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Analyses of databases derived from the Brookhaven Protein Data Bank have identified a set of related turn structures formed by the sequence Asx-Pro-Xxx(n). In a variety of flanking structural contexts, more than 60% of Asx-Pro sequences adopt a turn conformation stabilized by a set of alternative hydrogen bonds among the side chain O delta and backbone C = O carbonyl oxygens of Asx (residue i) and the backbone NH of residues i + 2, i + 3 and in some cases i + 4. In contrast, the structures adopted by Ser-Pro, His-Pro and other Xxx-Pro sequences reflect more heterogeneous hydrogen-bonding patterns. As expected, structures formed by Asx-Pro-Asx are similar to those formed by Asx-Pro-Xxx(n), but in some cases additional hydrogen bonds are formed between the Asx side chains. Hydrogen bond patterns within Asx-Pro and Asn-Pro-Asn turns are consistent with published NMR studies of helical (Asn-Pro-Asn-Ala)n peptides, indicating that a consensus structure reflecting these hydrogen bonds can serve as a partial model of the Asn-Pro-Asn-Ala tetrapeptide repeats of Plasmodium falciparum circumsporozoite protein.

protein engineering, design and selection

The 'Asx-Pro turn' as a local structural motif stabilized by alternative patterns of hydrogen bonds and a consensus-derived model of the sequence Asn-Pro-Asn