[Spatial structure of (1-36)bacterioopsin solubilized in a methanol-chloroform mixture with sodium dodecylsulfate...

Spatial structures of proteolytic segment A (sA) of bacterioopsin of Halobacterium halobium (residues 1-36) solubilized in the mixture of methanol-chloroform (1:1), 0.1 M LiClO4 or in perdeuteriated sodium dodecyl sulfate (SDS) micelles, were determined by 2D 1H-NMR techniques. Most of the resonances in 1H-NMR spectra of fragment A were assigned using DQF-COSY, TOCSY and NOESY spectra. Deuterium exchange rates for amide protons were measured in series of NOESY spectra. 324 and 400 NOESY cross-peak volumes were measured in NOESY spectra of sA in mixture of organic solvents and SDS micelles, respectively. The sA structure was determined by local structure analysis, distance geometry calculation with program DIANA and systematic search for energetically allowed side chain rotamers consistent with NOESY cross-peak volumes. The structures of sA are similar in both milieus. These structures have the right-handed alpha-helical region from Pro-8 to Met-32 with root mean square deviation (RMSD) of 0.25 A between back bone heavy atoms and fit well with Pro-8 to Met-32 alpha-helical region in electron cryo-microscopy (ECM) model of bacteriorhodopsin [4]. The C-terminal region Gly-33-Asp-36 is disordered in both milieus, while N-terminal region Ala-2-Gly-6 in organic solvents has a fixed structure (RMSD of 0.25 A) stabilized by the Thr-5 NH...O=C Gln-3 and Ile-4 NH...O = C Ala-2 hydrogen bonds. This region of sA in SDS micelles has disordered structure with RMSD of 1.44 A for back bone heavy atoms. Torsion angles chi 1 of sA were unequivocally determined for 72% of side chains in the alpha-helical region and are identical in both milieus.