Terminal residues in protein chains: residue preference, conformation, and interaction.

Abstract

The known protein structures have been analyzed to find out if there is any pattern in the type of residues used and their conformation at the two terminal positions of the polypeptide chains. While the N-terminal position is overwhelmingly occupied by Met (followed by Ala and Ser), the preference for the C-terminal is not as distinct, the residues with highest propensities being Lys, Arg, Gln, and Asn. Only one main-chain torsion angle, psi, can be defined for the N-terminal residue, which is found to be in the extended conformation due to a favorable electrostatic interaction between the charged amino group and the carbonyl oxygen atom. The distribution of the angle phi for the C-terminal residue, on the other hand, is not much different from that of the nonterminal residues. There are some differences in the distribution of the side-chain torsion angle chi1 of both the terminal residues from the general distribution. The terminal segments are generally flexible and there is a tendency for the more ordered residues to have lesser solvent exposure. About 40% of the terminal groups form a hydrogen bond with protein atoms--a slight preference is observed for the side-chain atoms (more than half of which belong to charged residues) over the main-chain ones. Although the terminal residues are not included in any regular secondary structure, the adjacent ones have a high preference to occur in the beta conformation. There is a higher chance of a beta-strand rather than an alpha-helix to start within the first 6 positions from the N-terminal end. It is suggested that the extended conformation observed for the N-terminal residue propagates along the chain leading to the formation of beta-strand. In the C-terminal end, on the other hand, as one moves upstream the alpha and beta structures are encountered in proportion similar to the average value for these structures in the database. The cleavage site of the zymogen structures has a conformation that can be retained by the N-terminal residue of the active enzyme.