Hydrogen bond with amino acids

Fig. 10. NMR structure of mPrP(121-231) with indication of the hydrophobic core and the hydrogen bonds with amino acid side chains. The polypeptide backbone is represented by white ribbons and tubes. The hydrophobic core containing the residues 134, 137,139,141,158,161,175,176,179,180,184,198, 203, 205, 206, 209, 210, 213, 214, and 215 is shown in a yellow translucent envelope. In a shell surrounding the core, hydrogen bonds involving side chains (drawn as violet stick models) are represented by dashed cyan lines and labeled by a code of lower case letters that are referenced in the text.

Specific attractive interactions between the dendrimer building blocks (e.g. hydrogen bonds between amino acid building blocks) or complexation of metal ions [86] by suitable functional groups in the dendrimer scaffold can favour the formation of chiral substructures and effect distortion or folding of the overall structure. Interactions with solvent molecules can also have a pronounced effect on the overall structure. 

Related to the a-helix the so-called 3 Q-helix with a higher pitch (1.94 A/residue vs. 1.56 for a-helix) exists (Scheme 8). It involves hydrogen bonds between amino acids that are three residues apart in the primary structure (cf. a-helix 4 residues) and is promoted by incorporation of a-aminoisobutyric acid (Aib, 51) residues. A transition from a-helix to 3io-helix can be induced in a model peptide by raising the temperature. The transition can be monitored by incorporating amino acids with suitable acceptor (Acc, 52) and donor (Don, 53) side chains for fluorescence studies (Chart 9). 

Helices that form pores will be amphiphilic because it is more favorable to have situated in the inner side of the pore hydrophilic amino acid side chains, while the outer side of the pore represents a more favorable environment for hydrophobic amino acid side chains since these are in contact with lipids. Some authors point to the possibility that such a structure contains hydrogen bonds between amino acid residues and the main chain in order to compensate opposite charges and oppositely oriented dipoles. A comparison between the strength of different interactions in the structure of soluble and membrane proteins leads to the conclusion that because of the decreased strength of hydrophobic interactions and increased strength of electrostatic interactions (because of the reduced dielectric constant), the electrostatic interactions play the main role in stabilizing the structure of membrane proteins. ... 

Class 1 aldolase mimics consist of amino acid catalysts that presumably activate the donor via enamine formation and the acceptor through a hydrogen bond with an acid functionality. Repotted hrst by Wiechert et al. and then by Hajos and Parrish,-proline was found to catalyze intramolecular asymmetric aldol reactions. However, the... 

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