Bridge helix

Figure 11.7 Structure of a transcribing RNA Pol II stalled at a CPD lesion, (a) RNA Pol II (gray) is shown with a template strand (dark blue), nontemplate strand (light blue), and growing mRNA strand (yellow). The translocation of the CPD lesion (red) on the template strand into the active site (active site metal is shown in magenta) is blocked by the bridge helix (purple). Tyr836,...

In the heptad sequence ate close to the hydrophobic core and can form salt bridges between the two a helices of a colled-coll structure, the e-resldue In one helix with the g-resldue In the second and vice versa. 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

One long a helix connects the two domains (purple). Thermostable mutants of this protein were constructed by introducing disulfide bridges at three different places (yellow). 

Figure 3.10 Stniciural details of the bridging units between pairs of bases in separate strands of the double helix of DNA (a) the thymine-adenine pair (b) the cytosine-guanine pair.

It is well known that native collagen containes tripeptide sequences, which alone are not capable of building up a triple helix (e.g. Gly-Pro-Leu, Gly-Pro-Ser) when they exist as homopolypeptides. The synthesis of threefold covalently bridged peptide chains opens up the possibility of investigating the folding properties of such weak helix formers, because the bridging reduces the entropy loss during triple-helix formation and thereby increases the thermodynamic stability of the tertiary structure. Therefore, we have... 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

In 1% aqueous acetic acid, the peptides of the sequence (Ala-Gly-Pro)n, bridged with Lys-Lys and beginning with n = 8 show a cooperative transition, which was interpreted as a triple helix-coil transition (see Figs. 35, 36). 

The covalent bridging of the three polypeptide chains with the sequence Ala-Gly-Pro has facilitated, as expected, the nucleation step for triple-helix formation. This is also... 

The effect of C ,C -disubstituted amino acids (aaAAs) on peptide secondary structure has been studied in recent years.2a d While longer side-chain C ,C -di-n-alkyl amino acids promote extended peptide conformation,23 alicyclic aaAAs, in which the Ca carbon forms a cyclic bridge with itself, such a 1-aminocyclopentane-l-carboxylic acid (Ac5c) and 1-aminocyclohexane-l-carboxylic acid (Ac6c), have helix-forming characteristics similar to those of 1 -aminoisobutyric acid (Aib).2ax... 

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