Spatial structure of (34-65)bacterioopsin polypeptide in SDS micelles determined from nuclear magnetic resonance data.
The spatial structure of a synthetic 32-residue polypeptide, an analog of the membrane-spanning segment B (residues 34-65) of bacterioopsin of Halobacterium halobium, incorporated into perdeuterated sodium dodecyl sulfate micelles, was determined from 1H NMR data. The structure determination included the following steps: (1) local structure analysis; (2) structure calculations using the distance geometry program DIANA; (3) systematic search for energetically allowed side-chain rotamers consistent with NOESY cross-peak volumes; (4) random generation of peptide conformations in allowed conformational space. The obtained structure has a right-handed alpha-helical region from Lys41 to Leu62 with a kink of 27 degrees at Pro50. The C-cap Gly63 adopts a conformation with phi = 87 +/- 6 degrees, psi = 43 +/- 10 degrees typical to a left-handed helix. The N-terminal part (residues 34-40) is exposed to the aqueous phase and lacks an ordered conformation. The secondary structure of segment B in micelles is consistent with the high-resolution electron cryomicroscopy model of bacteriorhodopsin (Henderson et al. (1990) J. Mol. Biol., 213, 899-929).
Lomize
A L
AL
M.M. Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
Pervushin
K V
KV
Arseniev
A S
AS
D001436:Bacteriorhodopsins / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008823:Micelles; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry
D008823:Micelles; D010446:Peptide Fragments; D012967:Sodium Dodecyl Sulfate; D001436:Bacteriorhodopsins; C017827:bacterio-opsin