title: Propagating structural perturbation inside bacteriorhodopsin: crystal structures of the M state and the D96A and T46V mutants.
abstract: The X-ray diffraction structure of the non-illuminated D96A bacteriorhodopsin mutant reveals structural changes as far away as 15 A from residue 96, at the retinal, Trp-182, Ala-215, and waters 501, 402, and 401. The Asp-to-Ala side-chain replacement breaks its hydrogen bond with Thr-46, and the resulting separation of the cytoplasmic ends of helices B and C is communicated to the retinal region through a chain of covalent and hydrogen bonds. The unexpected long-range consequences of the D96A mutation include breaking the hydrogen bond between O of Ala-215 and water 501 and the formation of a new hydrogen bond between water molecules 401 and 402 in the extracellular region. Because in the T46V mutant a new water molecule appears at Asp-96 and its hydrogen-bond to Ile-45 replaces Thr-46 as its link to helix B, the separation of helices B and C is smaller than that in D96A, and there are no atomic displacements elsewhere in the protein. Propagation of conformational changes along the chain between the retinal and Thr-46 had been observed earlier in the crystal structures of the D96N and E204Q mutants but in the trapped M state. Consistent with the perturbation of the retinal region in D96A, little change of the Thr-46 region occurs between the non-illuminated and M states of this mutant. It appears that a local perturbation can propagate along a track in both directions between the retinal and the Asp-96/Thr-46 pair, either from photoisomerization of the retinal in the wild-type protein in one case or from the D96A mutation in the other.
authors.affiliation: Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA. jlanyi@orion.oac.uci.edu
authors.forename: Janos K
authors.initials: JK
authors.lastname: Lanyi
authors.forename: Brigitte
authors.initials: B
authors.lastname: Schobert
mesh_terms: D019943:Amino Acid Substitution; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D007536:Isomerism; D020125:Mutation, Missense; D010777:Photochemistry; D017433:Protein Structure, Secondary / Q000235:genetics; D012172:Retinaldehyde / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D001436:Bacteriorhodopsins; D012172:Retinaldehyde