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Biochemistry. Biokhimiia Oct 2023The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites... (Review)
Review
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
Topics: Rhodopsin; Bacteriorhodopsins; Photochemistry
PubMed: 38105022
DOI: 10.1134/S0006297923100097 -
Biochimica Et Biophysica Acta Aug 2000
Topics: Bacteriorhodopsins; Membrane Proteins; Proton Pumps; Purple Membrane; Structure-Activity Relationship
PubMed: 10984585
DOI: 10.1016/s0005-2728(00)00124-9 -
Biophysical Chemistry 1995Photoaffinity labeling with bovine rhodopsin using a retinal with a fixed 11-cis-ene cross-linked exclusively to Trp-265/Leu-266 in helix F, showing that the beta-ionone... (Comparative Study)
Comparative Study Review
Photoaffinity labeling with bovine rhodopsin using a retinal with a fixed 11-cis-ene cross-linked exclusively to Trp-265/Leu-266 in helix F, showing that the beta-ionone C-3 is close to helix F. Moreover, since these labeled amino acids are in the middle of helix F, while the Schiff-base linkage to Lys-296 at the other terminus of the chromophore is also in the middle of helix G, the chromophore lies horizontally near the center of the lipid bilayer. In bacteriorhodopsin, photoaffinity studies using a retinal with a C-10 tritiated phenylazide appended through a 13 A spacer cross-linked to Arg-175/Asn-176 on the cytoplasmic side of helix F; this indicates that 9-Me points toward the extracellular space. This result agrees with our earlier studies with 9-sulfate analogs but is opposite to that deduced by biophysical measurements.
Topics: Affinity Labels; Amino Acid Sequence; Animals; Bacteriorhodopsins; Cross-Linking Reagents; Leucine; Lipid Bilayers; Models, Structural; Protein Structure, Secondary; Protein Structure, Tertiary; Rhodopsin; Schiff Bases; Tryptophan
PubMed: 7662862
DOI: 10.1016/0301-4622(95)00010-u -
Biochimica Et Biophysica Acta Mar 2015Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron... (Review)
Review
BACKGROUND
Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined.
SCOPE OF REVIEW
We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data.
MAJOR CONCLUSIONS
An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212.
GENERAL SIGNIFICANCE
A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
Topics: Bacteriorhodopsins; Crystallography, X-Ray; Light; Models, Molecular; Phylogeny; Protein Conformation; Protein Structure, Secondary; X-Rays
PubMed: 24918316
DOI: 10.1016/j.bbagen.2014.05.021 -
International Journal of Molecular... Jun 2022S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton...
S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficient photocycling. Here, we explored the specific binding of S-TGA-1 and PGP-Me with the bR trimer and elucidated how specific interactions modulate the bR trimeric structure and proton release and uptake using long-term atomistic molecular dynamic simulations. Our results showed that S-TGA-1 and PGP-Me are essential for stabilizing the bR trimer and maintaining the coherent conformational dynamics necessary for proton transfer. The specific binding of S-TGA-1 with W80 and K129 regulates proton release on the extracellular surface by forming a "Glu-shared" model. The interaction of PGP-Me with K40 ensures proton uptake by accommodating the conformation of the helices to recruit enough water molecules on the cytoplasmic side. The present study results could fill in the theoretical gaps of studies on the functional role of archaeal lipids and could provide a reference for other membrane proteins containing similar archaeal lipids.
Topics: Archaea; Bacteriorhodopsins; Lipids; Protein Structure, Secondary; Protons
PubMed: 35805918
DOI: 10.3390/ijms23136913 -
Proceedings of the National Academy of... Mar 2021Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the...
Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the most widely used assay and yields the change in unfolding free energy (ΔΔ). It has been applied to >80 different residues of bacteriorhodopsin (bR), a model membrane protein. However, such experiments have several key limitations: 1) a nonnative lipid environment, 2) a denatured state with significant secondary structure, 3) error introduced by extrapolation to zero denaturant, and 4) the requirement of globally reversible refolding. We overcame these limitations by reversibly unfolding local regions of an individual protein with mechanical force using an atomic-force-microscope assay optimized for 2 μs time resolution and 1 pN force stability. In this assay, bR was unfolded from its native bilayer into a well-defined, stretched state. To measure ΔΔ, we introduced two alanine point mutations into an 8-amino-acid region at the C-terminal end of bR's G helix. For each, we reversibly unfolded and refolded this region hundreds of times while the rest of the protein remained folded. Our single-molecule-derived ΔΔ for mutant L223A (-2.3 ± 0.6 kcal/mol) quantitatively agreed with past chemical denaturation results while our ΔΔ for mutant V217A was 2.2-fold larger (-2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to contact between Val and a natively bound squalene lipid, highlighting the contribution of membrane protein-lipid contacts not present in chemical denaturation assays. More generally, we established a platform for determining ΔΔ for a fully folded membrane protein embedded in its native bilayer.
Topics: Amino Acid Substitution; Bacteriorhodopsins; Halobacterium salinarum; Lipid Bilayers; Microscopy, Atomic Force; Point Mutation; Protein Folding; Single Molecule Imaging; Thermodynamics
PubMed: 33753487
DOI: 10.1073/pnas.2020083118 -
Molecules (Basel, Switzerland) Dec 2021Highly expressible bacteriorhodopsin (HEBR) is a light-triggered protein (optogenetic protein) that has seven transmembrane regions with retinal bound as their...
Highly expressible bacteriorhodopsin (HEBR) is a light-triggered protein (optogenetic protein) that has seven transmembrane regions with retinal bound as their chromophore to sense light. HEBR has controllable photochemical properties and regulates activity on proton pumping. In this study, we generated HEBR protein and incubated with lung cancer cell lines (A549 and H1299) to evaluate if there was a growth-inhibitory effect with or without light illumination. The data revealed that the HEBR protein suppressed cell proliferation and induced the G/G cell cycle arrest without light illumination. Moreover, the migration abilities of A549 and H1299 cells were reduced by ~17% and ~31% after incubation with HEBR (40 μg/mL) for 4 h. The Snail-1 gene expression level of the A549 cells was significantly downregulated by ~50% after the treatment of HEBR. In addition, HEBR significantly inhibited the gene expression of Sox-2 and Oct-4 in H1299 cells. These results suggested that the HEBR protein may inhibit cell proliferation and cell cycle progression of lung cancer cells, reduce their migration activity, and suppress some stemness-related genes. These findings also suggested the potential of HEBR protein to regulate the growth and migration of tumor cells, which may offer the possibility for an anticancer drug.
Topics: A549 Cells; Antineoplastic Agents; Bacteriorhodopsins; Cell Cycle Checkpoints; Cell Movement; Cell Proliferation; Humans; Lung Neoplasms; Protein Engineering
PubMed: 34885925
DOI: 10.3390/molecules26237344 -
Biochimica Et Biophysica Acta Aug 2000Light-induced changes of the proton affinities of amino acid side groups are the driving force for proton translocation in bacteriorhodopsin. Recent progress in... (Review)
Review
Light-induced changes of the proton affinities of amino acid side groups are the driving force for proton translocation in bacteriorhodopsin. Recent progress in obtaining structures of bacteriorhodopsin and its intermediates with an increasingly higher resolution, together with functional studies utilizing mutant pigments and spectroscopic methods, have provided important information on the molecular architecture of the proton transfer pathways and the key groups involved in proton transport. In the present paper I consider mechanisms of light-induced proton release and uptake and intramolecular proton transport and mechanisms of modulation of proton affinities of key groups in the framework of these data. Special attention is given to some important aspects that have surfaced recently. These are the coupling of protonation states of groups involved in proton transport, the complex titration of the counterion to the Schiff base and its origin, the role of the transient protonation of buried groups in catalysis of the chromophore's thermal isomerization, and the relationship between proton affinities of the groups and the pH dependencies of the rate constants of the photocycle and proton transfer reactions.
Topics: Amino Acids; Bacteriorhodopsins; Hydrogen-Ion Concentration; Light; Models, Chemical; Photochemistry; Proton Pumps; Schiff Bases
PubMed: 10984592
DOI: 10.1016/s0005-2728(00)00131-6 -
Proceedings of the National Academy of... Sep 2021Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in...
Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
Topics: Arginine; Aspartic Acid; Bacteriorhodopsins; Chlorides; Molecular Dynamics Simulation; Mutation; Protons; Quantum Theory; Water
PubMed: 34561302
DOI: 10.1073/pnas.2024803118 -
Biochemistry. Biokhimiia Apr 2017Photochemical reaction dynamics of the primary events in recombinant bacteriorhodopsin (bR) was studied by femtosecond laser absorption spectroscopy with 25-fs time... (Comparative Study)
Comparative Study
Photochemical reaction dynamics of the primary events in recombinant bacteriorhodopsin (bR) was studied by femtosecond laser absorption spectroscopy with 25-fs time resolution. bR was produced in an Escherichia coli expression system. Since bR was prepared in a DMPC-CHAPS micelle system in the monomeric form, its comparison with trimeric and monomeric forms of the native bacteriorhodopsin (bR and bR, respectively) was carried out. We found that bR intermediate I (excited state of bR) was formed in the range of 100 fs, as in the case of bR and bR. Further processes, namely the decay of the excited state I and the formation of intermediates J and K of bR, occurred more slowly compared to bR, but similarly to bR. The lifetime of intermediate I, judging from the signal of ΔA(470-480 nm), was 0.68 ps (78%) and 4.4 ps (22%) for bR, 0.52 ps (73%) and 1.7 ps (27%) for bR, and 0.45 ps (90%) and 1.75 ps (10%) for bR. The formation time of intermediate K, judging from the signal of ΔA(625-635 nm), was 13.5 ps for bR, 9.8 ps for bR, and 4.3 ps for bR. In addition, there was a decrease in the photoreaction efficiency of bR and bR as seen by a decrease in absorbance in the differential spectrum of the intermediate K by ~14%. Since photochemical properties of bR are similar to those of the monomeric form of the native protein, bR and its mutants can be considered as a basis for further studies of the mechanism of bacteriorhodopsin functioning.
Topics: Bacteriorhodopsins; Biopolymers; Chromatography, High Pressure Liquid; Circular Dichroism; Recombinant Proteins; Spectrophotometry, Ultraviolet
PubMed: 28371607
DOI: 10.1134/S0006297917040113