title: Conformation of pardaxin, the toxin of the flatfish Pardachirus marmoratus.
abstract: Pardaxin is the toxic component isolated from the secretion of the Red Sea flatfish Pardachirus marmoratus. Pardaxin has attracted considerable attention recently because of its use as shark repellent. Conformational information regarding the peptide backbone, disulfide bonds, and tyrosine chromophores was obtained using Raman and circular dichroism (CD) spectroscopy. Analysis of the Raman spectra indicates that the toxin consists of 39% alpha-helix, 23% beta-structure, and 39% random coil. The occurrence of a band at 510--512 cm-1 indicates the conformational geometry of the disulfide C-C-S-S-C-C linkages to be gauche-gauche-gauche. From the lack of a peak in the 2500--2700 cm-1 region we concluded that all half-cystines are involved in disulfide linkages. The far-ultraviolet CD spectrum of pardaxin showed positive 196 and negative 208 and 222 nm bands. The best fit secondary structure based on the CD ellipticities was found to be: 23% alpha-helix, 21% beta-structure, and 56% random coil. Under highly acidic and alkaline conditions the far-ultraviolet pardaxin spectra showed extensive, reversible loss of its helical structure. Due to certain biological characteristics of pardaxin the possible influence of salt on pardaxin's conformation was examined. No evidence of conformation perturbation was detected in either the CD or Raman spectra of pardaxin.
mesh_terms: D000818:Animals; D002942:Circular Dichroism; D005397:Fish Venoms; D005399:Fishes / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D011487:Protein Conformation; D012965:Sodium Chloride; D012996:Solutions; D013059:Spectrum Analysis, Raman
chemical_list: D005397:Fish Venoms; D012996:Solutions; D012965:Sodium Chloride; C017603:pardaxin