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Do TN, Sim JHN, Nguyen HL, Lu Y, Tan HS. Observing the Fluctuation Dynamics of Dative Bonds Using Two-Dimensional Electronic Spectroscopy. J Phys Chem Lett 2021; 12:165-170. [PMID: 33320689 DOI: 10.1021/acs.jpclett.0c03243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We perform two-dimensional electronic spectroscopy on chlorophyll (Chl) a and b molecules in aprotic solvents of different Lewis basicity. By analyzing the ultrafast spectral diffusion dynamics of the Qy transition, we show that a certain timescale of the spectral diffusion dynamics is affected by the solvents' Lewis basicity. Control experiments with Chlorin-e6-a Chl molecule analog-and ab initio time-dependent density functional theory calculations confirm that we are directly probing the fluctuation dynamics of the dative bond between the solvent's lone pair and the Mg2+ center in Chls that is responsible for the Lewis basicity. The observation is indicative of dative bond length and angular fluctuations with timescales ranging between ∼30 and 150 ps and the dative bond-strength-dependent perturbation on the Qy transition frequency of Chls.
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Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Jamie Hung Ni Sim
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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2
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Ebrey T. Brighter than the sun: Rajni Govindjee at 80 and her fifty years in photobiology. PHOTOSYNTHESIS RESEARCH 2015; 124:1-5. [PMID: 25739899 DOI: 10.1007/s11120-015-0106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
We celebrate distinguished photobiologist Rajni Govindjee for her pioneering research in photosynthesis and retinal proteins on the occasion of her 80th birthday.
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Affiliation(s)
- Thomas Ebrey
- University of Washington, Seattle, WA, 98109, USA,
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3
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Nakanishi K, Crouch R. Application of Artificial Pigments to Structure Determination and Study of Photoinduced Transformations of Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500030] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Gillespie NB, Ren L, Ramos L, Daniel H, Dews D, Utzat KA, Stuart JA, Buck CH, Birge RR. Characterization and Photochemistry of 13-Desmethyl Bacteriorhodopsin. J Phys Chem B 2005; 109:16142-52. [PMID: 16853051 PMCID: PMC1513633 DOI: 10.1021/jp052124+] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda > 590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --> P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --> P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the native protein.
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Affiliation(s)
- Nathan B. Gillespie
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
- W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Lei Ren
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
- W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Lavoisier Ramos
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
| | - Heather Daniel
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
| | - Deborah Dews
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
| | - Karissa A. Utzat
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
| | - Jeffrey A. Stuart
- W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Charles H. Buck
- W. M. Keck Center for Molecular Electronics and Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244-4100
| | - Robert R. Birge
- Departments of Chemistry and of Molecular and Cell Biology, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060
- *Address correspondence to this author (
) corresponding author: Robert R. Birge, Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269-3060: 860-486-6720; Fax(860-486-2981);
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5
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Abstract
[structure: see text] The preparations and spectroscopic characteristics of five all-trans halogenated canthaxanthins are described in this letter. The air/light-sensitive halogenated canthaxanthins were used to study alpha-crustacyanin, a blue astaxanthin-protein complex, which is isolated from the carapace of the lobster. Steric and electronegative effects of the halogen substituents on the noncovalent interaction between astaxanthin and the protein in alpha-crustacyanin were observed.
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Affiliation(s)
- Jin Liu
- Department of Chemistry, Murray State University, Murray, Kentucky 42071, USA.
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6
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Das J, Crouch RK, Govindjee R, Balashov S, Ebrey T. Studies on Pyry I retinal Analogues of Bacteriorhodopsin. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb08307.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Colmenares LU, Mead D, Yoshida W, Alam M, Liu RSH. An F NMR Study of Bis(trifluoromethyl)phenyl Bacteriorhodopsin Analogs. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952592r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. U. Colmenares
- Department of Chemistry, University of Hawaii, Honolulu, Hawaii 96822
| | - D. Mead
- Department of Chemistry, University of Hawaii, Honolulu, Hawaii 96822
| | - W. Yoshida
- Department of Chemistry, University of Hawaii, Honolulu, Hawaii 96822
| | - M. Alam
- Department of Chemistry, University of Hawaii, Honolulu, Hawaii 96822
| | - R. S. H. Liu
- Department of Chemistry, University of Hawaii, Honolulu, Hawaii 96822
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Liu RS, Krogh E, Li XY, Mead D, Colmenares LU, Thiel JR, Ellis J, Wong D, Asato AE. Analyzing the red-shift characteristics of azulenic, naphthyl, other ring-fused and retinyl pigment analogs of bacteriorhodopsin. Photochem Photobiol 1993; 58:701-5. [PMID: 8284326 DOI: 10.1111/j.1751-1097.1993.tb04955.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Prompted by the near infrared-absorbing properties of some of the azulenic bacteriorhodopsin (bR) analogs, we have analyzed their absorption characteristics along with 11 new related ring-fused analogs and the corresponding Schiff bases (SB) and protonated Schiff bases (PSB). The following three factors are believed to contribute to the total red shift of each of the pigment analogs (sigma RS): perturbation of the basic chromophore (SB shift, delta SB), protonation of the SB (PSB shift, PSBS) and protein perturbation (the opsin shift, OS). For each factor, effects of structural modifications were examined. For the red-shifted pigments, percent OS has been suggested as an alternate way of measuring protein perturbation. Computer-simulated chromophores provided evidence against any explanation involving altered shapes of the binding pocket as a major cause for absorption differences. Implications of the current bR results on preparation of further red-shifted bR and possible application to visual pigment analogs are discussed.
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Affiliation(s)
- R S Liu
- Department of Chemistry, University of Hawaii, Honolulu 96822
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9
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Electric light scattering study of apomembranes. J Electroanal Chem (Lausanne) 1992. [DOI: 10.1016/0022-0728(92)85107-e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Liu RS, Liu CW, Li XY, Asato AE. Butyl conformational reorganization as a possible explanation for the longitudinal flexibility of the binding site of bacteriorhodopsin. The azulene and C-22 retinoid analogs. Photochem Photobiol 1991; 54:625-31. [PMID: 1796116 DOI: 10.1111/j.1751-1097.1991.tb02066.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The UV-VIS absorption data of four bacteriorhodopsin (BR) analogs formed from azulene-retinals of varying polyene chain length show that the one-bond-shortened to one-bond-lengthened analogs possess comparable opsin shift values to that of BR. A two-bond-shortened analog exhibited a much smaller opsin shift. These data, combined with those reported for the C-22 retinal analog (Tokunaga et al., 1977, Biophys. J. 19, 191-198) were analyzed by molecular modelling and computer graphics in terms of a model where conformational flexibility of the appended butyl is the controlling factor in determining ease of pigment formation and protein/substrate interaction.
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Affiliation(s)
- R S Liu
- Department of Chemistry, University of Hawaii, Honolulu 96822
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11
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van den Berg R, Jang DJ, el-Sayed MA. Decay of the tryptophan fluorescence anisotropy in bacteriorhodopsin and its modified forms. Biophys J 1990; 57:759-64. [PMID: 2344462 PMCID: PMC1280777 DOI: 10.1016/s0006-3495(90)82596-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this work we study the decay of the polarization of the Trp fluorescence in native bacteriorhodopsin (bR), deionized bR (dlbR), and the retinal-free form of bR, bacterioopsin (bO), using picosecond laser/streak camera system. Two types of depolarization processes are observed, one around 250 ps, which is temperature independent around room temperature, and the other in the 1-3-ns range, which is sensitive to temperature and certain bR modifications. This suggests the presence of at least two different environments for the eight Trp molecules in bR. Native bR and deionized bR gave the same depolarization decay times, suggesting that the removal of metal cations does not change the microenvironment of the emitting Trp molecules. The slow component is faster in bO than in bR, suggesting a change in the environment of the Trp molecules upon the removal of the retinal chromophore. All these results are discussed in terms of the different mechanisms of Trp fluorescence depolarization. A comparison between the depolarization decay in rhodopsin and bR is made.
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Affiliation(s)
- R van den Berg
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
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12
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Lazarova T. Properties of apomembranes treated with sodium borohydride. J Electroanal Chem (Lausanne) 1989. [DOI: 10.1016/0022-0728(89)87302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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