-
Biophysical Journal Feb 2005
Comparative Study
Topics: Bacteriorhodopsins; Computer Simulation; Elasticity; Micromanipulation; Microscopy, Atomic Force; Models, Chemical; Models, Molecular; Motion; Physical Stimulation; Protein Denaturation; Protein Folding; Stress, Mechanical; Structure-Activity Relationship; Viscosity
PubMed: 15596486
DOI: 10.1529/biophysj.104.056242 -
Journal of Biochemistry Mar 1997The light-induced mechanism for proton pumping of bacteriorhodopsin was studied by Fourier transform infrared spectroscopy of the discrete sequential intermediate... (Review)
Review
The light-induced mechanism for proton pumping of bacteriorhodopsin was studied by Fourier transform infrared spectroscopy of the discrete sequential intermediate states, L, M, and N. Attention is focused on L in the early microsecond time range, as a transition state in which the Schiff base forms strong H-bonding with a water molecule coordinated with Asp85. This structure leads to transfer of the Schiff base proton to Asp85 in the L-to-M process, which then triggers proton release from Glu204 to the extracellular surface. H-bonding of Arg82 and water molecules are involved in this process. Chloride can replace Asp85 in the D85T mutant, and this anion will be then transported instead of a proton. In L, structural perturbations are induced also around Asp96, through a string of H-bonding mediated by internal water molecules and peptide carbonyls in helices B and C, and Trp182 in helix F. These may cause the structural changes that occur later in the M-to-N process. Similar interactions, through internal water molecules and the peptide bonds in helices B and C, take place in bovine rhodopsin. They transduce changes across the membrane from the Schiff base to the cytoplasmic surface, where the activation of the transducin occurs.
Topics: Animals; Bacteriorhodopsins; Cattle; Hydrogen Bonding; Membrane Proteins; Rhodopsin; Signal Transduction
PubMed: 9133606
DOI: 10.1093/oxfordjournals.jbchem.a021602 -
BMC Bioinformatics Jan 2023Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in...
BACKGROUND
Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in eukaryotes, bacteria, and archaea. Haloarchaeal rhodopsins are Type-I microbial rhodopsin that elicits various light-driven functions like proton pumping, chloride pumping and Phototaxis behaviour. The industrial application of Ion-pumping Haloarchaeal rhodopsins is limited by the lack of full-length rhodopsin sequence-based classifications, which play an important role in Ion-pumping activity. The well-studied Haloarchaeal rhodopsin is a proton-pumping bacteriorhodopsin that shows promising applications in optogenetics, biosensitized solar cells, security ink, data storage, artificial retinal implant and biohydrogen generation. As a result, a low-cost computational approach is required to identify Ion-pumping Haloarchaeal rhodopsin sequences and its subtype.
RESULTS
This study uses a support vector machine (SVM) technique to identify these ion-pumping Haloarchaeal rhodopsin proteins. The haloarchaeal ion pumping rhodopsins viz., bacteriorhodopsin, halorhodopsin, xanthorhodopsin, sensoryrhodopsin and marine prokaryotic Ion-pumping rhodopsins like actinorhodopsin, proteorhodopsin have been utilized to develop the methods that accurately identified the ion pumping haloarchaeal and other type I microbial rhodopsins. We achieved overall maximum accuracy of 97.78%, 97.84% and 97.60%, respectively, for amino acid composition, dipeptide composition and hybrid approach on tenfold cross validation using SVM. Predictive models for each class of rhodopsin performed equally well on an independent data set. In addition to this, similar results were achieved using another machine learning technique namely random forest. Simultaneously predictive models performed equally well during five-fold cross validation. Apart from this study, we also tested the own, blank, BLAST dataset and annotated whole-genome rhodopsin sequences of PWS haloarchaeal isolates in the developed methods. The developed web server ( https://bioinfo.imtech.res.in/servers/rhodopred ) can identify the Ion Pumping Haloarchaeal rhodopsin proteins and their subtypes. We expect this web tool would be useful for rhodopsin researchers.
CONCLUSION
The overall performance of the developed method results show that it accurately identifies the Ionpumping Haloarchaeal rhodopsin and their subtypes using known and unknown microbial rhodopsin sequences. We expect that this study would be useful for optogenetics, molecular biologists and rhodopsin researchers.
Topics: Bacteria; Bacteriorhodopsins; Light; Protons; Rhodopsin; Rhodopsins, Microbial; Machine Learning
PubMed: 36707759
DOI: 10.1186/s12859-023-05138-x -
Journal of Biomolecular NMR Jan 2020Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from...
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, C, C, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
Topics: Algorithms; Amino Acid Sequence; Bacteriorhodopsins; Models, Molecular; Nanoparticles; Peptide Mapping
PubMed: 31754899
DOI: 10.1007/s10858-019-00289-7 -
Biochimica Et Biophysica Acta Aug 2000A variety of neutron, X-ray and electron diffraction experiments have established that the transmembrane regions of bacteriorhodopsin undergo significant light-induced... (Review)
Review
A variety of neutron, X-ray and electron diffraction experiments have established that the transmembrane regions of bacteriorhodopsin undergo significant light-induced changes in conformation during the course of the photocycle. A recent comprehensive electron crystallographic analysis of light-driven structural changes in wild-type bacteriorhodopsin and a number of mutants has established that a single, large protein conformational change occurs within 1 ms after illumination, roughly coincident with the time scale of formation of the M(2) intermediate in the photocycle of wild-type bacteriorhodopsin. Minor differences in structural changes that are observed in mutants that display long-lived M(2), N or O intermediates are best described as variations of one fundamental type of conformational change, rather than representing structural changes that are unique to the optical intermediate that is accumulated. These observations support a model for the photocycle of wild-type bacteriorhodopsin in which the structures of the initial state and the early intermediates (K, L and M(1)) are well approximated by one protein conformation in which the Schiff base has extracellular accessibility, while the structures of the later intermediates (M(2), N and O) are well approximated by the other protein conformation in which the Schiff base has cytoplasmic accessibility.
Topics: Bacteriorhodopsins; Crystallography; Cytoplasm; Hydrogen-Ion Concentration; Light; Models, Molecular; Mutation; Photochemistry; Protein Conformation; Structure-Activity Relationship; Temperature
PubMed: 10984597
DOI: 10.1016/s0005-2728(00)00136-5 -
Biochimica Et Biophysica Acta Aug 2006The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane... (Review)
Review
The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.
Topics: Bacteriorhodopsins; Biological Transport; Hydrogen Bonding; Kinetics; Light; Models, Biological; Protons
PubMed: 16376293
DOI: 10.1016/j.bbabio.2005.11.003 -
Biochimica Et Biophysica Acta Aug 2000The folding mechanism of integral membrane proteins has eluded detailed study, largely as a result of the inherent difficulties in folding these proteins in vitro. The... (Review)
Review
The folding mechanism of integral membrane proteins has eluded detailed study, largely as a result of the inherent difficulties in folding these proteins in vitro. The seven-transmembrane helical protein bacteriorhodopsin has, however, allowed major advances to be made, not just on the folding of this particular protein, but also on the factors governing folding of transmembrane alpha-helical proteins in general. This review focusses on kinetic and equilibrium studies of bacteriorhodopsin folding in vitro. It covers what is currently known about secondary and tertiary structure formation as well as the events accompanying retinal binding, for protein in detergent and lipid systems, including native membrane samples.
Topics: Bacteriorhodopsins; Lipid Bilayers; Membrane Lipids; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary
PubMed: 10984586
DOI: 10.1016/s0005-2728(00)00125-0 -
Nature Communications Mar 2024Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it...
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.
Topics: Bacteriorhodopsins; Photochemistry; Proton Pumps; Light
PubMed: 38459010
DOI: 10.1038/s41467-024-46061-w -
Biochimica Et Biophysica Acta Aug 2000Atomic force microscopy (AFM) allows the observation of surface structures of purple membrane (PM) in buffer solution with subnanometer resolution. This offers the... (Review)
Review
Atomic force microscopy (AFM) allows the observation of surface structures of purple membrane (PM) in buffer solution with subnanometer resolution. This offers the possibility to classify the major conformations of the native bacteriorhodopsin (BR) surfaces and to map the variability of individual polypeptide loops connecting transmembrane alpha-helices of BR. The position, the variability and the flexibility of these loops depend on the packing arrangement of BR molecules in the lipid bilayer with significant differences observed between the trigonal and orthorhombic crystal forms. Cleavage of the Schiff base bond leads to a disassembly of the trigonal PM crystal, which is restored by regenerating the bleached PM. The combination of single molecule AFM imaging and single molecule force-spectroscopy provides an unique insight into the interactions between individual BR molecules and the PM, and between secondary structure elements within BR.
Topics: Bacteriorhodopsins; Crystallization; Halobacterium; Intracellular Membranes; Microscopy, Atomic Force; Models, Molecular; Molecular Structure; Purple Membrane
PubMed: 10984588
DOI: 10.1016/s0005-2728(00)00127-4 -
Journal of Bacteriology Mar 1993Site-specific mutagenesis has identified amino acids involved in bR proton transport. Biophysical studies of the mutants have elucidated the roles of two... (Review)
Review
Site-specific mutagenesis has identified amino acids involved in bR proton transport. Biophysical studies of the mutants have elucidated the roles of two membrane-embedded residues: Asp-85 serves as the acceptor for the proton from the isomerized retinylidene Schiff base, and Asp-96 participates in reprotonation of this group. The functions of Arg-82, Leu-93, Asp-212, Tyr-185, and other residues that affect bR properties when substituted are not as well understood. Structural characterization of the mutant proteins will clarify the effects of substitutions at these positions. Current efforts in the field remain directed at understanding how retinal isomerization is coupled to proton transport. In particular, there has been more emphasis on determining the structures of bR and its photointermediates. Since well-ordered crystals of bR have not been obtained, continued electron diffraction studies of purple membrane offer the best opportunity for structure refinement. Other informative techniques include solid-state nuclear magnetic resonance of isotopically labeled bR (56) and electron paramagnetic resonance of bR tagged with nitroxide spin labels (2, 3, 13, 15). Site-directed mutagenesis will be essential in these studies to introduce specific sites for derivatization with structural probes and to slow the decay of intermediates. Thus, combining molecular biology and biophysics will continue to provide solutions to fundamental problems in bR.
Topics: Amino Acid Sequence; Bacteriorhodopsins; Biological Transport; Halobacterium salinarum; Light; Molecular Sequence Data; Mutagenesis, Site-Directed; Protein Structure, Secondary; Protons
PubMed: 8383660
DOI: 10.1128/jb.175.6.1555-1560.1993