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Design of a heme-binding peptide motif adopting a beta-hairpin conformation

Nagarajan, Deepesh and Sukumaran, Sujeesh and Deka, Geeta and Krishnamurthy, Kiran and Atreya, Hanudatta S and Chandra, Nagasuma (2018) Design of a heme-binding peptide motif adopting a beta-hairpin conformation. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 293 (24). pp. 9412-9422.

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Official URL: https://dx.doi.org/10.1074/jbc.RA118.001768

Abstract

Heme-binding proteins constitute a large family of catalytic and transport proteins. Their widespread presence as globins and as essential oxygen and electron transporters, along with their diverse enzymatic functions, have made them targets for protein design. Most previously reported designs involved the use of -helical scaffolds, and natural peptides also exhibit a strong preference for these scaffolds. However, the reason for this preference is not well-understood, in part because alternative protein designs, such as those with -sheets or hairpins, are challenging to perform. Here, we report the computational design and experimental validation of a water-soluble heme-binding peptide, Pincer-1, composed of predominantly -scaffold secondary structures. Such heme-binding proteins are rarely observed in nature, and by designing such a scaffold, we simultaneously increase the known fold space of heme-binding proteins and expand the limits of computational design methods. For a -scaffold, two tryptophan zipper -hairpins sandwiching a heme molecule were linked through an N-terminal cysteine disulfide bond. -Hairpin orientations and residue selection were performed computationally. Heme binding was confirmed through absorbance experiments and surface plasmon resonance experiments (K-D = 730 +/- 160 nm). CD and NMR experiments validated the -hairpin topology of the designed peptide. Our results indicate that a helical scaffold is not essential for heme binding and reveal the first designed water-soluble, heme-binding -hairpin peptide. This peptide could help expand the search for and design space to cytoplasmic heme-binding proteins.

Item Type: Journal Article
Additional Information: Copyright of this article belong to AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Biological Sciences > Molecular Biophysics Unit
Division of Chemical Sciences > NMR Research Centre (Formerly Sophisticated Instruments Facility)
Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Depositing User: Id for Latest eprints
Date Deposited: 03 Jul 2018 14:49
Last Modified: 03 Jul 2018 14:49
URI: http://eprints.iisc.ac.in/id/eprint/60121

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