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Sephus CD, Fer E, Garcia AK, Adam ZR, Schwieterman EW, Kaçar B. Earliest photic zone niches probed by ancestral microbial rhodopsins. Mol Biol Evol 2022; 39:6582242. [PMID: 35524714 PMCID: PMC9117797 DOI: 10.1093/molbev/msac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
For billions of years, life has continuously adapted to dynamic physical conditions near the Earth’s surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth’s earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as “paleosensors” for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.
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Affiliation(s)
- Cathryn D Sephus
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Evrim Fer
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary R Adam
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Edward W Schwieterman
- Blue Marble Space Institute of Science, Seattle, WA, USA.,Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
| | - Betül Kaçar
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Huang HY, Syue ML, Chen IC, Yu TY, Chu LK. Influence of Lipid Compositions in the Events of Retinal Schiff Base of Bacteriorhodopsin Embedded in Covalently Circularized Nanodiscs: Thermal Isomerization, Photoisomerization, and Deprotonation. J Phys Chem B 2019; 123:9123-9133. [PMID: 31584816 DOI: 10.1021/acs.jpcb.9b07788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalently circularized nanodiscs using circular membrane scaffold protein (MSP) serve as a suitable membrane mimetic for transmembrane proteins by providing stability and tunability in lipid compositions, providing controllable biological environments for targeted proteins. In this work, monomeric bacteriorhodopsin (mbR) was embedded in lipid nanodiscs of different lipid compositions using negatively charged lipid dioleoyl phosphatidylglycerol (DOPG) and the zwitterion lipid dioleoyl phosphatidylcholine (DOPC), and the events associated with the retinal Schiff base, including the thermal isomerization during the dark adaptation, photoisomerization, and deprotonation, were investigated. The retinal thermal isomerization from all-trans, 15-anti to the 13-cis, 15-syn configuration during the dark adaptation was accelerated in the DOPG bilayer, whereas the processes in the DOPC bilayer and in Triton X-100 micelles were similar. This observation indicated that the negatively charged lipid reduced the barrier for retinal thermal isomerization at C13═C14-C15═N in the ground electronic state. Furthermore, the broader absorption contour of mbR in the DOPC nanodisc probably indicated various retinal isomers in the light-adapted state, consistent with the observed nontwo-state dark adaptation kinetics. Moreover, the kinetics of the photoisomerization of the retinal was slightly decelerated upon increasing the content of DOPC. However, the cascading deprotonation of the protonated Schiff base is not dependent on the types of the surrounding lipids in the nanodiscs. In summary, our research deepens the understanding of the coupling between lipid membrane and the photochemistry of bR retinal Schiff base. Combined with the results of our previous works (Lee, T.-Y.; Yeh, V.; Chuang, J.; Chan, J. C. C.; Chu, L.-K.; Yu, T.-Y. Biophys. J. 2015, 109, 1899-1906; Kao, Y.-M.; Cheng, C.-H.; Syue, M.-L.; Huang, H.-Y.; Chen, I-C.; Yu, T.-Y.; Chu, L.-K. J. Phys. Chem. B 2019, 123, 2032-2039), these outcomes extend our understanding of the control of photochemistry and biophysical events for other photosynthetic proteins via altering the lipid environments.
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Affiliation(s)
- Hsin-Yu Huang
- Department of Chemistry , National Tsing Hua University , 101, Sec. 2, Kuang-Fu Road , Hsinchu 30013 , Taiwan
| | - Ming-Lun Syue
- Department of Chemistry , National Tsing Hua University , 101, Sec. 2, Kuang-Fu Road , Hsinchu 30013 , Taiwan
| | - I-Chia Chen
- Department of Chemistry , National Tsing Hua University , 101, Sec. 2, Kuang-Fu Road , Hsinchu 30013 , Taiwan
| | - Tsyr-Yan Yu
- Institute of Atomic and Molecular Sciences, Academia Sinica , 1, Sec. 4, Roosevelt Road , Taipei 10617 , Taiwan.,International Graduate Program of Molecular Science and Technology , National Taiwan University , Taipei , Taiwan
| | - Li-Kang Chu
- Department of Chemistry , National Tsing Hua University , 101, Sec. 2, Kuang-Fu Road , Hsinchu 30013 , Taiwan
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3
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Kusumoto T, Kosumi D, Uragami C, Frank HA, Birge RR, Cogdell RJ, Hashimoto H. Femtosecond transient absorption spectroscopic study of a carbonyl-containing carotenoid analogue, 2-(all-trans-retinylidene)-indan-1,3-dione. J Phys Chem A 2011; 115:2110-9. [PMID: 21361262 DOI: 10.1021/jp111313f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photophysical properties of a carbonyl-containing carotenoid analogue in an s-cis configuration, relative to the conjugated π system, 2-(all-trans-retinylidene)-indan-1,3-dione (C20Ind), were investigated by femtosecond time-resolved spectroscopy in various solvents. The lifetime of the optically forbidden S(1) state of C20Ind becomes long as solvent polarity increases. This trend is completely opposite to the situation of S(1-ICT) dynamics of carbonyl-containing carotenoids, such as peridinin and fucoxanthin. Excitation energy dependence of the transient absorption measurements shows that the transient absorption spectra in nonpolar solvents were originated from two distinct transient species, while those in polar and protic solvents are due to a single transient species. By referring to the results of MNDO-PSDCI (modified neglect of differential overlap with partial single- and double-configuration interaction) calculations, we conclude: (1) in polar and protic solvents, the S(1) state is generated following excitation up to the S(2) state; (2) in nonpolar solvents, however, both the S(1) and the (1)nπ* states are generated; and (3) C20Ind does not generate the S(1-ICT) state, despite the fact that it has two conjugated carbonyl groups.
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Affiliation(s)
- Toshiyuki Kusumoto
- CREST/JST and Department of Physics, Graduated School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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4
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Wassenaar TA, Daura X, Padrós E, Mark AE. Calcium binding to the purple membrane: A molecular dynamics study. Proteins 2009; 74:669-81. [PMID: 18704943 DOI: 10.1002/prot.22182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca(2+) near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations.
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Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
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5
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Wanko M, Hoffmann M, Frähmcke J, Frauenheim T, Elstner M. Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins. J Phys Chem B 2008; 112:11468-78. [PMID: 18729405 DOI: 10.1021/jp802409k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The explicit treatment of polarization as a many-body interaction in condensed-phase systems represents a current problem in empirical force-field development. Although a variety of efficient models for molecular polarization have been suggested, polarizable force fields are still far from common use nowadays. In this work, we consider interactive polarization models employing Thole's short-range damping scheme and assess them for application on polypeptides. Despite the simplicity of the model, we find mean polarizabilities and anisotropies of amino acid side chains in excellent agreement with MP2/cc-pVQZ benchmark calculations. Combined with restrained electrostatic potential (RESP) derived atomic charges, the models are applied in a quantum-mechanical/molecular-mechanical (QM/MM) approach. An iterative scheme is used to establish a self-consistent mutual polarization between the QM and MM moieties. This ansatz is employed to study the influence of the protein polarizability on calculated optical properties of the protonated Schiff base of retinal in rhodopsin (Rh), bacterio-rhodopsin (bR), and pharaonis sensory rhodopsin II (psRII). The shifts of the excitation energy due to the instantaneous polarization response of the protein to the charge transfer on the retinal chromophore are quantified using the high level ab initio multireference spectroscopy-oriented configuration interaction (SORCI) method. The results are compared with those of previously published QM1/QM2/MM models for bR and psRII.
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6
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Wanko M, Hoffmann M, Frauenheim T, Elstner M. Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II. J Phys Chem B 2008; 112:11462-7. [PMID: 18698712 DOI: 10.1021/jp802408g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article.
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7
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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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Lee I, Greenbaum E, Budy S, Hillebrecht JR, Birge RR, Stuart JA. Photoinduced Surface Potential Change of Bacteriorhodopsin Mutant D96N Measured by Scanning Surface Potential Microscopy. J Phys Chem B 2006; 110:10982-90. [PMID: 16771351 DOI: 10.1021/jp052948r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the direct measurement of photoinduced surface potential differences of wild-type (WT) and mutant D96N bacteriorhodopsin (BR) membranes at pH 7 and 10.5. Atomic force microscopy (AFM) and scanning surface potential microscopy (SSPM) were used to measure the BR membrane with the extracellular side facing up. We present AFM and SSPM images of WT and mutant D96N in which the light-dark transition occurred in the mid-scan of a single BR membrane. Photosteady-state populations of the M state were generated to facilitate measurement in each sample. The photoinduced surface potential of D96N is 63 mV (peak to valley) at pH 10.5 and is 48 mV at pH 7. The photoinduced surface potential of WT is 37 mV at pH 10.5 and approximately 0 at pH 7. Signal magnitudes are proportional to the amount of M produced at each pH. The results indicated that the surface potentials were generated by photoformation of surface charges on the extracellular side of the membrane. Higher surface potential correlated with a longer lifetime of the charges. A mechanistic basis for these signals is proposed, and it is concluded that they represent a steady-state measurement of the B2 photovoltage.
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Affiliation(s)
- Ida Lee
- Department of Electrical and Computer Engineering, University of Tennessee, Knoxville, Tennessee 37996-2100, USA.
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9
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Acebal P, Blaya S, Carretero L, Fimia A. Upper limits of dielectric permittivity modulation in bacteriorhodopsin films. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:011909. [PMID: 16090003 DOI: 10.1103/physreve.72.011909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 11/09/2004] [Indexed: 05/03/2023]
Abstract
A theoretical study of light-induced modulation of the dielectric permittivity in bacteriorhodopsin films has been done (including B--> M and B --> Q transitions). Analysis of dielectric permittivity modulation enables us to determine the fundamental limits of BR to be used in a holographic data storage system, together with the optimum experimental and material conditions. In order to carry out this analysis, the macroscopic dielectric permittivity was related to the microscopic polarizability of the three states of BR considered (B, M and Q). This parameter was calculated using a modelization procedure that includes the effect of ASP85, TRP86, and TYR185 amino acid residues (the B3LYP/6-31+ G(*) method was used for the calculations). Good concordance between theoretical calculations and experimental data was found for the linear optical properties (absorption wavelength, transition dipole moment, and dielectric permittivity modulation). The theoretical upper limits of Deltaepsilson at 750 nm (far from the resonance of the molecule) in a randomly oriented material are about 0.01 and 0.012 for B--> M and B--> Q transitions, respectively. The values of Deltaepsilon obtained were used to simulate diffraction efficiencies (eta) of a volume phase hologram recorded in a BR film. The high absorptive losses at low wavelengths (about 625 nm ) cause an interesting behavior, since the highest Deltaepsilom do not produce the greatest eta. The highest eta is produced for a hologram thickness in the range of 900-1000 microm and working wavelength of 700-750 nm.
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Affiliation(s)
- P Acebal
- Departamento de Ciencia y Tecnología de Materiales, Universidad Miguel Hernández, Elx (Alicante), Spain
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10
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Hufen J, Sugihara M, Buss V. How the Counterion Affects Ground- and Excited-State Properties of the Rhodopsin Chromophore. J Phys Chem B 2004. [DOI: 10.1021/jp046147k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Hufen
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
| | - Minoru Sugihara
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
| | - Volker Buss
- Institute of Theoretical Chemistry and Institute of Theoretical Low-Temperature Physics, University of Duisburg-Essen, D47048 Duisburg, Germany
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11
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Saitô H, Yamaguchi S, Ogawa K, Tuzi S, Márquez M, Sanz C, Padrós E. Glutamic acid residues of bacteriorhodopsin at the extracellular surface as determinants for conformation and dynamics as revealed by site-directed solid-state 13C NMR. Biophys J 2004; 86:1673-81. [PMID: 14990495 PMCID: PMC1304003 DOI: 10.1016/s0006-3495(04)74236-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We recorded (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled bacteriorhodopsin (bR) and a variety of its mutants, E9Q, E74Q, E194Q/E204Q (2Glu), E9Q/E194Q/E204Q (3Glu), and E9Q/E74Q/E194Q/E204Q (4Glu), to clarify contributions of the extracellular (EC) Glu residues to the conformation and dynamics of bR. Replacement of Glu-9 or Glu-74 and Glu-194/204 at the EC surface by glutamine(s) induced significant conformational changes in the cytoplasmic (CP) surface structure. These changes occurred in the C-terminal alpha-helix and loops, and also those of the EC surface, as viewed from (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled proteins. Additional conformational changes in the transmembrane alpha-helices were induced as modified retinal-protein interactions for multiple mutants involving the E194Q/E204Q pair. Significant dynamic changes were induced for the triple or quadruple mutants, as shown by broadened (13)C NMR peaks of [1-(13)C]Val-labeled proteins. These changes were due to acquired global fluctuation motions of the order of 10(-4)-10(-5) s as a result of disorganized trimeric form. In such mutants (13)C NMR signals from Val residues of [1-(13)C]Val-labeled triple and quadruple mutants near the CP and EC surfaces (including 8.7-A depth from the surface) were substantially suppressed, as shown by comparative (13)C NMR studies with and without 40 micro M Mn(2+) ion. We conclude that these Glu residues at the EC surface play an important role in maintaining the native secondary structure of bR in the purple membrane.
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Affiliation(s)
- Hazime Saitô
- Department of Life Science, Graduate School of Science, Himeji Institute of Technology, Harima Science Garden City, Kamgiori, Hyogo, Japan 678-1297.
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Yan ECY, Kazmi MA, Ganim Z, Hou JM, Pan D, Chang BSW, Sakmar TP, Mathies RA. Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin. Proc Natl Acad Sci U S A 2003; 100:9262-7. [PMID: 12835420 PMCID: PMC170906 DOI: 10.1073/pnas.1531970100] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biological function of Glu-181 in the photoactivation process of rhodopsin is explored through spectroscopic studies of site-specific mutants. Preresonance Raman vibrational spectra of the unphotolyzed E181Q mutant are nearly identical to spectra of the native pigment, supporting the view that Glu-181 is uncharged (protonated) in the dark state. The pH dependence of the absorption of the metarhodopsin I (Meta I)-like photoproduct of E181Q is investigated, revealing a dramatic shift of its Schiff base pKa compared with the native pigment. This result is most consistent with the assignment of Glu-181 as the primary counterion of the retinylidene protonated Schiff base in the Meta I state, implying that there is a counterion switch from Glu-113 in the dark state to Glu-181 in Meta I. We propose a model where the counterion switch occurs by transferring a proton from Glu-181 to Glu-113 through an H-bond network formed primarily with residues on extracellular loop II (EII). The resulting reorganization of EII is then coupled to movements of helix III through a conserved disulfide bond (Cys110-Cys187); this process may be a general element of G protein-coupled receptor activation.
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Affiliation(s)
- Elsa C Y Yan
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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13
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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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14
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Shima S, Ilagan RP, Gillespie N, Sommer BJ, Hiller RG, Sharples FP, Frank HA, Birge RR. Two-Photon and Fluorescence Spectroscopy and the Effect of Environment on the Photochemical Properties of Peridinin in Solution and in the Peridinin-Chlorophyll-Protein from Amphidinium carterae. J Phys Chem A 2003. [DOI: 10.1021/jp022648z] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sumie Shima
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Robielyn P. Ilagan
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Nathan Gillespie
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Brandi J. Sommer
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Roger G. Hiller
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Frank P. Sharples
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Harry A. Frank
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Robert R. Birge
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060, and School of Biological Sciences, Macquarie University, NSW 2109, Australia
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15
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Ren L, Martin CH, Wise KJ, Gillespie NB, Luecke H, Lanyi JK, Spudich JL, Birge RR. Molecular mechanism of spectral tuning in sensory rhodopsin II. Biochemistry 2001; 40:13906-14. [PMID: 11705380 DOI: 10.1021/bi0116487] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sensory rhodopsin II (SRII) is unique among the archaeal rhodopsins in having an absorption maximum near 500 nm, blue shifted roughly 70 nm from the other pigments. In addition, SRII displays vibronic structure in the lambda(max) absorption band, whereas the other pigments display fully broadened band maxima. The molecular origins responsible for both photophysical properties are examined here with reference to the 2.4 A crystal structure of sensory rhodopsin II (NpSRII) from Natronobacterium pharaonis. We use semiempirical molecular orbital theory (MOZYME) to optimize the chromophore within the chromophore binding site, and MNDO-PSDCI molecular orbital theory to calculate the spectroscopic properties. The entire first shell of the chromophore binding site is included in the MNDO-PSDCI SCF calculation, and full single and double configuration interaction is included for the chromophore pi-system. Through a comparison of corresponding calculations on the 1.55 A crystal structure of bacteriorhodopsin (bR), we identify the principal molecular mechanisms, and residues, responsible for the spectral blue shift in NpSRII. We conclude that the major source of the blue shift is associated with the significantly different positions of Arg-72 (Arg-82 in bR) in the two proteins. In NpSRII, this side chain has moved away from the chromophore Schiff base nitrogen and closer to the beta-ionylidene ring. This shift in position transfers this positively charged residue from a region of chromophore destabilization in bR to a region of chromophore stabilization in NpSRII, and is responsible for roughly half of the blue shift. Other important contributors include Asp-201, Thr-204, Tyr-174, Trp-76, and W402, the water molecule hydrogen bonded to the Schiff base proton. The W402 contribution, however, is a secondary effect that can be traced to the transposition of Arg-72. Indeed, secondary interactions among the residues contribute significantly to the properties of the binding site. We attribute the increased vibronic structure in NpSRII to the loss of Arg-72 dynamic inhomogeneity, and an increase in the intensity of the second excited (1)A(g)(-) -like state, which now appears as a separate feature within the lambda(max) band profile. The strongly allowed (1)B(u)(+)-like state and the higher-energy (1)A(g)(-) -like state are highly mixed in NpSRII, and the latter state borrows intensity from the former to achieve an observable oscillator strength.
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Affiliation(s)
- L Ren
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA
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Dolan PM, Miller D, Cogdell RJ, Birge RR, Frank HA. Linear Dichroism and the Transition Dipole Moment Orientation of the Carotenoid in the LH2 Antenna Complex in Membranes of Rhodopseudomonas acidophila Strain 10050. J Phys Chem B 2001. [DOI: 10.1021/jp010271b] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pamela M. Dolan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, and Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Deborah Miller
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, and Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Richard J. Cogdell
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, and Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Robert R. Birge
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, and Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
| | - Harry A. Frank
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, and Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, United Kingdom
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Sanz C, Márquez M, Perálvarez A, Elouatik S, Sepulcre F, Querol E, Lazarova T, Padrós E. Contribution of extracellular Glu residues to the structure and function of bacteriorhodopsin. Presence of specific cation-binding sites. J Biol Chem 2001; 276:40788-94. [PMID: 11524418 DOI: 10.1074/jbc.m104836200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Single and multiple mutants of extracellular Glu side chains of bacteriorhodopsin were analyzed by acid and calcium titration, differential scanning calorimetry, and thermal difference spectrophotometry. Acid titration spectra show that the second group protonating with Asp(85) is revealed in E204Q in the absence of Cl(-) but is not observed in the triple mutant E9Q/E194Q/E204Q or in the quadruple mutant E9Q/E74Q/E194Q/E204Q. The results point to Glu(9) as the second group protonating cooperatively with Asp(85). Comparison of the apparent pK(a) of Asp(85) protonation in water and in the deionized forms and results of calcium titration suggest that cation-binding sites are of low affinity in the multiple Glu mutants. Like for deionized wild type bacteriorhodopsin, differential scanning calorimetry reveals a lack of the pretransition in the multiple mutants, whereas in E9Q it appears at lower temperature and with lower cooperativity. Additionally, at neutral pH the band at 630 nm arising from cation release upon temperature increase is absent for the multiple mutants. Based on these results, we propose the presence of two cation-binding sites in the extracellular region of bacteriorhodopsin having as ligands Glu(9), Glu(194), Glu(204), and water molecules.
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Affiliation(s)
- C Sanz
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona 08193, Spain
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18
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Hayashi S, Tajkhorshid E, Pebay-Peyroula E, Royant A, Landau EM, Navarro J, Schulten K. Structural Determinants of Spectral Tuning in Retinal ProteinsBacteriorhodopsin vs Sensory Rhodopsin II#. J Phys Chem B 2001. [DOI: 10.1021/jp011362b] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Kusnetzow A, Dukkipati A, Babu KR, Singh D, Vought BW, Knox BE, Birge RR. The photobleaching sequence of a short-wavelength visual pigment. Biochemistry 2001; 40:7832-44. [PMID: 11425310 DOI: 10.1021/bi010387y] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photobleaching pathway of a short-wavelength cone opsin purified in delipidated form (lambda(max) = 425 nm) is reported. The batho intermediate of the violet cone opsin generated at 45 K has an absorption maximum at 450 nm. The batho intermediate thermally decays to the lumi intermediate (lambda(max) = 435 nm) at 200 K. The lumi intermediate decays to the meta I (lambda(max) = 420 nm) and meta II (lambda(max) = 388 nm) intermediates at 258 and 263 K, respectively. The meta II intermediate decays to free retinal and opsin at >270 K. At 45, 75, and 140 K, the photochemical excitation of the violet cone opsin at 425 nm generates the batho intermediate at high concentrations under moderate illumination. The batho intermediate spectra, generated via decomposing the photostationary state spectra at 45 and 140 K, are identical and have properties typical of batho intermediates of other visual pigments. Extended illumination of the violet cone opsin at 75 K, however, generates a red-shifted photostationary state (relative to both the dark and the batho intermediates) that has as absorption maximum at approximately 470 nm, and thermally reverts to form the normal batho intermediate when warmed to 140 K. We conclude that this red-shifted photostationary state is a metastable state, characterized by a higher-energy protein conformation that allows relaxation of the all-trans chromophore into a more planar conformation. FTIR spectroscopy of violet cone opsin indicates conclusively that the chromophore is protonated. A similar transformation of the rhodopsin binding site generates a model for the VCOP binding site that predicts roughly 75% of the observed blue shift of the violet cone pigment relative to rhodopsin. MNDO-PSDCI calculations indicate that secondary interactions involving the binding site residues are as important as the first-order chromophore protein interactions in mediating the wavelength maximum.
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Affiliation(s)
- A Kusnetzow
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06268-3060, USA
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20
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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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21
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Vought BW, Salcedo E, Chadwell LV, Britt SG, Birge RR, Knox BE. Characterization of the primary photointermediates of Drosophila rhodopsin. Biochemistry 2000; 39:14128-37. [PMID: 11087361 DOI: 10.1021/bi001135k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Invertebrate opsins are unique among the visual pigments because the light-activated conformation, metarhodopsin, is stable following exposure to light in vivo. Recovery of the light-activated pigment to the dark conformation (or resting state) occurs either thermally or photochemically. There is no evidence to suggest that the chromophore becomes detached from the protein during any stage in the formation or recovery processes. Biochemical and structural studies of invertebrate opsins have been limited by the inability to express and purify rhodopsins for structure-function studies. In this study, we used Drosophila to produce an epitope-tagged opsin, Rh1-1D4, in quantities suitable for spectroscopic and photochemical characterization. When expressed in Drosophila, Rh1-1D4 is localized to the rhabdomere membranes, has the same spectral properties in vivo as wild-type Rh1, and activates the phototransduction cascade in a normal manner. Purified Rh1-1D4 visual pigment has an absorption maximum of the dark-adapted state of 474 nm, while the metarhodopsin absorption maximum is 572 nm. However, the metarhodopsin state is not stable as purified in dodecyl maltoside but decays with kinetics that require a double-exponential fit having lifetimes of 280 and 2700 s. We investigated the primary properties of the pigment at low temperature. At 70 K, the pigment undergoes a temperature-induced red shift to 486 nm. Upon illumination with 435 nm light, a photostationary state mixture is formed consisting of bathorhodopsin (lambda(max) = 545 nm) and isorhodopsin (lambda(max) = 462 nm). We also compared the spectroscopic and photochemical properties of this pigment with other vertebrate pigments. We conclude that the binding site of Drosophila rhodopsin is similar to that of bovine rhodopsin and is characterized by a protonated Schiff base chromophore stabilized via a single negatively charged counterion.
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Affiliation(s)
- B W Vought
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
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Abstract
The photon-driven proton translocator bacteriorhodopsin is considered to be the best understood membrane protein so far. It is nowadays regarded as a model system for photosynthesis, ion pumps and seven transmembrane receptors. The profound knowledge came from the applicability of a variety of modern biophysical techniques which have often been further developed with research on bacteriorhodopsin and have delivered major contributions also to other areas. Most prominent examples are electron crystallography, solid-state NMR spectroscopy and time-resolved vibrational spectroscopy. The recently introduced method of crystallising a membrane protein in the lipidic cubic phase led to high-resolution structures of ground state bacteriorhodopsin and some of the photocycle intermediates. This achievement in combination with spectroscopic results will strongly advance our understanding of the functional mechanism of bacteriorhodopsin on the atomic level. We present here the current knowledge on specific aspects of the structural and functional dynamics of the photoreaction of bacteriorhodopsin with a focus on techniques established in our institute.
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Heberle J. Proton transfer reactions across bacteriorhodopsin and along the membrane. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:135-47. [PMID: 10812029 DOI: 10.1016/s0005-2728(00)00064-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin is probably the best understood proton pump so far and is considered to be a model system for proton translocating membrane proteins. The basis of a molecular description of proton translocation is set by having the luxury of six highly resolved structural models at hand. Details of the mechanism and reaction dynamics were elucidated by a whole variety of biophysical techniques. The current molecular picture of catalysis by BR will be presented with examples from time-resolved spectroscopy. FT-IR spectroscopy monitors single proton transfer events within bacteriorhodopsin and judiciously positioned pH indicators detect proton migration at the membrane surface. Emerging properties are briefly outlined that underlie the efficient proton transfer across and along biological membranes.
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Affiliation(s)
- J Heberle
- Research Centre Jülich, IBI-2: Structural Biology, D-52425, Jülich, Germany.
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