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

Ramagopal, Udupi A and Ramakumar, Suryanarayanarao and Sahal, Dinkar and Chauhan, Virander S (2001) De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions. In: Proceedings of the National Academy of Sciences of the United States of America, 98 (3). 870-874.

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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.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to National Academy of Sciences.
Department/Centre: Division of Information Sciences > BioInformatics Centre
Division of Physical & Mathematical Sciences > Physics
Date Deposited: 25 Oct 2007
Last Modified: 19 Sep 2010 04:40
URI: http://eprints.iisc.ernet.in/id/eprint/12219

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