Side chain locations

Fig. 14. Structural prediction and modeling of a fragment of FHA from B. pertussis containing Rl-repeats. (A) Successive stages in the modeling. From top to bottom identification of the consensus sequence repeat, generation of 2D template of the coil, and the modeled 3D structure. In the consensus sequence, letters indicate residues that are conserved at the level of >60% identity, x is any residue and filled circles represent bulky nonpolar residues. Apolar residues are in red glycine in green. In the 2D template, open circles denote any (but mainly polar) residues, while filled circles denote conserved, mainly nonpolar, residues. Circles inside the coil contour indicate side chains located inside the structure and circles outside the contour denote side chains facing the solvent. Arrows indicate /(-strands. (B) A fragment of the crystal structure of FHA (Clantin et al, 2004) (on the top, in green color) and the 3D model (bottom, in brown).

From our considerations above, we can see just how important the interactions of various amino acid side-chains are to the structure and shape of proteins. These interactions tend to be located inside the protein molecule, stabilizing a particular conformation and generating the overall shape as in a globular protein. However, it is obvious that there are also going to be many amino acid side-chains located on the surface of a protein, and these in turn will be capable of interacting with other molecules. These interactions will be intermolecular, rather than the intramolecular interactions that contribute to protein structure. 

The acylation of peptides with fatty acids is easily achieved by acylation of a free amino group that can be N-terminal or side-chain located. After the discovery that short tri-palmitoylated peptides can elicit strong immunological responses against the peptide,[90,91]... 

Ala286 point mutations caused 19-and 28-fold respective losses in affinity for bradykinin. Close inspection of the bradykinin Arg1 side chain location and surrounding receptor interactions led to the suspicion that Asp286 and Asp268... 

Frickel225 has provided a comprehensive review of the chemistry of the retinoids which shows that most of the literature relates to molecular modifications aimed at pharmaceutical purposes. It has been rare to find a retinoid designed to include a polar element at a side chain location, although some work has been done on substituting fluorine into the side chain. Dawson Hobbs226 updated Frickel s review to 1994 and noted some additional work... 

Several pharmaceutical enzymes belong to the group of serine-histidine estero-proteolytic enzymes (serine proteases), which display their catalytic activity with the aid of an especially reactive serine residue, whoso p-hydroxyi group forms a covalent bond with the substrate molecule. This reaction takes place by cooperation with the imidazole base of histidine. The specificity of the enzymes is achieved by the characteristic strocture of their substrate-binding centers, which in these proteases are built according to the same principle. They consist of a hydrophobic slit formed by apolar aide chains of amino acids and a dissociated side chain-located carboxyl group of an aspartic add residue at the bottom. 

Figure 10 Close-up of the four layers of side chains located on /3-strands of the C-terminal (/3/a)g barrel, which define the interior surface of the ammonia tunnel in Saccharomyces cerevisiae IGP synthase (10X5). The PRFAR binding site is at the top of the tunnel, where the PRFAR ligand is shown asaCPK model C-gray, O-red, N - blue, and P-orange. Image rendered in PYMOL.

We have found that these deviations are greatest in locus noticeable enough in loci S2, S3, and S2, and differ but slightly from unity for other positions (Fig.l). Therefore, the active site of pepsin is adjusted to accomodate specifically at least five amino acid residues three toward the NH2-terminal from the sensitive bond and two toward the COOH-terminal. The most strict requirements are imposed on the structure of the side chain located in the locus S]. ... 

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