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Mostafa HIA. Detection of bacteriorhodopsin trimeric rotation at thermal phase transitions of purple membrane in suspension. Biophys Chem 2023; 300:107074. [PMID: 37421867 DOI: 10.1016/j.bpc.2023.107074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/24/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
Bacteriorhodopsin (bR) of purple membrane (PM) is a retinal protein that forms aggregates in the form of trimers constituting, together with archaeal lipids, the crystalline structure of PM. The rotary motion of bR inside PM may be pertinent in understanding the essence of the crystalline lattice. An attempt has been made to determine the rotation of bR trimers which has been found to be detected solely at thermal phase transitions of PM, namely lipid, crystalline lattice and protein melting phase transitions. The temperature dependences of dielectric versus electronic absorption spectra of bR have been determined. The results suggest that the rotation of bR trimers, together with concomitant bending of PM, are most likely brought by structural changes in bR which might be driven by retinal isomerization and mediated by lipid. The rupturing of the lipid-protein contact might consequently lead to rotation of trimers associated with bending, curling or vesicle formation of PM. So the retinal reorientation may underlie the concomitant rotation of trimers. Most importantly, rotation of trimers might play a role, in terms of the essence of the crystalline lattice, in the functional activity of bR and may serve physiological relevance.
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Affiliation(s)
- Hamdy I A Mostafa
- Department of Biophysics, Faculty of Science, Cairo University, 11757 Giza, Egypt.
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2
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Ghimire GD, Sugiyama H, Sonoyama M, Mitaku S. Regeneration of Bacteriorhodopsin from Thermally Unfolded Bacterio-Opsin and All-transRetinal at High Temperatures. Biosci Biotechnol Biochem 2014; 69:252-4. [PMID: 15665500 DOI: 10.1271/bbb.69.252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The temperature dependence of regeneration of bacteriorhodopsin (bR) from its apoprotein, bacterio-opsin (bO), and all-trans retinal was investigated using two different procedures to probe the structural properties of bO at high temperatures. Regeneration experiments performed at 25 degrees C after incubation of bO within the temperature range of 35-75 degrees C indicate that irreversible thermal unfolding begins at 50 degrees C. When bO is incubated for one hour and mixed with retinal at the same elevated temperatures, however, a greater extent of regeneration to bR occurs, even at temperatures ranging from 50 to 65 degrees C. These experimental results indicate that regeneration of bR occurs from thermally unfolded bO and suggest dynamic structural fluctuation of bO in the unfolded state.
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Affiliation(s)
- Ganga D Ghimire
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Tokyo, Japan
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3
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Sugiyama H, Sonoyama M, Ghimire GD, Mitaku S. Heterogeneity in Regeneration of Bacteriorhodopsin from Bacterio-Opsin and All-transRetinal at High Temperatures: Implications for Dynamic Structural Fluctuations. Biosci Biotechnol Biochem 2014; 70:1350-5. [PMID: 16794313 DOI: 10.1271/bbb.50629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Measurements of regeneration kinetics were performed in order to investigate the regeneration mechanisms of bacteriorhodopsin (bR) from thermally unfolded bacterio-opsin (bO) and all-trans retinal. Regeneration kinetics data were successfully fitted to a single exponential function when regeneration was performed at 25 degrees C after incubation at high temperatures. Conversely, the process of regeneration after the addition of retinal to bO at high temperatures occurred at two different rate constants. These findings strongly suggest that the slower regeneration of bR at high temperatures occurs as a result of dynamic structural fluctuation of bO, whereas the faster process corresponds to regeneration from bO, which retains a native structure capable of retinal binding.
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Affiliation(s)
- Hiroyuki Sugiyama
- Department of Applied Physics, Graduate School of Engineering, Nagoya University
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4
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Saitô H, Kira A, Arakawa T, Tanio M, Tuzi S, Naito A. Suppressed or recovered intensities analysis in site-directed 13C NMR: Assessment of low-frequency fluctuations in bacteriorhodopsin and D85N mutants revisited. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:167-76. [DOI: 10.1016/j.bbamem.2009.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 06/08/2009] [Accepted: 06/30/2009] [Indexed: 11/16/2022]
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5
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Abstract
Biology relies on the precise self-assembly of its molecular components. Generic principles of protein folding have emerged from extensive studies on small, water-soluble proteins, but it is unclear how these ideas are translated into more complex situations. In particular, the one-third of cellular proteins that reside in biological membranes will not fold like water-soluble proteins because membrane proteins need to expose, not hide, their hydrophobic surfaces. Here, we apply the powerful protein engineering method of Phi-value analysis to investigate the folding transition state of the alpha-helical membrane protein, bacteriorhodopsin, from a partially unfolded state. Our results imply that much of helix B of the seven-transmembrane helical protein is structured in the transition state with single-point alanine mutations in helix B giving Phi values >0.8. However, residues Y43 and T46 give lower Phi values of 0.3 and 0.5, respectively, suggesting a possible reduction in native structure in this region of the helix. Destabilizing mutations also increase the activation energy of folding, which is accompanied by an apparent movement of the transition state toward the partially unfolded state. This apparent transition state movement is most likely due to destabilization of the structured, unfolded state. These results contrast with the Hammond effect seen for several water-soluble proteins in which destabilizing mutations cause the transition state to move toward, and become closer in energy to, the folded state. We thus introduce a classic folding analysis method to membrane proteins, providing critical insight into the folding transition state.
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Rhinow D, Hampp NA. Light- and pH-Dependent Conformational Changes in Protein Structure Induce Strong Bending of Purple Membranes—Active Membranes Studied by Cryo-SEM. J Phys Chem B 2008; 112:13116-20. [DOI: 10.1021/jp803510t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Rhinow
- Department of Chemistry, University of Marburg, and Material Sciences Center, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Norbert A. Hampp
- Department of Chemistry, University of Marburg, and Material Sciences Center, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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Kawase Y, Tanio M, Kira A, Yamaguchi S, Tuzi S, Naito A, Kataoka M, Lanyi JK, Needleman R, Saitô H. Alteration of conformation and dynamics of bacteriorhodopsin induced by protonation of Asp 85 and deprotonation of Schiff base as studied by 13C NMR. Biochemistry 2000; 39:14472-80. [PMID: 11087400 DOI: 10.1021/bi0015820] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
According to previous X-ray diffraction studies, the D85N mutant of bacteriorhodopsin (bR) with unprotonated Schiff base assumes a protein conformation similar to that in the M photointermediate. We recorded (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled D85N and D85N/D96N mutants at ambient temperature to examine how conformation and dynamics of the protein backbone are altered when the Schiff base is protonated (at pH 7) and unprotonated (at pH 10). Most notably, we found that the peak intensities of three to four [3-(13)C]Ala-labeled residues from the transmembrane alpha-helices, including Ala 39, 51, and 53 (helix B) and 215 (helix G), were suppressed in D85N and D85N/D96N both from CP-MAS (cross polarization-magic angle spinning) and DD-MAS (dipolar decoupled-magic angle spinning) spectra, irrespective of the pH. This is due to conformational change and subsequent acquisition of intermediate time-range motions, with correlation times in the order of 10(-)(5) or 10(-)(4) s, which interferes with proton decoupling frequency or frequency of magic angle spinning, respectively, essential for an attempted peak-narrowing to achieve high-resolution NMR signals. Greater changes were achieved, however, at pH 10, which indicate large-amplitude motions of transmembrane helices upon deprotonation of Schiff base and the formation of the M-like state in the absence of illumination. The spectra detected more rapid motions in the extracellular and/or cytoplasmic loops, with correlation times increasing from 10(-)(4) to 10(-)(5) s. Conformational changes in the transmembrane helices were located at helices B, G, and D as viewed from the above-mentioned spectral changes, as well as at 1-(13)C-labeled Val 49 (helix B), 69 (B-C loop), and [3-(13)C]Ala-labeled Ala 126 (D-helix) signals, in addition to the cytoplasmic and extracellular loops. Further, we found that in the M-like state the charged state of Asp 96 at the cytoplasmic side substantially modulated the conformation and dynamics of the extracellular region through long-distance interaction.
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Affiliation(s)
- Y Kawase
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Harima Science Garden City, Kouto 3-chome, Kamigori, Hyogo, Japan
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Saranak J, Foster KW. Reducing agents and light break an S-S bond activating rhodopsin in vivo in Chlamydomonas. Biochem Biophys Res Commun 2000; 275:286-91. [PMID: 10964659 DOI: 10.1006/bbrc.2000.3296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Light induces retinal synthesis via photoactivation of a small amount of Chlamydomonas rhodopsin pigment (Foster et al., Proc. Natl. Acad. Sci. USA 85, 6379-6383). A reducing agent [dithiothreitol (DDT) or mercaptoacetic acid (MAA)] also induces retinal synthesis in the dark via a rhodopsin with a chromophore. If the opsin is saturated with retinal and is bleached with light in the presence of a thiol trapping agent, the bleaching becomes irreversible. We conclude that the reducing agent as well as light break a disulfide bond resulting in activation of the rhodopsin and induction of carotenogenesis. Both the chemical and light induction is inhibited by GDPbetaS and pertussis toxin. Breaking the bridge between the 3rd and 5th helix may lead to increased proton accessibility of Asp134 leading to the rolling of the 3rd helix and MetaIIb formation.
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Affiliation(s)
- J Saranak
- Department of Physics, Syracuse University, Syracuse, New York 13244-1130, USA
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Abstract
The detailed mechanism of retinal binding to bacterio-opsin is important to understanding retinal pigment formation as well as to the process of membrane protein folding. We have measured the temperature dependence of bacteriorhodopsin formation from bacterio-opsin and all-trans retinal. An Arrhenius plot of the apparent second-order rate constants gives an activation energy of 11.6 +/- 0.7 kcal/mol and an activation entropy of -4 +/- 2 cal/mol deg. Comparison of the activation entropy to model compound reactions suggests that chromophore formation in bacteriorhodopsin involves a substantial protein conformational change. Cleavage of the polypeptide chain between residues 71 and 72 has little effect on the activation energy or entropy, indicating that the connecting loop between helices B and C is not involved in this conformational change.
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Affiliation(s)
- R Renthal
- Division of Earth and Physical Sciences, University of Texas at San Antonio 78249, USA.
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Subramaniam S, Lindahl M, Bullough P, Faruqi AR, Tittor J, Oesterhelt D, Brown L, Lanyi J, Henderson R. Protein conformational changes in the bacteriorhodopsin photocycle. J Mol Biol 1999; 287:145-61. [PMID: 10074413 DOI: 10.1006/jmbi.1999.2589] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report a comprehensive electron crystallographic analysis of conformational changes in the photocycle of wild-type bacteriorhodopsin and in a variety of mutant proteins with kinetic defects in the photocycle. Specific intermediates that accumulate in the late stages of the photocycle of wild-type bacteriorhodopsin, the single mutants D38R, D96N, D96G, T46V, L93A and F219L, and the triple mutant D96G/F171C/F219L were trapped by freezing two-dimensional crystals in liquid ethane at varying times after illumination with a light flash. Electron diffraction patterns recorded from these crystals were used to construct projection difference Fourier maps at 3.5 A resolution to define light-driven changes in protein conformation. Our experiments demonstrate that in wild-type bacteriorhodopsin, a large protein conformational change occurs within approximately 1 ms after illumination. Analysis of structural changes in wild-type and mutant bacteriorhodopsins under conditions when either the M or the N intermediate is preferentially accumulated reveals that there are only small differences in structure between M and N intermediates trapped in the same protein. However, a considerably larger variation is observed when the same optical intermediate is trapped in different mutants. In some of the mutants, a partial conformational change is present even prior to illumination, with additional changes occurring upon illumination. Selected mutations, such as those in the D96G/F171C/F219L triple mutant, can sufficiently destabilize the wild-type structure to generate almost the full extent of the conformational change in the dark, with minimal additional light-induced changes. We conclude that the differences in structural changes observed in mutants that display long-lived M, 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. Our observations thus support a simplified view of the photocycle of wild-type bacteriorhodopsin in which the structures of the initial state and the early intermediates (K, L and M1) are well approximated by one protein conformation, while the structures of the later intermediates (M2, N and O) are well approximated by the other protein conformation. We propose that in wild-type bacteriorhodopsin and in most mutants, this conformational change between the M1 and M2 states is likely to make an important contribution towards efficiently switching proton accessibility of the Schiff base from the extracellular side to the cytoplasmic side of the membrane.
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Affiliation(s)
- S Subramaniam
- MRC Laboratory for Molecular Biology, Cambridge, England.
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DeLange F, Klaassen CH, Wallace-Williams SE, Bovee-Geurts PH, Liu XM, DeGrip WJ, Rothschild KJ. Tyrosine structural changes detected during the photoactivation of rhodopsin. J Biol Chem 1998; 273:23735-9. [PMID: 9726981 DOI: 10.1074/jbc.273.37.23735] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present the first Fourier transform infrared (FTIR) analysis of an isotope-labeled eukaryotic membrane protein. A combination of isotope labeling and FTIR difference spectroscopy was used to investigate the possible involvement of tyrosines in the photoactivation of rhodopsin (Rho). Rho --> MII difference spectra were obtained at 10 degrees C for unlabeled recombinant Rho and isotope-labeled L-[ring-2H4]Tyr-Rho expressed in Spodoptera frugiperda cells grown on a stringent culture medium containing enriched L-[ring-2H4]Tyr and isolated using a His6 tag. A comparison of these difference spectra revealed reproducible changes in bands that correspond to tyrosine and tyrosinate vibrational modes. A similar pattern of tyrosine/tyrosinate bands has also been observed in the bR --> M transition in bacteriorhodopsin, although the sign of the bands is reversed. In bacteriorhodopsin, these bands were assigned to Tyr-185, which along with Pro-186 in the F-helix, may form a hinge that facilitates alpha-helix movement.
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Affiliation(s)
- F DeLange
- Department of Biochemistry, Institute of Cellular Signalling, University of Nijmegen, 6500 HB, Nijmegen, The Netherlands
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Oesterhelt D. The structure and mechanism of the family of retinal proteins from halophilic archaea. Curr Opin Struct Biol 1998; 8:489-500. [PMID: 9729742 DOI: 10.1016/s0959-440x(98)80128-0] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Retinal proteins from halophilic archaea provide a unique opportunity to analyze vectorial ion translocation. Studies on its structure, conformational changes, proton conduction and electrogenic steps have helped to elucidate the catalytic cycle of bacteriorhodopsin in increasing detail. Experimental modulation of the vectoriality and ion specificity by altering the substrate availability, point mutations and light conditions for the different retinal proteins allows the proposal of a general model of ion transport for this protein family.
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Affiliation(s)
- D Oesterhelt
- Max-Planck-Institut für Biochemie, Martinsried, Germany.
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