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De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions

By Udupi A Ramagopal, Suryanarayanarao Ramakumar, Dinkar Sahal and VS Chauhan

Abstract

Design of helical super secondary structural motifs is expected to provide important scaffolds to incorporate functional sites, thus allowing the engineering of novel miniproteins with function. An $\alpha ,\beta$ -dehydrophenylalanine containing 21-residue apolar peptide was designed to mimic the helical hairpin motif by using a simple geometrical design strategy. The synthetic peptide folds into the desired structure as assessed crystallographically at 1.0-\AA resolution. The two helices of the helical-hairpin motif, connected by a flexible $(Gly)_4$ linker, are docked to each other by the concerted influence of weak interactions. The folding of the peptide without binary patterning of amino acids, disulfide bonds, or metal ions is a remarkable observation. The results demonstrate that preferred interactions among the hydrophobic residues selectively discriminate their putative partners in space, leading to the unique folding of the peptide, also a hallmark of the unique folding of hydrophobic core in globular proteins. We demonstrate here the engineering of molecules by using weak interactions pointing to their possible further exploitation in the de novo design of protein super secondary structural elements

Topics: BioInformatics Centre, Physics
Publisher: National Academy of Sciences
Year: 2001
OAI identifier: oai:eprints.iisc.ac.in:12219
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