The structural basis of the functioning of bacteriorhodopsin: An overview

Ovchinnikov, Yu.A.; Abdulaev, N.G.; Feigina, M.Yu.; Kiselev, A. P.; Lobanov, Nikolai A.

doi:10.1016/0014-5793(79)80338-5

Cited by 476 publications

(219 citation statements)

References 13 publications

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“…The amino-terminal glutamine residue would then become blocked by a post-translational process. Several other proteins with an amino-terminal pyroglutamic acid are known, such as bacteriorhodopsin (Ovchinnikov et al, 1979) and a proline-rich phosphoprotein from human saliva (Wong, Hofmann and Bennick, 1979).…”

Section: The Protein Sequencementioning

confidence: 99%

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

Jou

Verhoeyen

Devos

et al. 1980

Cell

219

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SummaryThe complete sequence of a hemagglutinin (HA) gene of a recent human influenza A strain, A/Victoria/3/75, is 1768 nucleotides long and contains the information for 567 amino acids. It codes for a signal peptide of 16 amino acids, the HA1 chain of the mature hemagglutinin of 329 amino acids, a connecting region between HA1 and HA2 consisting of a single arginine residue and the HA2 portion of 221 amino acids. The sequence is compared with the hemagglutinin of two members of other subtypes, the human H2 strain A/Jap/305/57 and the avian Havl strain A/FPV/Rostock/34, and with one of the same H3 subtype, A/Memphis/3/72. To align the HA1 chain of different major subtypes several deletions/insertions of single amino acids must be invoked, but two more extensive differences are found at both ends, one leading to an extension of the amino terminal sequence of HA1 and the other (four residues) occurring in the region processed away between HA1 and HA2. Comparison of the HA1 of two H3 strains suggests that drift probably depends on single base mutations, some of which change antigenic determinants. The HA2 region, which apparently is not involved in the immune response, is highly conserved even between different subtypes, and single base substitutions account for all the observed diversity. A hydrophobic segment of 24 residues is present in the same position close to the carboxyl terminus of HA2 in both Victoria and FPV, and presumably functions in implantation into the lipid bilayer. The many conserved features not only in HA2 but also in HA1 suggest a rather rigid architecture for the whole hemagglutinin molecule.

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Section: The Protein Sequencementioning

confidence: 99%

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

Jou

Verhoeyen

Devos

et al. 1980

Cell

219

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“…In order to avoid a possible loss of the label through the cleavage of the retinyl-opsin bond (-in 2) so laboriously constructed,we have developed a protocol for the oxidative transformation of a retinyl moiety into a carboxymethyl group. The tritNote: The lysine is in position 216 as in 171 but would correspond to 215 in [6] molecular mass 26 000 on sodium dodecyl sulphate/ polyacrylamide gel electrophoresis.…”

Section: Hooc-c -Nh -Proteinmentioning

confidence: 99%

“…Extending our studies on the development of methods for the structural analysis of the chromophore-binding sites in various rhodopsins [l-5] we now report experiments showing that in bacteriorhodopsin the retinal-moiety is attached to Lyszrb in the primary sequence recently established by the painstaking work of the Russian [6] and American groups [7]. The two main features of our original strategy to explore the nature and location of the retinal-opsin bond involved labelling the rhodopsin active-site with [ 1 5-3 HIretinal and then fixing the Schiff-base in the reconstituted species with NaBHa n31.…”

Section: Introductionmentioning

confidence: 99%

The identification of Lys₂₁₆ as the retinal binding residue in bacteriorhodopsin

1981

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“…The detailed description of this, so-called cis-photocycle can be found in [19,20,21,22,23,24]. Figure 3 here A widely accepted model for the three-dimensional structure of bR has been provided by Henderson and coworkers using electron-microscopy at low temperature [25,26] together with bR's amino acid sequence [27,28]. The obversations resulted in a structure for the membrane-spanning helical portion of bR at a resolution of 3Å in a direction parallel to the membrane and at a resolution of 10Å perpendicular to the membrane.…”

Section: Introductionmentioning

confidence: 99%

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Logunov

Schulten

1996

Quantum Mechanical Simulation Methods for Studying Biological Systems

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1A combination of molecular dynamics and quantum chemistry techniques have been employed to study the electronic excitation and conformational potential surface of retinal in the binding site of bacteriorhodopsin (bR). The CASSCF(6,9)/6-31G level of ab initio calculations (within Gaussian92) has been used for the treatment of both the ground (S0) and excited (S1) states of retinal. Charges of all atoms in the protein are represented by spherical Gaussians and explicitly included in the electronic Hamiltonian of retinal. Spectral properties have been analyzed for the native bR pigment as well as for its D85N mutant.The calculated relative shift in the absorption maxima between the two pigments is in better agreement with experiment than the computed absolute parameters of the absorption line shapes. The dark adaptation processes in bacteriorhodopsin (which involves rotation around the 13-14 and the 15-N retinal double bonds) has been modelled by following the pre-defined reaction coordinate. Our simulations support the notion that the isomerization process is catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin. 2 IntroductionBacteriorhodopsin (bR) spans the cell membrane of Halobacterium halobium and functions as a light-driven proton pump. bR contains seven α-helices which enclose the prosthetic group, all-trans retinal, bound via a protonated Schiff base linkage to Lys-216. Figure 1a shows the chemical structure of retinal and its conventional numbering scheme. The bR structure is presented in Fig. 2a. Retinal absorbs light and undergoes a photoisomerization process; the thermal reversal of this reaction is coupled to transfer of a proton from the cytoplasmic side (top in Fig. 2a) to the extracellular side (bottom in Fig. 2a) of the protein.Recent reviews that discuss the structure and function of bR are [1,2,3,4,5,6,7]. Figure 1 here Bacteriorhodopsin accomplishes its function through a cyclic process initiated by absorption of a photon. This photon triggers an isomerization of retinal, which proceeds then through several intermediate states identified by their absorption spectra. An accepted kinetic scheme for this cycle is an unbranched series of intermediates, shown in Fig. 3. Photoisomerization occurs in the bR 568 → J 625 transition. During the L 550 → M 412 transition the Schiff base proton is transferred to Asp-85 and, subsequently, to the outside of the cell [8,9,10,11,12,13]. During the M 412 → N 520 transition, a proton is transferred to the Schiff base from Asp-96, which then takes up a proton from the cytoplasmic environment [13]. The reaction cycle is completed as the protein returns to bR 568 via the O 640 intermediate. Figure 2 here When bR is allowed to equilibrate in the dark, it converts within an hour to a 2:1 mixture containing 13-cis retinal and all-trans retinal bR [14]. The protein containing the 13-cis retinal isomer of bRis referred to as the dark adapted (DA) pigment of bR, bR 548 , which absorbs at 548 nm. bR 548 contains, actually, retinal in a 1...

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The structural basis of the functioning of bacteriorhodopsin: An overview

Cited by 476 publications

References 13 publications

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

The identification of Lys₂₁₆ as the retinal binding residue in bacteriorhodopsin

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

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The structural basis of the functioning of bacteriorhodopsin: An overview

Cited by 476 publications

References 13 publications

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA

The identification of Lys216 as the retinal binding residue in bacteriorhodopsin

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

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The identification of Lys₂₁₆ as the retinal binding residue in bacteriorhodopsin