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Current Opinion in Structural Biology Aug 2001High-resolution maps from X-ray diffraction of bacteriorhodopsin and some of its photointermediates have yielded insights into how the isomerization of the bound retinal... (Review)
Review
High-resolution maps from X-ray diffraction of bacteriorhodopsin and some of its photointermediates have yielded insights into how the isomerization of the bound retinal drives ion transport. Although important mechanistic details are still undecided, the events of the photochemical cycle are now understood to reflect changes in specific hydrogen bonds of protein groups and bound water molecules in response to motions of the retinal chain.
Topics: Bacteriorhodopsins; Ion Transport; Isomerism; Light; Membrane Proteins; Models, Structural; Protein Conformation; Proton Pumps; Purple Membrane; Retinaldehyde; Water; X-Ray Diffraction
PubMed: 11495732
DOI: 10.1016/s0959-440x(00)00226-8 -
Annual Review of Physiology 2004Fourier transform infrared and Raman spectroscopy, solid-state NMR, and X-ray crystallography have contributed detailed information about the structural changes in the... (Review)
Review
Fourier transform infrared and Raman spectroscopy, solid-state NMR, and X-ray crystallography have contributed detailed information about the structural changes in the proton transport cycle of the light-driven pump, bacteriorhodopsin. The results over the past few years add up to a step-by-step description of the configurational changes of the photoisomerized retinal, how these changes result in internal proton transfers and the release of a proton to the extracellular surface and uptake on the other side, as well as the conservation and transformation of excess free energy during the cycle.
Topics: Bacteriorhodopsins; Biological Transport; Extracellular Space; Isomerism; Light; Molecular Structure; Protons; Schiff Bases
PubMed: 14977418
DOI: 10.1146/annurev.physiol.66.032102.150049 -
International Review of Cytology 1999Bacteriorhodopsin is a seven-transmembrane helical protein that contains all-trans retinal. In this light-driven pump, a reaction cycle initiated by photoisomerization... (Review)
Review
Bacteriorhodopsin is a seven-transmembrane helical protein that contains all-trans retinal. In this light-driven pump, a reaction cycle initiated by photoisomerization to 13-cis causes translocation of a proton across the membrane. Local changes in the geometry of the protonated Schiff base and the proton acceptor Asp85, and the proton conductivities of the half channels that lead from this active site to the two membrane surfaces, interact so as to allow timely proton transfers that result in proton release on the extracellular side and proton uptake on the cytoplasmic one. The details of the steps in this photocycle, and the underlying principles that ensure unidirectionality of the movement of a proton across the protein, provide strong clues to how ion pumps function.
Topics: Bacteriorhodopsins; Cytoplasm; Protein Conformation; Protons; Schiff Bases
PubMed: 10212980
DOI: 10.1016/s0074-7696(08)62418-3 -
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 -
Current Microbiology Aug 2017Haloarchaea are known for its adaptation in extreme saline environment. Halophilic archaea produces carotenoid pigments and proton pumps to protect them from extremes of... (Review)
Review
Haloarchaea are known for its adaptation in extreme saline environment. Halophilic archaea produces carotenoid pigments and proton pumps to protect them from extremes of salinity. Bacteriorhodopsin (bR) is a light-driven proton pump that resides in the membrane of haloarchaea Halobacterium salinarum. The photocycle of Bacteriorhodopsin passes through several states from K to O, finally liberating ATP for host's survival. Extensive studies on Bacteriorhodopsin photocycle has provided in depth knowledge on their sequential mechanism of converting solar energy into chemical energy inside the cell. This ability of Bacteriorhodopsin to harvest sunlight has now been experimented to exploit the unexplored and extensively available solar energy in various biotechnological applications. Currently, bacteriorhodopsin finds its importance in dye-sensitized solar cell (DSSC), logic gates (integrated circuits, IC's), optical switching, optical memories, storage devices (random access memory, RAM), biosensors, electronic sensors and optical microcavities. This review deals with the optical and electrical applications of the purple pigment Bacteriorhodopsin.
Topics: Bacteriorhodopsins; Chemical Phenomena; Electronics; Halobacterium salinarum; Optics and Photonics; Solar Energy
PubMed: 28573340
DOI: 10.1007/s00284-017-1271-5 -
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 -
Nature Aug 2000
Topics: Bacteriorhodopsins; Cell Membrane; Proton Pumps; Retinaldehyde
PubMed: 10949279
DOI: 10.1038/35020654 -
Applied Microbiology and Biotechnology Jun 2000Bacteriorhodopsin (BR) is the key protein for the halobacterial photosynthetic capabilities and is one of the very rare molecules which occur in crystalline form in... (Review)
Review
Bacteriorhodopsin (BR) is the key protein for the halobacterial photosynthetic capabilities and is one of the very rare molecules which occur in crystalline form in nature. Since its discovery, which was reported in 1971, many efforts have been made to exploit the obvious technical potential of this molecule. Successful application of gene technology methods for the modification of the physical function of a biomolecule was first demonstrated with BR. This approach points the way to a new class of materials derived from evolutionary optimized biomaterials by genetic re-engineering. Mutated BRs proved to have significant advantages over the wild type in optical applications. The current status of potential technical applications of BR is reviewed. BR is employed as a photoelectric, photochromic or energy-converting element. First systems now exist which demonstrate the successful integration of this new material into existing technologies. Analyzing the patents filed, which claim the processing or application of BR, gives an indication to areas where further technical uses are to be expected in the near future.
Topics: Bacteriorhodopsins; Electronics; Holography; Mutation; Optics and Photonics; Patents as Topic; Protein Engineering; Transducers
PubMed: 10919318
DOI: 10.1007/s002539900311 -
Trends in Biotechnology Sep 2002Bacteriorhodopsin (BR) is the photoactive proton pump found in the purple membrane of the salt marsh archaeon Halobacterium salinarum. Evolution has optimized this... (Review)
Review
Bacteriorhodopsin (BR) is the photoactive proton pump found in the purple membrane of the salt marsh archaeon Halobacterium salinarum. Evolution has optimized this protein for high photochemical efficiency, thermal stability and cyclicity, as the organism must be able to function in a hot, stagnant and resource-limited environment. Photonic materials generated via organic chemistry have yet to surpass the native protein in terms of quantum efficiency or cyclicity. However, the native protein still lacks the overall efficiency necessary for commercial viability and virtually all successful photonic devices using bacteriorhodopsin are based on chemical or genetic variants of the native protein. We show that genetic engineering can provide significant improvement in the device capabilities of proteins and, in the case of bacteriorhodopsin, a 700-fold improvement has been realized in volumetric data storage. We conclude that semi-random mutagenesis and directed evolution will play a prominent role in future efforts in bioelectronic optimization.
Topics: Bacteriorhodopsins; Biocompatible Materials; Directed Molecular Evolution; Electrochemistry; Electronics; Halobacterium salinarum; Imaging, Three-Dimensional; Information Storage and Retrieval; Light; Miniaturization; Mutagenesis, Site-Directed; Nanotechnology; Optics and Photonics; Photochemistry; Protein Engineering; Quality Control
PubMed: 12175770
DOI: 10.1016/s0167-7799(02)02023-1 -
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