Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: $3_{10}$-helix, \alpha-helix, and \beta-bend ribbon

Karle, Isabella L and Flippen-Anderson, Judith and Sukumar, Muppalla and Balaram, Padmanabhan (1987) Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: $3_{10}$-helix, \alpha-helix, and \beta-bend ribbon. In: Proceedings of the National Academy of Sciences of the United States of America, 84 (15). pp. 5087-5091.

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Abstract

Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-Ala-Aib-Pro-Aib-Pro-Phe-OMe (where Boc is t-butoxycarbonyl and Aib is \alpha-aminoisobutyric acid), a synthetic apolar analog of the membrane-active fungal peptide antibiotic zervamycin IIA, crystallizes in space group P1 with Z = 1 and cell parameters a = 9.086 \pm 0.002 A, b = 10.410 \pm 0.002 A, c = 28.188 \pm 0.004 A, \alpha = 86.13 \pm 0.01 deg, \beta = 87.90 \pm 0.01 deg, and \gamma = 89.27 \pm 0.01 deg; overall agreement factor R = 7.3% for 7180 data ($F_o$ > 3\sigma) and 0.91-A resolution. The peptide backbone makes a continuous spiral that begins as a $3_{10}$-helix at the N-terminus, changes to an \alpha-helix for two turns, and ends in a spiral of three beta-bends in a ribbon. Each of the \beta-bends contains a proline residue at one of the corners. The torsion angles ${\phi}_i$ range from -51 deg to -91 deg (average value -64 deg), and the torsion angles ${\psi}_i$ range from -1 deg to -46 deg (average value -31 deg). There are 10 intramolecular NH...OC hydrogen bonds in the helix and two direct head-to-tail hydrogen bonds between successive molecules. Two $H_2O$ and two ${CH}_3OH$ solvent molecules fill additional space with appropriate hydrogen bonding in the head-to-tail region, and two additional $H_2O$ molecules form hydrogen bonds with carbonyl oxygens near the curve in the helix at Pro-10. Since there is only one peptide molecule per cell in space group P1, the molecules repeat only by translation, and consequently the helices pack parallel to each other.

Item Type:	Journal Article
Publication:	Proceedings of the National Academy of Sciences of the United States of America
Publisher:	National Academy of Sciences
Additional Information:	Copyright for this article belongs to National Academy of Sciences.
Keywords:	x-ray structure analysis;hydrogen bonds;parallel packing of helices;peptaibophol antibiotics
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	28 Feb 2005
Last Modified:	19 Sep 2010 04:18
URI:	http://eprints.iisc.ac.in/id/eprint/2851

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