trp29 bound to helix B on the distal heme side. Figure prepared with rihhons ... 

Fig. 4. Conformational transformations from random-coil to helix through interrupted...

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