Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. (1/1144)
The high-affinity cation-binding sites of bacteriorhodopsin (bR) were examined by solid-state 13C NMR of samples labeled with [3-13C]Ala and [1-13C]Val. We found that the 13C NMR spectra of two kinds of blue membranes, deionized (pH 4) and acid blue at pH 1.2, were very similar and different from that of the native purple membrane. This suggested that when the surface pH is lowered, either by removal of cations or by lowering the bulk pH, substantial change is induced in the secondary structure of the protein. Partial replacement of the bound cations with Na+, Ca2+, or Mn2+ produced additional spectral changes in the 13C NMR spectra. The following conclusions were made. First, there are high-affinity cation-binding sites in both the extracellular and the cytoplasmic regions, presumably near the surface, and one of the preferred cation-binding sites is located at the loop between the helix F and G (F-G loop) near Ala196, consistent with the 3D structure of bR from x-ray diffraction and cryoelectron microscopy. Second, the bound cations undergo rather rapid exchange (with a lifetime shorter than 3 ms) among various types of cation-binding sites. As expected from the location of one of the binding sites, cation binding induced conformational alteration of the F-G interhelical loop. (+info)Distortion of the L-->M transition in the photocycle of the bacteriorhodopsin mutant D96N: a time-resolved step-scan FTIR investigation. (2/1144)
The D96N mutant of bacteriorhodopsin has often been taken as a model system to study the M intermediate of the wild type photocycle due to the long life time of the corresponding intermediate of the mutant. Using time-resolved step-scan FTIR spectroscopy in combination with a sample changing wheel we investigated the photocycle of the mutant with microsecond time resolution. Already after several microseconds an intermediate similar to the MN state is observed, which contrasts with the M state of the wild type protein. At reduced hydration M and N intermediates similar to those of wild type BR can be detected. These results have a bearing on the interpretation of the photocycle of this mutant. A mechanism is suggested for the fast rise of MN which provides some insight into the molecular events involved in triggering the opening of the cytosolic channel also of the wild type protein. (+info)Molecular modeling of mu opioid receptor and receptor-ligand interaction. (3/1144)
AIM: To construct the 3D structural model of mu opioid receptor (mu OR) and study the interaction between mu OR and fentanyl derivatives. METHODS: The 3D structure of mu OR was modeled using the bacteriorhodopsin (bRh) as a template, in which the alignments of transmembrane (TM) of bRh and mu OR were achieved by scoring the alignment between the amino acid sequence of mu OR and the structure of bRh. The fentanyl derivatives were docked into the 7 helices of mu OR and the binding energies were calculated. RESULTS: (1) The receptor-ligand interaction models were obtained for fentanyl derivatives. (2) In these models, the fundamental binding sites were possibly Asp147 and His297. The negatively charged oxygen of Asp147 and the positively charged ammonium group of ligand formed the potent electrostatic and hydrogen-binding interactions. Whereas the interactions between the positively charged nitrogen of His297 and the carbonyl oxygen of ligand were weak. In addition, there were some pi-pi interactions between the receptor and the ligand. (3) The binding energies of the receptor-ligand complexes had a good correlation with the analgesic activities (-lg ED50) of the fentanyl derivatives. CONCLUSION: This model is helpful for understanding the receptor-ligand interaction and for designing novel mu OR selective ligands. (+info)Molecular modeling of interaction between delta opioid receptor and 3-methylfentanylisothiocyanate. (4/1144)
AIM: To construct a 3D structural model of delta opioid receptor (delta OR) and study its interaction with 3-methylfentanylisothiocyanate (SuperFIT). METHODS: Using the bacteriohodopsin as a template, the 3D structure of delta OR was modeled; SuperFIT was docked into its inside. RESULTS: The interaction model between delta OR and (3R, 4S)-SuperFIT was achieved, in which the important binding sites possibly were Asp128, Ser106, Phe104, Tyr308, and Pro315. Asp128 formed the electrostatic and hydrogen-binding interactions with the protonated nitrogen on piperidine of the ligand. Ser106 formed the electrostatic interaction with the N atom of isothiocyano group of the ligand; whereas Phe104, Tyr308, and Pro315 formed the hydrophobic interactions with the S atom of isothiocyano group. In addition, there were some other interactions between delta OR and the ligand. CONCLUSION: The residues Phe104, Tyr308, Pro315, and Ser106 of delta OR are crucial to the delta selectivity of the ligand, which is beneficial for designing novel delta-selective ligand. (+info)Interpretation of the spatial charge displacements in bacteriorhodopsin in terms of structural changes during the photocycle. (5/1144)
We have recently introduced a method, made possible by an improved orienting technique using a combination of electric and magnetic fields, that allows the three-dimensional detection of the intramolecular charge displacements during the photocycle of bacteriorhodopsin. This method generates electric asymmetry, a prerequisite for the detection of electric signal on the macroscopic sample, in all three spatial dimensions. Purple membrane fragments containing bacteriorhodopsin were oriented so that their permanent electric dipole moment vectors were perpendicular to the membrane plane and pointed in the same direction. The resulting cylindrical symmetry was broken by photoselection, i. e., by flash excitation with low intensity linearly polarized light. From the measured electric signals, the three-dimensional motion of the electric charge center in the bacteriorhodopsin molecules was calculated for the first 400 microseconds. Simultaneous absorption kinetic recording provided the time-dependent concentrations of the intermediates. Combining the two sets of data, we determined the discrete dipole moments of intermediates up to M. When compared with the results of current molecular dynamics calculations, the data provided a decisive experimental test for selecting the optimal theoretical model for the proton transport and should eventually lead to a full description of the mechanism of the bacteriorhodopsin proton pump. (+info)Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. (6/1144)
In dark-adapted bacteriorhodopsin (bR) the retinal moiety populates two conformers: all-trans and (13,15)cis. Here we examine factors influencing the thermodynamic equilibrium and conformational transition between the two forms, using molecular mechanics and dynamics calculations. Adiabatic potential energy mapping indicates that whereas the twofold intrinsic torsional potentials of the C13==C14 and C15==N16 double bonds favor a sequential torsional pathway, the protein environment favors a concerted, bicycle-pedal mechanism. Which of these two pathways will actually occur in bR depends on the as yet unknown relative weight of the intrinsic and environmental effects. The free energy difference between the conformers was computed for wild-type and modified bR, using molecular dynamics simulation. In the wild-type protein the free energy of the (13,15)cis retinal form is calculated to be 1.1 kcal/mol lower than the all-trans retinal form, a value within approximately kBT of experiment. In contrast, in isolated retinal the free energy of the all-trans state is calculated to be 2.1 kcal/mol lower than (13,15)cis. The free energy differences are similar to the adiabatic potential energy differences in the various systems examined, consistent with an essentially enthalpic origin. The stabilization of the (13,15)cis form in bR relative to the isolated retinal molecule is found to originate from improved protein-protein interactions. Removing internal water molecules near the Schiff base strongly stabilizes the (13,15)cis form, whereas a double mutation that removes negative charges in the retinal pocket (Asp85 to Ala; Asp212 to Ala) has the opposite effect. (+info)Chloride ion binding to bacteriorhodopsin at low pH: an infrared spectroscopic study. (7/1144)
Bacteriorhodopsin (bR) and halorhodopsin (hR) are light-induced ion pumps in the cell membrane of Halobacterium salinarium. Under normal conditions bR is an outward proton transporter, whereas hR is an inward Cl- transporter. There is strong evidence that at very low pH and in the presence of Cl-, bR transports Cl- ions into the cell, similarly to hR. The chloride pumping activity of bR is connected to the so-called acid purple state. To account for the observed effects in bR a tentative complex counterion was suggested for the protonated Schiff base of the retinal chromophore. It would consist of three charged residues: Asp-85, Asp-212, and Arg-82. This quadruplet (including the Schiff base) would also serve as a Cl- binding site at low pH. We used Fourier transform infrared difference spectroscopy to study the structural changes during the transitions between the normal, acid blue, and acid purple states. Asp-85 and Asp-212 were shown to participate in the transitions. During the normal-to-acid blue transition, Asp-85 protonates. When the pH is further lowered in the presence of Cl-, Cl- binds and Asp-212 also protonates. The binding of Cl- and the protonation of Asp-212 occur simultaneously, but take place only when Asp-85 is already protonated. It is suggested that HCl is taken up in undissociated form in exchange for a neutral water molecule. (+info)Time-resolved absorption and photothermal measurements with sensory rhodopsin I from Halobacterium salinarum. (8/1144)
An expansion accompanying the formation of the first intermediate in the photocycle of transducer-free sensory rhodopsin I (SRI) was determined by means of time-resolved laser-induced optoacoustic spectroscopy. For the native protein (SRI-WT), the absolute value of the expansion is approximately 5.5 mL and for the mutant SRI-D76N, approximately 1.5 mL per mol of phototransformed species (in 0.5 M NaCl), calculated by using the formation quantum yield for the first intermediate (S610) of Phi610 = 0.4 +/- 0.05 for SRI-WT and 0.5 +/- 0.05 for SRI-D76N, measured by laser-induced optoacoustic spectroscopy and by laser flash photolysis. The similarity in Phi610 and in the determined value of the energy level of S610, E610 = (142 +/- 12) kJ/mol for SRI-WT and SRI-D76N indicates that Asp76 is not directly involved in the first step of the phototransformation. The increase with pH of the magnitude of the structural volume change for the formation of S610 in SRI-WT and in SRI-D76N upon excitation with 580 nm indicates also that amino acids other than Asp76, and other than those related to the Schiff base, are involved in the process. The difference in structural volume changes as well as differences in the activation parameters for the S610 decay should be attributed to differences in the rigidity of the cavity surrounding the chromophore. Except for the decay of the first intermediate, which is faster than in the SRI-transducer complex, the rate constants of the photocycle for transducer-free SRI in detergent suspension are strongly retarded with respect to wild-type membranes (this comparison should be done with great care because the preparation of both samples is very different). (+info)Bacteriorhodopsins are a type of protein found in certain archaea, a group of single-celled microorganisms. They are most commonly found in the archaea of the genus Halobacterium, which live in extremely salty environments such as salt lakes and solar salterns.
Bacteriorhodopsins are embedded in the cell membrane of these archaea and contain a retinal molecule, which is a type of vitamin A derivative. When exposed to light, the retinal changes shape, which causes a conformational change in the bacteriorhodopsin protein. This leads to the pumping of protons (hydrogen ions) across the cell membrane, generating a proton gradient.
The proton gradient created by bacteriorhodopsins can be used to generate ATP, which is the main energy currency of the cell. Bacteriorhodopsins are therefore involved in energy production in these archaea and are often referred to as light-driven proton pumps. They have also been studied extensively for their potential applications in optoelectronics and biotechnology.
Bacteriorhodopsin
Archaea
Proton pump
Model lipid bilayer
Lysosomal cystine transporter family
Retinal
Rhodopsin
Har Gobind Khorana
Opsin
Coherent control
Dieter Oesterhelt
Microbial rhodopsin
Proteorhodopsin
Pyroglutamic acid
Site-directed spin labeling
Halobacteriaceae
Halobacteriales
Spizellomyces punctatus
Photoacoustic effect
Phototaxis
Bis-tris propane
Electrochemical gradient
Baruch Fischer
Laura Eisenstein
Bacterial motility
George W. Rayfield
Adaptation (eye)
Halobacterium
Shiladitya DasSarma
Purple Earth hypothesis
Bacteriorhodopsin - Wikipedia
Bacteriorhodopsin Analogs from Diphenylpolyene Chromophores¶
Photobleaching of Bacteriorhodopsin Solubilized with Triton X-100
Bacteriorhodopsin - Proteopedia, life in 3D
Bacteriorhodopsin
The use of bacteriorhodopsin as a dynamic holographic media. Esprit basic research programme. Project no. 6863, POPAM</em>...
Vibrational Spectroscopy of Bacteriorhodopsin Mutants: Chromophore Isomerization Perturbs Tryptophan-86<...
The photocycle and ultrafast vibrational dynamics of bacteriorhodopsin in lipid nanodiscs :: MPG.PuRe
Holdings: Zeitaufgelöste Laser induzierte optoakustische Spektroskopie des photochromen Systems Bacteriorhodopsin.
DNP enhanced frequency-selective TEDOR experiments in bacteriorhodopsin | Griffin Group
RESONANCE RAMAN STUDIES OF BACTERIORHODOPSIN ANALOGUES<...
Genetic Transfer of the Pigment Bacteriorhodopsin Into the Eukaryote Schizosaccharomyces-Pombe - edoc
SFB749 - Polarization effects stabilize bacteriorhodopsin's chromophore binding pocket: A molecular dynamics study
Enthalpy changes during the photochemical cycle of bacteriorhodopsin<...
Efficient in-gel digestion procedure using 5-cyclohexyl-1-pentyl-beta-D-maltoside as an additive for gel-based membrane...
PDB 1PXR | Chain STRUCTURE OF PRO50ALA MUTANT OF BACTERIORHODOPSIN | 1PXR A | 3D Structure | Cancer
Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle - Mendeley Data
pigmentation - How does bacteriorhodopsin differ from the rhodopsin present in mammalian eyes? - Biology Stack Exchange
Bacteriorhodopsin: A high-resolution structural view of vectorial proton transport - Fingerprint - UTMB Health Research...
Light-driven activation of mitochondrial proton-motive force improves motor behaviors in a Drosophila model of Parkinson's...
A MICROSECOND KINETIC STUDY OF THE PHOTOGENERATED MEMBRANE POTENTIAL OF BACTERIORHODOPSIN WITH A FAST RESPONDING DYE<...
The effect of temperature and protein content on the dispersive properties of bacteriorhodopsin from H. halobium in...
PDB 6G7J | Chain RETINAL ISOMERIZATION IN BACTERIORHODOPSIN REVEALED BY A FEMTOSECOND X-RAY LASER: 457-646 FS STATE STRUCTURE |...
Localisation of structural changes of the alpha-helices during the photoreaction of bacteriorhodopsin by FTIR-difference...
Examining the Dynamic Evolution of G Protein-Coupled Receptors | SpringerLink
Staff Listing - The University of Nottingham
CHRNS SURF Presentations | NIST
SCOPe 2.08: Domain d1tn5a : 1tn5 A
Proton pump6
- Bacteriorhodopsin is a light-driven proton pump. (wikipedia.org)
- Xanthorhodopsin: a bacteriorhodopsin-like proton pump with a carotenoid antenna. (proteopedia.org)
- Abstract- Bacteriorhodopsin is a light activated proton pump which generates proton and electric gradients across the cytoplasmic membrane of Halobacterium halobium. (biu.ac.il)
- bacteriorhodopsin-like proton pump from a eukaryote. (springer.com)
- Bacteriorhodopsin is a retinal-containing protein that functions as a light-driven proton pump. (ias.ac.in)
- In the early 1970s , the first described member of this protein family is the light-driven proton-pump Bacteriorhodopsin from Halobacterium salinarum [2]. (hu-berlin.de)
Retinal4
- The nine stages are: bR + photon → K ⇌ L ⇌ M1 ⇌ M2 ⇌ M2' ⇌ N ⇌ N' ⇌ O ⇌ bR Bacteriorhodopsin in the ground state absorbs a photon and the retinal changes isomerization from all-trans 15-anti to the strained 13-cis 15-anti in the K state. (wikipedia.org)
- ABSTRACT BR-photoreaction-at various pHs-in-0MKCl-2022elThe proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with telThe proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. (mendeley.com)
- The triggering of the potential is not the formation of the M 412 intermediate, which was hitherto considered to be the first species in the bacteriorhodopsin cycle which has an unprotonated Schiff base linkage at the retinal chromophore. (biu.ac.il)
- Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukaryotic G-protein-coupled receptors. (springer.com)
Photocycle3
- 2014). The photocycle and ultrafast vibrational dynamics of bacteriorhodopsin in lipid nanodiscs. (mpg.de)
- The photocycle and vibrational dynamics of bacteriorhodopsin in a lipid nanodisc microenvironment have been studied by steady-state and time-resolved spectroscopies. (mpg.de)
- By comparing the formation kinetics of the potential to those of the long‐lived intermediate species in the bacteriorhodopsin photocycle, M 412 , both in H 2 O and 2 H 2 O suspensions, we can draw the following conclusion: the electric potential onset time is 20 μs after initiation of the illumination. (biu.ac.il)
Protein9
- Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by haloarchaea, a class of the Euryarchaeota. (wikipedia.org)
- Bacteriorhodopsin is a 27 kDa integral membrane protein usually found in two-dimensional crystalline patches known as "purple membrane", which can occupy almost 50% of the surface area of the archaeal cell. (wikipedia.org)
- Bacteriorhodopsin is synthesized as a protein precursor, known as bacterio-opsin, which is extensively modified after translation. (wikipedia.org)
- Both rhodopsin and bacteriorhodopsin belong to the 7TM receptor family of proteins, but rhodopsin is a G protein-coupled receptor and bacteriorhodopsin is not. (wikipedia.org)
- Chromophore-modified bacteriorhodopsin (bR) analogs are prepared, to study the nature of chromophore-protein interaction as well as to develop new bR analogs that can find applications as photoactive element in molecular electronic devices. (bioone.org)
- Bacteriorhodopsin (Br) is a membrane protein in Archaea which moves protons across the cell membrane [1] . (proteopedia.org)
- The key difference between them is that rhodopsin is a G-protein-coupled receptor , and this is not the case with bacteriorhodopsin. (stackexchange.com)
- Using this approach, he discovered the sequence of the protein bacteriorhodopsin, among others. (chemistryviews.org)
- The protein Bacteriorhodopsin from Halobacterium absorbs light and converts it into energy for the metabolism of the cell: The colour of the bacteriorhodopsin changes from violet to yellow in the process. (vaam.de)
Membrane5
- We have used a capacitor microphone calorimeter to measure rapid enthalpy changes that occur when bacteriorhodopsin-containing membrane fragments are excited with short flashes of light. (illinois.edu)
- The excel file ' BR-photoreaction-at various Temperatures-at-pH5.9-20220420b.xlsx' contains raw data of flash-induced absorption changes in bacteriorhodopsin (bR) at various temperatures in low-salt membrane suspensions (5 mM Mes) at pH 5.9. (mendeley.com)
- In this study, a dye whose fluorescence intensity responds rapidly to membrane potential was used to follow the evolution of the potential on liposomes reconstituted with bacteriorhodopsin, in the microseconds time domain. (biu.ac.il)
- Here we investigate the membrane properties reported by the light-induced proton pumping activity of bacteriorhodopsin (bR) reconstituted in three vesicle systems of different membrane composition. (dtu.dk)
- They are critical in understanding the function of various proton pumps such as bacteriorhodopsin (BR) and cytochrome oxidase C. Their light or redox driven action and unidirectional proton pumping mechanism motivates the structural study of these membrane proteins. (lu.se)
Halobacterium2
- Bacteriorhodopsin is a light-driven H+ ion transporter found in some haloarchaea, most notably Halobacterium salinarum (formerly known as syn. (wikipedia.org)
- After the discovery of the bacteriorhodopsin from Halobacterium salinarum , a new field of research developed: optogenetics. (vaam.de)
Molecule3
- Cleavage of the signal peptide, the first 13 amino acids at the N-terminus, and the conversion of residue Gln14 to pyroglutamate Removal of residue Asp262 at the C-terminus Bacteriorhodopsin molecule is purple and is most efficient at absorbing green light (in the wavelength range 500-650 nm). (wikipedia.org)
- Bacteriorhodopsin, the molecule that essentially defined your career, was discovered in San Francisco. (mpg.de)
- Featured Molecule: Bacteriorhodopsin http://www.bio.com/Redirectors/LinkRedirect03_19.jhtml?link=7 Photosynthesis requires a complex collection of molecular antennas and photosystems. (bio.net)
Rhodopsin4
- Bacteriorhodopsin belongs to the microbial rhodopsin family. (wikipedia.org)
- however, the functions of rhodopsin and bacteriorhodopsin are different, and there is limited similarity in their amino acid sequences. (wikipedia.org)
- These results suggest that the binding site of bacteriorhodopsin near the Schiff base moiety is different from that of rhodopsin. (elsevierpure.com)
- How does bacteriorhodopsin differ from the rhodopsin present in mammalian eyes? (stackexchange.com)
Schiff1
- The protonated Schiff base ‐C=NH‐ stretching frequency of 5.6‐dihydro‐bR lies at 1660 cm ‐1 which is unusually high for a bacteriorhodopsin based pigment. (elsevierpure.com)
Archaea2
- By expressing bacteriorhodopsin, the archaea cells are able to synthesise ATP in the absence of a carbon source. (wikipedia.org)
- Since their recent discovery, several other bacteria and archaea have been found to have bacteriorhodopsins with different adsorption spectra, allowing them to live at different water depths where the wavelengths of light available are filtered as depth increases. (dummies.com)
Lipid2
- In the current studies, we examined the effects of hexagonal lattice formation with lipid membranes on the structural stability of native bacteriorhodopsin (bR). (bioone.org)
- Oriented Incorporation of Bacteriorhodopsin into the Lipid Shell of Phospholipid-coated Polymer Particles. (mpg.de)
Channelrhodopsin1
- After 2000, the bacteriorhodopsin-related light-sensitive pump halorhodopsin and the channelrhodopsin discovered by Peter Hegemann was introduced into tissue using genetic engineering. (mpg.de)
Rhodopsins1
- Bacteriorhodopsin is similar to vertebrate rhodopsins, the pigments that sense light in the retina. (wikipedia.org)
Chromophore2
- Abstract- We present the results of resonance Raman measurements on a series of bacteriorhodopsin (bR) analogues formed from synthetic retinals which have replaced the native chromophore in the active site. (elsevierpure.com)
- Here, we show for the case of bacteriorhodopsin (BR) that MM−MD descriptions with standard nonpolarizable force fields entail a collapse of the chromophore binding pocket. (sfb749.de)
Halorhodopsin1
- Halorhodopsin is a molecular pump similar to bacteriorhodopsin. (mpg.de)
Dieter Oesterhelt1
- The discovery of the import role of bacteriorhodopsin from H. salinarum was made by the biochemist Dieter Oesterhelt in 1971. (vaam.de)
Abstract1
- abstract = "Fourier transform infrared difference spectra have been obtained for the bR → K and bR → M photoreactions of bacteriorhodopsin mutants with Phe replacements for Trp residues 10, 12, 80, 86, 138, 182, and 189 and Cys replacements for Trp residues 137 and 138. (syr.edu)
Structural1
- inproceedings{Hauser1997Local-16461, year={1997}, title={Localisation of structural changes of the alpha-helices during the photoreaction of bacteriorhodopsin by FTIR-difference-spectroscopy of site-directed isotope labelled T46C-BR-mutants}, isbn={0-7923-4685-8}, publisher={Kluwer Academic}, address={Dordrecht [u.a.]}, booktitle={Spectroscopy of biological molecules : modern trends. (uni-konstanz.de)
Absorption1
- Resonance Raman and femtosecond dynamic absorption spectroscopy are being used to elucidate the molecular mechanism of bacteriorhodopsin. (ias.ac.in)
Carbon1
- The exact mechanisms of bacteriorhodopsin-driven carbon fixation are still being studied. (dummies.com)
Amino1
- Amino acid sequence of bacteriorhodopsin. (chemistryviews.org)
Absence1
- Proton translocation by bacteriorhodopsin in the absence of substantial conformational changes. (mpg.de)
Molecular1
- These results are integrated into an explicit molecular model (the C-T Model) for proton pumping in bacteriorhodopsin. (ias.ac.in)
Mechanism1
- The proton-conducting pathway of bacteriorhodopsin (BR) contains at University, PO Box 124 least nine internal water molecules that are thought to be key players in SE-22100 Lund, Sweden the proton translocation mechanism. (lu.se)
Essentially1
- The downward shift upon deuteration is 16 cm ‐1 , essentially identical to that measured for bacteriorhodopsin. (elsevierpure.com)
Title1
- title = "The use of bacteriorhodopsin as a dynamic holographic media. (dtu.dk)
Systems1
- Holdings: Zeitaufgelöste Laser induzierte optoakustische Spektroskopie des photochromen Systems Bacteriorhodopsin. (fz-juelich.de)