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Smitienko OA, Feldman TB, Petrovskaya LE, Nekrasova OV, Yakovleva MA, Shelaev IV, Gostev FE, Cherepanov DA, Kolchugina IB, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin. J Phys Chem B 2021; 125:995-1008. [PMID: 33475375 DOI: 10.1021/acs.jpcb.0c07763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.
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Affiliation(s)
| | - Tatiana B Feldman
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Oksana V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | | | - Ivan V Shelaev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | | | - Irina B Kolchugina
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Dolgikh
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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2
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Haque S, Kikukawa T, Tamaoki N. Photoisomerization of azobenzene units drives the photochemical reaction cycles of proteorhodopsin and bacteriorhodopsin analogues. Org Biomol Chem 2020; 18:6312-6327. [PMID: 32748909 DOI: 10.1039/d0ob01486a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study we substituted the retinal units in proteorhodopsin (PR) and bacteriorhodopsin (BR) with azo chromophores to investigate the mechanism of photoinduced proton pumping in rhodopsins and potentially develop new artificial molecular pumps. We used an indium tin oxide electrode to investigate the photoinduced proton transfer of the azo analogues of PR and BR. We also employed flash photolysis to determine the characteristic photocycles, comprising multiple transient intermediates, of the azo chromophore-bound PR and BR. Moreover, our studies of the photoinduced proton pumping functions of azo-proteoopsin and azo-bacterioopsin complexes revealed that they did not pump protons upon illumination, even though they underwent photoinduced proton transfer and the characteristic photocycle. Mutational analysis suggested that the proton pumping malfunction of the azo analogues of PR and BR resulted from the absence of proton transfer reactions through cytoplasmic channels, even though these reactions were evoked in extracellular channels. Based on our experimental findings, we propose herein a putative model of the proton transfer reaction mechanism for the azo analogues of PR and BR.
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Affiliation(s)
- Shariful Haque
- Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, Japan. and Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan and Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 001-0021, Japan
| | - Nobuyuki Tamaoki
- Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, Japan. and Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Japan
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3
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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin. J Phys Chem B 2019; 123:4242-4250. [PMID: 30998011 PMCID: PMC6526469 DOI: 10.1021/acs.jpcb.9b01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Microbial rhodopsins
constitute a key protein family in optobiotechnological
applications such as optogenetics and voltage imaging. Spectral tuning
of rhodopsins into the deep-red and near-infrared spectral regions
is of great demand in such applications because more bathochromic
light into the near-infrared range penetrates deeper in living tissue.
Recently, retinal analogues have been successfully used in ion transporting
and fluorescent rhodopsins to achieve red-shifted absorption, activity,
and emission properties. Understanding their photochemical mechanism
is essential for further design of appropriate retinal analogues but
is yet only poorly understood for most retinal analogue pigments.
Here, we report the photoreaction dynamics of red-shifted analogue
pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto-
to submillisecond transient absorption spectroscopy. We found that
the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510
nm light illumination, which is comparable to the native retinal (A1)
in PR. On the other hand, the deprotonation of the A2 pigment Schiff
base was observed with a dominant time constant of 67 μs, which
is significantly slower than the A1 pigment. In the MOA2 pigment,
no isomerization or photoproduct formation was detected upon 520 nm
excitation, implying that all the excited molecules returned to the
initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very
slow excited state dynamics similar to the previously studied MMAR
pigment, but only very little photoproduct was formed. The low efficiency
of the photoproduct formation likely is the reason why DMAR analogue
pigments of PR showed very weak proton pumping activity.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands
| | - Sean Frehan
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Miroslav Kloz
- ELI-Beamlines , Institute of Physics , Na Slovance 2 , Praha 8 182 21 , Czech Republic
| | - Willem J de Grip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands.,Department of Biochemistry , Radboud University Medical Center , Nijmegen 6500 HB , The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
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4
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Köhler T, Weber I, Glaubitz C, Wachtveitl J. Proteorhodopsin Photocycle Kinetics Between pH 5 and pH 9. Photochem Photobiol 2017; 93:762-771. [DOI: 10.1111/php.12753] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Köhler
- Institute of Physical and Theoretical Chemistry; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Ingrid Weber
- Institut für Biophysikalische Chemie; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Clemens Glaubitz
- Institut für Biophysikalische Chemie; Goethe Universität Frankfurt am Main; Frankfurt Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Goethe Universität Frankfurt am Main; Frankfurt Germany
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5
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Tamogami J, Sato K, Kurokawa S, Yamada T, Nara T, Demura M, Miyauchi S, Kikukawa T, Muneyuki E, Kamo N. Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH. Biochemistry 2016; 55:1036-48. [DOI: 10.1021/acs.biochem.5b01196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Tamogami
- College
of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keitaro Sato
- Department
of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Sukuna Kurokawa
- Department
of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Takumi Yamada
- Department
of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Toshifumi Nara
- College
of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Makoto Demura
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Seiji Miyauchi
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Faculty
of Pharmaceutical Sciences, Toho University, Funabashi 274-8510, Japan
| | - Takashi Kikukawa
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Eiro Muneyuki
- Department
of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Naoki Kamo
- College
of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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6
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Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2015. [PMID: 26216996 DOI: 10.1073/pnas.1507713112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Channelrhodopsin-2 from Chlamydomonas reinhardtii is a light-gated ion channel. Over recent years, this ion channel has attracted considerable interest because of its unparalleled role in optogenetic applications. However, despite considerable efforts, an understanding of how molecular events during the photocycle, including the retinal trans-cis isomerization and the deprotonation/reprotonation of the Schiff base, are coupled to the channel-opening mechanism remains elusive. To elucidate this question, changes of conformation and configuration of several photocycle and conducting/nonconducting states need to be determined at atomic resolution. Here, we show that such data can be obtained by solid-state NMR enhanced by dynamic nuclear polarization applied to (15)N-labeled channelrhodopsin-2 carrying 14,15-(13)C2 retinal reconstituted into lipid bilayers. In its dark state, a pure all-trans retinal conformation with a stretched C14-C15 bond and a significant out-of-plane twist of the H-C14-C15-H dihedral angle could be observed. Using a combination of illumination, freezing, and thermal relaxation procedures, a number of intermediate states was generated and analyzed by DNP-enhanced solid-state NMR. Three distinct intermediates could be analyzed with high structural resolution: the early [Formula: see text] K-like state, the slowly decaying late intermediate [Formula: see text], and a third intermediate populated only under continuous illumination conditions. Our data provide novel insight into the photoactive site of channelrhodopsin-2 during the photocycle. They further show that DNP-enhanced solid-state NMR fills the gap for challenging membrane proteins between functional studies and X-ray-based structure analysis, which is required for resolving molecular mechanisms.
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7
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Inoue K, Kato Y, Kandori H. Light-driven ion-translocating rhodopsins in marine bacteria. Trends Microbiol 2015; 23:91-8. [PMID: 25432080 DOI: 10.1016/j.tim.2014.10.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/14/2014] [Accepted: 10/27/2014] [Indexed: 12/25/2022]
Abstract
Microbial rhodopsins are the photoreceptive membrane proteins found in diverse microorganisms from within Archaea, Eubacteria, and eukaryotes. They have a hep-tahelical transmembrane structure that binds to an all-trans retinal chromophore. Since 2000, thousands of proteorhodopsins, genes of light-driven proton pump rhodopsins, have been identified from various species of marine bacteria. This suggests that they are used for the conversion of light into chemical energy, contribut-ing to carbon circulation related to ATP synthesis in the ocean. Furthermore, novel types of rhodopsin (sodium and chloride pumps) have recently been discovered. Here, we review recent progress in our understanding of ion-transporting rhodopsins of marine bacteria, based mainly on biophysical and biochemical research.
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8
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Functional consequences of the oligomeric assembly of proteorhodopsin. J Mol Biol 2015; 427:1278-1290. [PMID: 25597999 PMCID: PMC4374980 DOI: 10.1016/j.jmb.2015.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/21/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022]
Abstract
The plasma membrane is the crucial interface between the cell and its exterior, packed with embedded proteins experiencing simultaneous protein-protein and protein-membrane interactions. A prominent example of cell membrane complexity is the assembly of transmembrane proteins into oligomeric structures, with potential functional consequences that are not well understood. From the study of proteorhodopsin (PR), a prototypical seven-transmembrane light-driven bacterial proton pump, we find evidence that the inter-protein interaction modulated by self-association yields functional changes observable from the protein interior. We also demonstrate that the oligomer is likely a physiologically relevant form of PR, as crosslinking of recombinantly expressed PR reveals an oligomeric population within the Escherichia coli membrane (putatively hexameric). Upon chromatographic isolation of oligomeric and monomeric PR in surfactant micelles, the oligomer exhibits distinctly different optical absorption properties from monomeric PR, as reflected in a prominent decrease in the pKa of the primary proton acceptor residue (D97) and slowing of the light-driven conformational change. These functional effects are predominantly determined by specific PR-PR contacts over nonspecific surfactant interactions. Interestingly, varying the surfactant type alters the population of oligomeric states and the proximity of proteins within an oligomer, as determined by sparse electron paramagnetic resonance distance measurements. Nevertheless, the dynamic surfactant environment retains the key function-tuning property exerted by oligomeric contacts. A potentially general design principle for transmembrane protein function emerges from this work, one that hinges on specific oligomeric contacts that can be modulated by protein expression or membrane composition.
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9
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Mehler M, Scholz F, Ullrich SJ, Mao J, Braun M, Brown LJ, Brown RCD, Fiedler SA, Becker-Baldus J, Wachtveitl J, Glaubitz C. The EF loop in green proteorhodopsin affects conformation and photocycle dynamics. Biophys J 2014; 105:385-97. [PMID: 23870260 DOI: 10.1016/j.bpj.2013.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 11/20/2022] Open
Abstract
The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.
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Affiliation(s)
- Michaela Mehler
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Germany
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10
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Tamogami J, Kikukawa T, Nara T, Shimono K, Demura M, Kamo N. Photoinduced proton release in proteorhodopsin at low pH: the possibility of a decrease in the pK(a) of Asp227. Biochemistry 2012; 51:9290-301. [PMID: 23095117 DOI: 10.1021/bi300940p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteorhodopsin (PR) is one of the microbial rhodopsins that are found in marine eubacteria and likely functions as an outward light-driven proton pump. Previously, we [Tamogami, J., et al. (2009) Photochem. Photobiol.85, 578-589] reported the occurrence of a photoinduced proton transfer in PR between pH 5 and 10 using a transparent ITO (indium-tin oxide) or SnO(2) electrode that works as a time-resolving pH electrode. In the study presented here, the proton transfer at low pH (<4) was investigated. Under these conditions, Asp97, the primary counterion to the protonated Schiff base, is protonated. We observed a first proton release that was followed by an uptake; during this process, however, the M intermediate did not form. Through the use of experiments with several PR mutants, we found that Asp227 played an essential role in proton release. This residue corresponds to the Asp212 residue of bacteriorhodopsin, the so-called secondary Schiff base counterion. We estimated the pK(a) of this residue in both the dark and the proton-releasing photoproduct to be ~3.0 and ~2.3, respectively. The pK(a) value of Asp227 in the dark was also estimated spectroscopically and was approximately equal to that determined with the ITO experiments, which may imply the possibility of the release of a proton from Asp227. In the absence of Cl(-), we observed the proton release in D227N and found that Asp97, the primary counterion, played a key role. It is inferred that the negative charge is required to stabilize the photoproducts through the deprotonation of Asp227 (first choice), the binding of Cl(-) (second choice), or the deprotonation of Asp97. The photoinduced proton release (possibly by the decrease in the pK(a) of the secondary counterion) in acidic media was also observed in other microbial rhodopsins with the exception of the Anabaena sensory rhodopsin, which lacks the dissociable residue at the position of Asp212 of BR or Asp227 of PR and halorhodopsin. The implication of this pK(a) decrease is discussed.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.
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11
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Herz J, Verhoefen MK, Weber I, Bamann C, Glaubitz C, Wachtveitl J. Critical role of Asp227 in the photocycle of proteorhodopsin. Biochemistry 2012; 51:5589-600. [PMID: 22738119 DOI: 10.1021/bi3003764] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photocycle of the proton acceptor complex mutant D227N of the bacterial retinal protein proteorhodopsin is investigated employing steady state pH-titration experiments in the UV-visible range as well as femtosecond-pump-probe spectroscopy and flash photolysis in the visible spectral range. The evaluation of the pH-dependent spectra showed that the neutralization of the charge at position 227 has a remarkable influence on the ground state properties of the protein. Both the pK(a) values of the primary proton acceptor and of the Schiff base are considerably decreased. Femtosecond-time-resolved measurements demonstrate that the general S(1) deactivation pathway; that is, the K-state formation is preserved in the D227N mutant. However, the pH-dependence of the reaction rate is lost by the substitution of Asp227 with an asparagine. Also no significant kinetic differences are observed upon deuteration. This is explained by the lack of a strongly hydrogen-bonded water in the vicinity of Asp97, Asp227, and the Schiff base or a change in the hydrogen bonding of it (Ikeda et al. (2007) Biochemistry 46, 5365-5373). The flash photolysis measurements prove a considerably elongated photocycle with pronounced pH-dependence. Interestingly, at pH 9 the M-state is visible until the end of the reaction cycle, leading to the conclusion that the mutation does not only lower the pK(a) of the Schiff base in the unphotolyzed ground state but also prevents an efficient reprotonation reaction.
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Affiliation(s)
- Julia Herz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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12
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Low temperature FTIR spectroscopy provides new insights in the pH-dependent proton pathway of proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1583-90. [DOI: 10.1016/j.bbabio.2011.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
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13
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Ranaghan MJ, Schwall CT, Alder NN, Birge RR. Green proteorhodopsin reconstituted into nanoscale phospholipid bilayers (nanodiscs) as photoactive monomers. J Am Chem Soc 2011; 133:18318-27. [PMID: 21951206 PMCID: PMC3218432 DOI: 10.1021/ja2070957] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over 4000 putative proteorhodopsins (PRs) have been identified throughout the oceans and seas of the Earth. The first of these eubacterial rhodopsins was discovered in 2000 and has expanded the family of microbial proton pumps to all three domains of life. With photophysical properties similar to those of bacteriorhodopsin, an archaeal proton pump, PRs are also generating interest for their potential use in various photonic applications. We perform here the first reconstitution of the minimal photoactive PR structure into nanoscale phospholipid bilayers (nanodiscs) to better understand how protein-protein and protein-lipid interactions influence the photophysical properties of PR. Spectral (steady-state and time-resolved UV-visible spectroscopy) and physical (size-exclusion chromatography and electron microscopy) characterization of these complexes confirms the preparation of a photoactive PR monomer within nanodiscs. Specifically, when embedded within a nanodisc, monomeric PR exhibits a titratable pK(a) (6.5-7.1) and photocycle lifetime (∼100-200 ms) that are comparable to the detergent-solubilized protein. These ndPRs also produce a photoactive blue-shifted absorbance, centered at 377 or 416 nm, that indicates that protein-protein interactions from a PR oligomer are required for a fast photocycle. Moreover, we demonstrate how these model membrane systems allow modulation of the PR photocycle by variation of the discoidal diameter (i.e., 10 or 12 nm), bilayer thickness (i.e., 23 or 26.5 Å), and degree of saturation of the lipid acyl chain. Nanodiscs also offer a highly stable environment of relevance to potential device applications.
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Affiliation(s)
- Matthew J. Ranaghan
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 (USA)
| | - Christine T. Schwall
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 (USA)
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 (USA)
| | - Robert R. Birge
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 (USA)
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269 (USA)
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14
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Kralj JM, Hochbaum DR, Douglass AD, Cohen AE. Electrical spiking in Escherichia coli probed with a fluorescent voltage-indicating protein. Science 2011; 333:345-8. [PMID: 21764748 DOI: 10.1126/science.1204763] [Citation(s) in RCA: 253] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteria have many voltage- and ligand-gated ion channels, and population-level measurements indicate that membrane potential is important for bacterial survival. However, it has not been possible to probe voltage dynamics in an intact bacterium. Here we developed a method to reveal electrical spiking in Escherichia coli. To probe bacterial membrane potential, we engineered a voltage-sensitive fluorescent protein based on green-absorbing proteorhodopsin. Expression of the proteorhodopsin optical proton sensor (PROPS) in E. coli revealed electrical spiking at up to 1 hertz. Spiking was sensitive to chemical and physical perturbations and coincided with rapid efflux of a small-molecule fluorophore, suggesting that bacterial efflux machinery may be electrically regulated.
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Affiliation(s)
- Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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15
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Dai G, Ohno Y, Ikeda Y, Tamogami J, Kikukawa T, Kamo N, Iwasa T. Photoreaction Cycle of Phoborhodopsin (Sensory Rhodopsin II) from Halobacterium salinarum Expressed in Escherichia coli. Photochem Photobiol 2010; 86:571-9. [DOI: 10.1111/j.1751-1097.2009.00687.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lörinczi É, Verhoefen MK, Wachtveitl J, Woerner AC, Glaubitz C, Engelhard M, Bamberg E, Friedrich T. Voltage- and pH-Dependent Changes in Vectoriality of Photocurrents Mediated by Wild-type and Mutant Proteorhodopsins upon Expression in Xenopus Oocytes. J Mol Biol 2009; 393:320-41. [DOI: 10.1016/j.jmb.2009.07.055] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 06/15/2009] [Accepted: 07/17/2009] [Indexed: 10/20/2022]
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17
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Abstract
Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II) is a seven transmembrane helical retinal protein. ppR forms a signaling complex with pharaonis Halobacterial transducer II (pHtrII) in the membrane that transmits a light signal to the sensory system in the cytoplasm. The M-state during the photocycle of ppR (lambda(max) = 386 nm) is one of the active (signaling) intermediates. However, progress in characterizing the M-state at physiological temperature has been slow because its lifetime is very short (decay half-time is approximately 1 s). In this study, we identify a highly stable photoproduct that can be trapped at room temperature in buffer solution containing n-octyl-beta-d-glucoside, with a decay half-time and an absorption maximum of approximately 2 h and 386 nm, respectively. HPLC analysis revealed that this stable photoproduct contains 13-cis-retinal as a chromophore. Previously, we reported that water-soluble hydroxylamine reacts selectively with the M-state, and we found that this stable photoproduct also reacts selectively with that reagent. These results suggest that the physical properties of the stable photoproduct (named the M-like state) are very similar with the M-state during the photocycle. By utilizing the high stability of the M-like state, we analyzed interactions of the M-like state and directly estimated the pK(a) value of the Schiff base in the M-like state. These results suggest that the dissociation constant of the ppR(M-like)/pHtrII complex greatly increases (to 5 muM) as the pK(a) value greatly decreases (from 12 to 1.5). The proton transfer reaction of ppR from the cytoplasmic to the extracellular side is proposed to be caused by this change in pK(a).
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18
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Initial reaction dynamics of proteorhodopsin observed by femtosecond infrared and visible spectroscopy. Biophys J 2008; 94:4796-807. [PMID: 18326639 DOI: 10.1529/biophysj.107.125484] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a comparative study using femtosecond pump/probe spectroscopy in the visible and infrared of the early photodynamics of solubilized proteorhodopsin (green absorbing variant) in D(2)O with deprotonated (pD 9.2) and protonated (pD 6.4) primary proton acceptor Asp-97. The vis-pump/vis-probe experiments show a kinetic isotope effect that is more pronounced for alkaline conditions, thus decreasing the previously reported pH-dependence of the primary reaction of proteorhodopsin in H(2)O. This points to a pH dependent H-bonding network in the binding pocket of proteorhodopsin, that directly influences the primary photo-induced dynamics. The vis-pump/IR-probe experiments were carried out in two different spectral regions and allowed to monitor the retinal C=C (1500 cm(-1)-1580 cm(-1)) and C=N stretching vibration as well as the amide I mode of the protein (1590 cm(-1)-1680 cm(-1)). Like the FTIR spectra of the K intermediate (PR(K)-PR difference spectra) in this spectral range, the kinetic parameters and also the quantum efficiency of photo-intermediate formation are found to be virtually independent of the pD value.
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Xi B, Tetley WC, Marcy DL, Zhong C, Whited G, Birge RR, Stuart JA. Evaluation of Blue and Green Absorbing Proteorhodopsins as Holographic Materials. J Phys Chem B 2008; 112:2524-32. [DOI: 10.1021/jp0740752] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bangwei Xi
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - William C. Tetley
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Duane L. Marcy
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Cheng Zhong
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Gregg Whited
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Robert R. Birge
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Jeffrey A. Stuart
- W.M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, Syracuse, New York 13244; Department of Electrical & Computer Engineering, Syracuse University, Syracuse, New York 13244; Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269; Genencor International, Inc., Palo Alto, California 94304; and Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
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Klyszejko AL, Shastri S, Mari SA, Grubmüller H, Muller DJ, Glaubitz C. Folding and Assembly of Proteorhodopsin. J Mol Biol 2008; 376:35-41. [DOI: 10.1016/j.jmb.2007.11.030] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
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21
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Characterization of the primary photochemistry of proteorhodopsin with femtosecond spectroscopy. Biophys J 2008; 94:4020-30. [PMID: 18234812 DOI: 10.1529/biophysj.107.121376] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteorhodopsin is an ion-translocating member of the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization, leading to transmembrane translocation of a proton toward the extracellular side of the cytoplasmic membrane. Here we report a study on the photoisomerization dynamics of the retinal chromophore of proteorhodopsin, using femtosecond time-resolved spectroscopy, by probing in the visible- and in the midinfrared spectral regions. Experiments were performed both at pH 9.5 (a physiologically relevant pH value in which the primary proton acceptor of the protonated Schiff base, Asp(97), is deprotonated) and at pH 6.5 (with Asp(97) protonated). Simultaneous analysis of the data sets recorded in the two spectral regions and at both pH values reveals a multiexponential excited state decay, with time constants of approximately 0.2 ps, approximately 2 ps, and approximately 20 ps. From the difference spectra associated with these dynamics, we conclude that there are two chromophore-isomerization pathways that lead to the K-state: one with an effective rate of approximately (2 ps)(-1) and the other with a rate of approximately (20 ps)(-1). At high pH, both pathways are equally effective, with an estimated quantum yield for K-formation of approximately 0.7. At pH 6.5, the slower pathway is less productive, which results in an isomerization quantum yield of 0.5. We further observe an ultrafast response of residue Asp(227), which forms part of the counterion complex, corresponding to a strengthening of its hydrogen bond with the Schiff base on K-state formation; and a feature that develops on the 0.2 ps and 2 ps timescale and probably reflects a response of an amide II band in reaction to the isomerization process.
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22
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Pfleger N, Lorch M, Woerner AC, Shastri S, Glaubitz C. Characterisation of Schiff base and chromophore in green proteorhodopsin by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2008; 40:15-21. [PMID: 17968661 DOI: 10.1007/s10858-007-9203-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 09/27/2007] [Accepted: 10/01/2007] [Indexed: 05/25/2023]
Abstract
The proteorhodopsin family consists of hundreds of homologous retinal containing membrane proteins found in bacteria in the photic zone of the oceans. They are colour tuned to their environment and act as light-driven proton pumps with a potential energetic and regulatory function. Precise structural details are still unknown. Here, the green proteorhodopsin variant has been selected for a chemical shift analysis of retinal and Schiff base by solid-state NMR. Our data show that the chromophore exists in mainly all-trans configuration in the proteorhodopsin ground state. The optical absorption maximum together with retinal and Schiff base chemical shifts indicate a strong interaction network between chromophore and opsin.
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Affiliation(s)
- Nicole Pfleger
- Institute for Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany
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Lenz MO, Woerner AC, Glaubitz C, Wachtveitl J. Photoisomerization in proteorhodopsin mutant D97N. Photochem Photobiol 2007; 83:226-31. [PMID: 16808594 DOI: 10.1562/2006-05-31-ra-909] [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: 11/19/2022]
Abstract
The first steps of the photocycle of the D97N mutant of proteorhodopsin (PR) have been investigated by means of ultrafast transient absorption spectroscopy. A comparison with the primary dynamics of native PR and D85N mutant of bacteriorhodopsin is given. Upon photoexcitation of the covalently bound all-trans retinal the excited state decays biexponentially with time constants of 1.4 and 20 ps via a conical intersection, resulting in a 13-cis isomerized retinal. Neither of the two-deactivation channels is significantly preferred. The dynamics is slowed down in comparison with native PR at pH 9 and reaction rates are even lower than for native PR at pH 6, where the primary proton acceptor (Asp97) is protonated. Therefore, the ultrafast isomerization is not only controlled by the charge distribution within the retinal binding pocket. This study shows that in addition to direct electrostatics other effects have to be taken into account to explain the catalytic function of Asp97 in PR on the ultrafast isomerization reaction. This may include sterical interactions and/or bound water molecules within the retinal binding pocket.
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Affiliation(s)
- Martin O Lenz
- Institute for Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität Frankfurt, Germany
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Shastri S, Vonck J, Pfleger N, Haase W, Kuehlbrandt W, Glaubitz C. Proteorhodopsin: characterisation of 2D crystals by electron microscopy and solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3012-9. [PMID: 17964280 DOI: 10.1016/j.bbamem.2007.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 09/29/2007] [Accepted: 10/02/2007] [Indexed: 11/15/2022]
Abstract
Proteorhodopsin (PR) a recent addition to retinal type 1 protein family, is a bacterial homologue of archaeal bacteriorhodopsin. It was found to high abundance in gamma-proteobacteria in the photic zone of the oceans and has been shown to act as a photoactive proton pump. It is therefore involved in the utilisation of light energy for energy production within the cell. Based on data from biodiversity screens, hundreds of variants were discovered worldwide, which are spectrally tuned to the available light at different locations in the sea. Here, we present a characterisation of 2D crystals of the green variant of proteorhodopsin by electron microscopy and solid state NMR. 2D crystal formation with hexagonal protein packing was observed under a very wide range of conditions indicating that PR might be also closely packed under native conditions. A low-resolution 2D projection map reveals a ring-shaped oligomeric assembly of PR. The protein state was analysed by 15N MAS NMR on lysine, tryptophan and methionine labelled samples. The chemical shift of the protonated Schiff base was almost identical to non-crystalline preparations. All residues could be cross-polarised in non-frozen samples. Lee-Goldberg cross-polarisation has been used to probe protein backbone mobility.
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Affiliation(s)
- Sarika Shastri
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe University, Max von Laue Str. 9, D-60438 Frankfurt am Main, Germany
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25
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Abstract
Xanthorhodopsin (XR), the light-driven proton pump of the halophilic eubacterium Salinibacter ruber, exhibits substantial homology to bacteriorhodopsin (BR) of archaea and proteorhodopsin (PR) of marine bacteria, but unlike them contains a light-harvesting carotenoid antenna, salinixanthin, as well as retinal. We report here the pH-dependent properties of XR. The pKa of the retinal Schiff base is as high as in BR, i.e. > or =12.4. Deprotonation of the Schiff base and the ensuing alkaline denaturation cause large changes in the absorption bands of the carotenoid antenna, which lose intensity and become broader, making the spectrum similar to that of salinixanthin not bound to XR. A small redshift of the retinal chromophore band and increase of its extinction, as well as the pH-dependent amplitude of the M intermediate indicate that in detergent-solubilized XR the pKa of the Schiff base counterion and proton acceptor is about 6 (compared to 2.6 in BR, and 7.5 in PR). The protonation of the counterion is accompanied by a small blueshift of the carotenoid absorption bands. The pigment is stable in the dark upon acidification to pH 2. At pH < 2 a transition to a blueshifted species absorbing around 440 nm occurs, accompanied by loss of resolution of the carotenoid absorption bands. At pH < 3 illumination of XR with continuous light causes accumulation of long-lived photoproduct(s) with an absorption maximum around 400 nm. The photocycle of XR was examined between pH 4 and 10 in solubilized samples. The pH dependence of recovery of the initial state slows at both acid and alkaline pH, with pKas of 6.0 and 9.3. The decrease in the rates with pKa 6.0 is apparently caused by protonation of the counterion and proton acceptor, and that at high pH reflects the pKa of the internal proton donor, Glu94, at the times in the photocycle when this group equilibrates with the bulk.
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Affiliation(s)
| | - Sergei P. Balashov
- To whom correspondence should be addressed: Department of Physiology & Biophysics, D-340 Medical Science I, University of California, Irvine, CA 92697-4560 , Phone: (949) 824-7783, Fax: (949) 824-8540,
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27
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Lenz MO, Huber R, Schmidt B, Gilch P, Kalmbach R, Engelhard M, Wachtveitl J. First steps of retinal photoisomerization in proteorhodopsin. Biophys J 2006; 91:255-62. [PMID: 16603495 PMCID: PMC1479053 DOI: 10.1529/biophysj.105.074690] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The early steps (<1 ns) in the photocycle of the detergent solubilized proton pump proteorhodopsin are analyzed by ultrafast spectroscopic techniques. A comparison to the first primary events in reconstituted proteorhodopsin as well as to the well known archaeal proton pump bacteriorhodopsin is given. A dynamic Stokes shift observed in fs-time-resolved fluorescence experiments allows a direct observation of early motions on the excited state potential energy surface. The initial dynamics is dominated by sequentially emerging stretching (<150 fs) and torsional (approximately 300 fs) modes of the retinal. The different protonation states of the primary proton acceptor Asp-97 drastically affect the reaction rate and the overall quantum efficiencies of the isomerization reactions, mainly evidenced for time scales above 1 ps. However, no major influence on the fast time scales (approximately 150 fs) could be seen, indicating that the movement out of the Franck-Condon region is fairly robust to electrostatic changes in the retinal binding pocket. Based on fs-time-resolved absorption and fluorescence spectra, ground and exited state contributions can be disentangled and allow to construct a reaction model that consistently explains pH-dependent effects in solubilized and reconstituted proteorhodopsin.
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Affiliation(s)
- Martin O Lenz
- Institut für Physikalische und Theoretische Chemie, Johann-Wolfgang-Goethe-Universität, Frankfurt, Germany
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