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Terpugov EL, Degtyareva OV, Fesenko EE. Microwave-Induced Structural Changes in Bacteriorhodopsin: Studies by Optical and Fourier Transform Infrared Difference Spectroscopy. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918050226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Calcium binding proteins and calcium signaling in prokaryotes. Cell Calcium 2014; 57:151-65. [PMID: 25555683 DOI: 10.1016/j.ceca.2014.12.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.
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TAVASOLI ELHAM, FATTAHI ALIREZA. DFT STUDY OF BOND ENERGIES AND ATTACHMENT SITES OF SAMPLE DIVALENT CATIONS (Mg2+, Ca2+, Zn2+) TO HISTIDINE IN THE GAS PHASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609004642] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine– M 2+ ( M 2+ = Mg 2+, Ca 2+, Zn 2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg 2+, Ca 2+, Zn 2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH 2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn 2+ to Mg 2+ and Ca 2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic.
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Affiliation(s)
- ELHAM TAVASOLI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
| | - ALIREZA FATTAHI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
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Neebe M, Rhinow D, Schromczyk N, Hampp NA. Thermochromism of Bacteriorhodopsin and Its pH Dependence. J Phys Chem B 2008; 112:6946-51. [DOI: 10.1021/jp7111389] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Neebe
- Department of Chemistry, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Daniel Rhinow
- Department of Chemistry, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Nina Schromczyk
- Department of Chemistry, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Norbert A. Hampp
- Department of Chemistry, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
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Rhinow D, Hampp NA. Sugar-induced blue membrane: release of divalent cations during phase transition of purple membranes observed in sugar-derived glasses. J Phys Chem B 2008; 112:4613-9. [PMID: 18358028 DOI: 10.1021/jp710694s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of blue membrane from purple membranes (PM) has been observed in glassy films made from PM and various sugars. The phase transition of PM at about 70 degrees C causes the complexation of divalent cations to be weakened. The vicinal diol structures in sugars are capable to complex divalent cations and delocalize them throughout the matrix as long as its glass transition temperature is lower than the phase transition temperature of PM. The loss of divalent cations from bacteriorhodopsin (BR), the only protein in PM, causes the formation of blue membrane (BM), which is accompanied by a loss of beta-sheet structure observable in the infrared spectrum. Glassy sugars are particular useful to observe this transition, as sugar entrapment does not restrict conformational changes of BR but rather retards them. The material obtained was named sugar-induced blue membrane (SIBM). The formation of SIBM is inhibited by the addition of divalent cations. Furthermore, SIBM is reverted immediately to PM by addition of water. A characteristic time dependence of the thermal reversion of SIBM to PM proves that the phase transition of PM triggers the release and uptake of divalent cations and the corresponding color change.
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Affiliation(s)
- Daniel Rhinow
- Department of Chemistry, and Material Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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Ai H, Zhang C, Li Y, Zhang L, Li F. Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter. J Phys Chem B 2007; 111:13786-96. [DOI: 10.1021/jp074198m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Chong Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Yun Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Liang Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
| | - Fang Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, People's Republic of China, Department of Chemistry and Technology, Liaocheng University, Liaocheng, 252059, People's Republic of China, and Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China
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Wang J, El-Sayed MA. The Effect of Metal Cation Binding on the Protein, Lipid and Retinal Isomeric Ratio in Regenerated Bacteriorhodopsin of Purple Membrane¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730564teomcb2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Ai H, Li Y, Zhang C, Feng J. The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ai H, Bu Y, Li P, Yan S. The peptide-chain size dependence of positive dissociation energy effect in metallized and protonated polydentate oligoglycine peptides. J Chem Phys 2005; 123:134307. [PMID: 16223288 DOI: 10.1063/1.2042449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The dependence of the positive dissociation energy (PDE) on the size of both protonated and various metal cationized (M+/2+=Na+, K+, Mg2+, and Ca2+) oligoglycines GnHM (G=glycine; n=1-5, and including 6 for GnHK) in the gas phase has been first determined at the B3LYP level with different basis sets. Results show that these PDEs become negative ones when n>or=5 for GnHNa, n>or=6 for GnHK, n>or=2 for GnHMg, and n>or=3 for GnHCa. Moreover, the PDE effect decreases gradually along the increase of oligoglycine size for all these PDE systems. More charge transfer to the ambient ligand and large electrostatic effect of the two divalent cation (Mg2+ and Ca2+) involved systems make them lose the PDE effect more rapidly, and hold more compact and oblate shapes than the monovalent ones. Differently, polydentate GnHK prefers a spherical to oblate shape along with the increase of oligoglycine size.
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Affiliation(s)
- Hongqi Ai
- School of Chemistry and Chemical Engineering, Jinan University, Jinan, 250022, People's Republic of China
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Whitmire SE, Wolpert D, Markelz AG, Hillebrecht JR, Galan J, Birge RR. Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. Biophys J 2003; 85:1269-77. [PMID: 12885670 PMCID: PMC1303244 DOI: 10.1016/s0006-3495(03)74562-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Accepted: 03/28/2003] [Indexed: 10/21/2022] Open
Abstract
Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.
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Affiliation(s)
- S E Whitmire
- Physics Department, University at Buffalo, State University of New York, Buffalo, New York, USA
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Saga Y, Ishikawa T, Watanabe T. Effect of metal ion exchange on the photocurrent response from bacteriorhodopsin on tin oxide electrodes. Bioelectrochemistry 2002; 57:17-22. [PMID: 12049752 DOI: 10.1016/s1567-5394(01)00173-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The transient photocurrent response from bacteriorhodopsin (bR) on tin oxide electrodes was strongly influenced by metal ions bound to bR molecules. The photocurrent polarity reversal pH, which corresponded to the pH value for the reversal of the proton release/uptake sequence in the bR photocycle, of cation-substituted purple membrane (PM) was shifted to lower pH with the increase in the cation affinities to carboxyl groups and a close correlation was noted between the two values. This suggests that the metal ion present in the extracellular region of a bR molecule modulates the pK(a) of proton release groups of bR by stabilizing the ionized state of the proton-releasing glutamic acids. The behavior of photocurrents at light-off in alkaline media, reflecting the proton uptake by bR, was unchanged by binding monovalent (Na(+) and K(+)) or divalent cations (Mg(2+) and Ca(2+)), but was drastically changed by binding La(3+) ions. This can be explained by invoking a substantial slowing of the proton uptake process in the presence of La(3+).
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Affiliation(s)
- Yoshitaka Saga
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Abstract
The Asp-85 residue, located in the vicinity of the retinal chromophore, plays a key role in the function of bacteriorhodopsin (bR) as a light-driven proton pump. In the unphotolyzed pigment the protonation of Asp-85 is responsible for the transition from the purple form (lambda(max) = 570 nm) to the blue form (lambda(max) = 605 nm) of bR. This transition can also be induced by deionization (cation removal). It was previously proposed that the cations bind to the bR surface and raise the surface pH, or bind to a specific site in the protein, probably in the retinal vicinity. We have reexamined these possibilities by evaluating the interaction between Mn(2+) and a nitroxyl radical probe covalently bound to several mutants in which protein residues were substituted by cystein. We have found that Mn(2+), which binds to the highest-affinity binding site, significantly affects the EPR spectrum of a spin label attached to residue 74C. Therefore, it is concluded that the highest-affinity binding site is located in the extracellular side of the protein and its distance from the spin label at 74C is estimated to be approximately 9.8 +/- 0.7 A. At least part of the three to four low-affinity cation binding sites are located in the cytoplasmic side, because Mn(2+) bound to these binding sites affects spin labels attached to residues 103C and 163C located in the cytoplasmic side of the protein. The results indicate specific binding sites for the color-controlling cations, and suggest that the binding sites involve negatively charged lipids located on the exterior of the bR trimer structure.
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Affiliation(s)
- T Eliash
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Wang G, Hu KS. Effects of pH and acetylation on Hg(2+)-induced purple to blue transition in bacteriorhodopsin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2001; 60:97-101. [PMID: 11470564 DOI: 10.1016/s1011-1344(01)00126-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Effects of Hg(2+) ions on the absorption spectrum of bacteriorhodopsin have been measured at different pH values and after acetylation. UV-difference spectroscopy and CD spectra show that Hg(2+)-induced color change is essentially similar to that caused by removal of cations or acidification. The ability of Hg(2+)-induced purple-to-blue transition is pH-dependent and exhibits a maximum at pH 5.5. Acetylation influences the absorption in the same way as Hg(2+) ions and accelerates Hg(2+)-induced purple to blue transition. All these results strongly suggest that the Hg(2+) effect is not a specific binding but just a replacement of intrinsic cations on the membrane surface, where they form a double layer. The composition of the double layer determines the surface pH on the membrane, which affects the color of the bacteriorhodopsin.
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Affiliation(s)
- G Wang
- Institute of Biophysics, Academia Sinica, 15 Datun Road, 100101, Beijing, China
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Wang J, El-Sayed MA. Time-resolved Fourier transform infrared spectroscopy of the polarizable proton continua and the proton pump mechanism of bacteriorhodopsin. Biophys J 2001; 80:961-71. [PMID: 11159463 PMCID: PMC1301294 DOI: 10.1016/s0006-3495(01)76075-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Nanosecond-to-microsecond time-resolved Fourier transform infrared (FTIR) spectroscopy in the 3000-1000-cm(-1) region has been used to examine the polarizable proton continua observed in bacteriorhodopsin (bR) during its photocycle. The difference in the transient FTIR spectra in the time domain between 20 ns and 1 ms shows a broad absorption continuum band in the 2100-1800-cm(-1) region, a bleach continuum band in the 2500-2150-cm(-1) region, and a bleach continuum band above 2700 cm(-1). According to Zundel (G., J. Mol. Struct. 322:33-42), these continua appear in systems capable of forming polarizable hydrogen bonds. The formation of a bleach continuum suggests the presence of a polarizable proton in the ground state that changes during the photocycle. The appearance of a transient absorption continuum suggests a change in the polarizable proton or the appearance of new ones. It is found that each continuum has a rise time of less than 80 ns and a decay time component of approximately 300 micros. In addition, it is found that the absorption continuum in the 2100-1800-cm(-1) region has a slow rise component of 190 ns and a fast decay component of approximately 60 micros. Using these results and those of the recent x-ray structural studies of bR(570) and M(412) (H. Luecke, B. Schobert, H.T. Richter, J.-P. Cartailler, and J. K., Science 286:255-260), together with the already known spectroscopic properties of the different intermediates in the photocycle, the possible origins of the polarizable protons giving rise to these continua during the bR photocycle are proposed. Models of the proton pump are discussed in terms of the changes in these polarizable protons and the hydrogen-bonded chains and in terms of previously known results such as the simultaneous deprotonation of the protonated Schiff base (PSB) and Tyr185 and the disappearance of water molecules in the proton release channel during the proton pump process.
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Affiliation(s)
- J Wang
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Wang J, el-Sayed MA. The Effect of Metal Cation Binding on the Protein, Lipid and Retinal Isomeric Ratio in Regenerated Bacteriorhodopsin of Purple Membrane¶. Photochem Photobiol 2001; 73:564-71. [PMID: 11367581 DOI: 10.1562/0031-8655(2001)073<0564:teomcb>2.0.co;2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The effect of metal cation binding on bacteriorhodopsin (bR) in purple membrane has been examined using in situ attenuated total reflection-Fourier transform infrared difference spectroscopy in aqueous media. It is known that adding metal cations to deionized bR regenerates the purple state from its blue state and recovers the proton pump function. During this process, infrared spectral changes in the frequency region of 1800-1000 cm-1 are monitored. The results reveal that metal cation binding affects the protein conformation, the retinal isomeric composition as well as lipid head groups. It is also observed that metal cation binding induces conformational changes in the alpha 1-helix region of bR, converting the portion of its alpha 1-helical domain into beta-turn or disordered coil. In addition, the influence of Ho3+ binding on the protein and lipid is observed to be larger than that of Ca2+. These results suggest that some of the metal cation binding sites are on the membrane lipid domain, while others could be on the intrahelical domain or interhelical loops where the Asp and Glu are located (binding with their COO- groups). Our results also suggest that the removal of the C-terminal of bR increase the accessibility of the binding site of metal cations, which affects protein conformational structure. All these observations are discussed in terms of the two proposals given in the literature regarding the metal cation binding sites.
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Affiliation(s)
- J Wang
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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Pebay-Peyroula E, Neutze R, Landau EM. Lipidic cubic phase crystallization of bacteriorhodopsin and cryotrapping of intermediates: towards resolving a revolving photocycle. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:119-32. [PMID: 10984595 DOI: 10.1016/s0005-2728(00)00134-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Bacteriorhodopsin is a small retinal protein found in the membrane of the halophilic bacterium Halobacterium salinarum, whose function is to pump protons across the cell membrane against an electrostatic potential, thus converting light into a proton-motive potential needed for the synthesis of ATP. Because of its relative simplicity, exceptional stability and the fundamental importance of vectorial proton pumping, bacteriorhodopsin has become one of the most important model systems in the field of bioenergetics. Recently, a novel methodology to obtain well-diffracting crystals of membrane proteins, utilizing membrane-like bicontinuous lipidic cubic phases, has been introduced, providing X-ray structures of bacteriorhodopsin and its photocycle intermediates at ever higher resolution. We describe this methodology, the new insights provided by the higher resolution ground state structures, and review the mechanistic implications of the structural intermediates reported to date. A detailed understanding of the mechanism of vectorial proton transport across the membrane is thus emerging, helping to elucidate a number of fundamental issues in bioenergetics.
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Affiliation(s)
- E Pebay-Peyroula
- Institut de Biologie Structurale, CEA-CNrS-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
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Abstract
Adding Ca2+ or other cations to deionized bacteriorhodopsin causes a blue to purple color shift, a result of deprotonation of Asp85. It has been proposed by different groups that the protonation state of Asp85 responds to the binding of Ca2+ either 1) directly at a specific site in the protein or 2) indirectly through the rise of the surface pH. We tested the idea of specific binding of Ca2+ and found that the surface pH, as determined from the ionization state of eosin covalently linked to engineered cysteine residues, rises about equally at both extracellular and cytoplasmic surfaces when only one Ca2+ is added. This precludes binding to a specific site and suggests that rather than decreasing the pKa of Asp85 by direct interaction, Ca2+ increases the surface pH by binding to anionic lipid groups. As Ca2+ is added the surface pH rises, but deprotonation of Asp85 occurs only when the surface pH approaches its pKa. The nonlinear relationship between Ca2+ binding and deprotonation of Asp85 from this effect is different in the wild-type protein and in various mutants and explains the observed complex and varied spectral titration curves.
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Affiliation(s)
- G Váró
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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Kusnetzow A, Singh DL, Martin CH, Barani IJ, Birge RR. Nature of the chromophore binding site of bacteriorhodopsin: the potential role of Arg82 as a principal counterion. Biophys J 1999; 76:2370-89. [PMID: 10233056 PMCID: PMC1300211 DOI: 10.1016/s0006-3495(99)77394-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nature of the chromophore binding site of light-adapted bacteriorhodopsin is analyzed by using modified neglect of differential overlap with partial single and double configuration interaction (MNDO-PSDCI) molecular orbital theory to interpret previously reported linear and nonlinear optical spectroscopic measurements. We conclude that in the absence of divalent metal cations in close interaction with Asp85 and Asp212, a positively charged amino acid must be present in the same vicinity. We find that models in which Arg82 is pointed upward into the chromophore binding site and directly stabilizes Asp85 and Asp212 are successful in rationalizing the observed one-photon and two-photon properties. We conclude further that a water molecule is strongly hydrogen bonded to the chromophore imine proton. The chromophore "1Bu*+" and "1Ag*-" states, despite extensive mixing, exhibit significantly different configurational character. The lowest-lying "1Bu*+" state is dominated by single excitations, whereas the second-excited "1Ag*-" state is dominated by double excitations. We can rule out the possibility of a negatively charged binding site, because such a site would produce a lowest-lying "1Ag*-" state, which is contrary to experimental observation. The possibility that Arg82 migrates toward the extracellular surface during the photocycle is examined.
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Affiliation(s)
- A Kusnetzow
- Department of Chemistry and W. M. Keck Center for Molecular Electronics, Syracuse University, Syracuse, New York 13244, USA
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Tallent JR, Stuart JA, Song QW, Schmidt EJ, Martin CH, Birge RR. Photochemistry in dried polymer films incorporating the deionized blue membrane form of bacteriorhodopsin. Biophys J 1998; 75:1619-34. [PMID: 9746505 PMCID: PMC1299835 DOI: 10.1016/s0006-3495(98)77605-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The preparation and photochemical properties of dried deionized blue membrane (dIbR600; lambdamax approximately 600 nm, epsilon approximately 54, 760 cm-1 M-1, f approximately 1.1) in polyvinyl alcohol films are studied. Reversible photoconversion from dIbR600 to the pink membrane (dIbR485; lambdamax approximately 485 nm) is shown to occur in these films under conditions of strong 647-nm laser irradiation. The pink membrane analog, dIbR485, has a molar extinction coefficient of approximately 39,000 cm-1 M-1 (f approximately 1.2). The ratio of pink --> blue and blue --> pink quantum efficiencies is 33 +/- 5. We observe an additional blue-shifted species (dIbR455, lambdamax approximately 455 nm) with a very low oscillator strength (f approximately 0.6, epsilon approximately 26,000 cm-1 M-1). This species is the product of fast thermal decay of dIbR485. Molecular modeling indicates that charge/charge and charge/dipole interactions introduced by the protonation of ASP85 are responsible for lowering the excited-state all-trans --> 9-cis barrier to approximately 6 kcal mol-1 while increasing the corresponding all-trans --> 13-cis barrier to approximately 4 kcal mol-1. Photochemical formation of both 9-cis and 13-cis photoproducts are now competitive, as is observed experimentally. We suggest that dIbR455 may be a 9-cis, 10-s-distorted species that partially divides the chromophore into two localized conjugated segments with a concomitant blue shift and decreased oscillator strength of the lambdamax absorption band.
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Affiliation(s)
- J R Tallent
- Department of Chemistry and W. M. Keck Center for Molecular Electronics, Syracuse University, Syracuse, New York 13244-4100 USA
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Pardo L, Sepulcre F, Cladera J, Duñach M, Labarta A, Tejada J, Padrós E. Experimental and theoretical characterization of the high-affinity cation-binding site of the purple membrane. Biophys J 1998; 75:777-84. [PMID: 9675179 PMCID: PMC1299752 DOI: 10.1016/s0006-3495(98)77567-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Binding of Mn2+ or Mg2+ to the high-affinity site of the purple membrane from Halobacterium salinarium has been studied by superconducting quantum interference device magnetometry or by ab initio quantum mechanical calculations, respectively. The binding of Mn2+ cation, in a low-spin state, to the high-affinity site occurs through a major octahedral local symmetry character with a minor rhombic distortion and a coordination number of six. A molecular model of this binding site in the Schiff base vicinity is proposed. In this model, a Mg2+ cation interacts with one oxygen atom of the side chain of Asp85, with both oxygen atoms of Asp212 and with three water molecules. One of these water molecules is hydrogen bonded to both the nitrogen of the protonated Schiff base and the Asp85 oxygen. It could serve as a shuttle for the Schiff base proton to move to Asp85 in the L-M transition.
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Affiliation(s)
- L Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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21
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Immaraporn B, Isaacson AD. Calculation of Rate Constants for Proton Transfer between Tethered Oxygens. J Phys Chem A 1998. [DOI: 10.1021/jp972722r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Alan D. Isaacson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
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Sakar K, Vacek G, Luthi HP, Nagashima U. The Importance of Charge Transfer between the Retinal Chromophore and the Protein Environment in Bacteriorhodopsin: A Theoretical Analysis on Reduced and Oxidized Chromophores. Photochem Photobiol 1997. [DOI: 10.1111/j.1751-1097.1997.tb03185.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Friedman N, Rousso I, Sheves M, Fu X, Bressler S, Druckmann S, Ottolenghi M. Time-resolved titrations of ASP-85 in bacteriorhodopsin: the multicomponent kinetic mechanism. Biochemistry 1997; 36:11369-80. [PMID: 9298956 DOI: 10.1021/bi970646c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Asp-85 residue, located in the vicinity of the retinal chromophore, plays a key role in the function of bacteriorhodopsin (bR) as a light-driven proton pump. In the unphotolyzed pigment the protonation of Asp-85 is responsible for the transition from the purple form (lambdamax = 570 nm) to the blue form (lambdamax = 605 nm) of bR (pKa = 3.5 in 20 mM NaCl). The Purple <=> Blue transition can also be induced by deionization (cation removal). These color changes offer a unique opportunity for time resolving the titration of a protein residue using conventional stopped-flow methodologies. We have studied the Purple <=> Blue equilibration kinetics in bR by exposing the system to pH and to cation jumps. Independently of the equilibration direction (Purple-->Blue or Blue-->Purple) and of the inducing concentration jump ([H+] or [cation]), the kinetics are found to exhibit analogous multicomponent features. Analysis of the data over a range of cation concentrations and pH values leads to the conclusion that the rate-determining step in the overall titration of Asp-85 is proton translocation through a specific proton channel. The multicomponent kinetics, extending over a wide time range (10(-2)-10(4) s), are accounted for in terms of a pH-dependent heterogeneity of proton channels. A model is presented in which the relative weight of four proton channels is determined by the state of protonation of two interacting, channel-controlling, protein residues A1 and A2. These findings bear on the mechanism of the vectorial proton translocation associated with the photocycle of bR.
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Affiliation(s)
- N Friedman
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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