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Biophysical Journal 86:3687-3699 (2004)
© 2004 The Biophysical Society

Peptaibol Zervamicin IIB Structure and Dynamics Refinement from Transhydrogen Bond J Couplings

Z. O. Shenkarev, T. A. Balashova, Z. A. Yakimenko, T. V. Ovchinnikova and A. S. Arseniev

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia

Correspondence: Address reprint requests to A. S. Arseniev, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia. Fax: 7-095-3355033; E-mail: aars{at}nmr.ru.

Zervamicin IIB (Zrv-IIB) is a channel-forming peptaibol antibiotic of fungal origin. The measured transhydrogen bond 3hJNC' couplings in methanol solution heaving average value of –0.41 Hz indicate that the stability of the Zrv-IIB helix in this milieu is comparable to the stability of helices in globular proteins. The N-terminus of the peptide forms an {alpha}-helix, whereas 310-helical hydrogen bonds stabilize the C-terminus. However, two weak transhydrogen bond peaks are observed in a long-range HNCO spectrum for HN Aib12. Energy calculations using the Empirical Conformation Energy Program for Peptides (ECEPP)/2 force field and the implicit solvent model show that the middle of the peptide helix accommodates a bifurcated hydrogen bond that is simultaneously formed between HN Aib12 and CO Leu8 and CO Aib9. Several lowered 3hJNC' on a polar face of the helix correlate with the conformational exchange process observed earlier and imply dynamic distortions of a hydrogen bond pattern with the predominant population of a properly folded helical structure. The refined structure of Zrv-IIB on the basis of the observed hydrogen bond pattern has a small (~20°) angle of helix bending that is virtually identical to the angle of bending in dodecylphosphocholine (DPC) micelles, indicating the stability of a hinge region in different environments. NMR parameters (1HN chemical shifts and transpeptide bond 1JNC' couplings) sensitive to hydrogen bonding along with the solvent accessible surface area of carbonyl oxygens indicate a large polar patch on the convex side of the helix formed by three exposed backbone carbonyls of Aib7, Aib9, and Hyp10 and polar side chains of Hyp10, Gln11, and Hyp13. The unique structural features, high helix stability and the enhanced polar patch, set apart Zrv-IIB from other peptaibols (for example, alamethicin) and possibly underlie its biological and physiological properties.






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Copyright © 2004 by the Biophysical Society.