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Shafiei G, Levenberg A, Lujan MA, Picorel R, Zazubovich V. Evidence of Simultaneous Spectral Hole Burning Involving Two Tiers of the Protein Energy Landscape in Cytochrome b6f. J Phys Chem B 2019; 123:10930-10938. [PMID: 31763829 DOI: 10.1021/acs.jpcb.9b09515] [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
Cytochrome b6f, with one chlorophyll molecule per protein monomer, is a simple model system whose studies can help achieve a better understanding of nonphotochemical spectral hole burning (NPHB) and single-complex spectroscopy results obtained in more complicated photosynthetic chlorophyll-protein complexes. We are reporting new data and proposing an alternative explanation for spectral dynamics that was recently observed in cytochrome b6f using NPHB. The relevant distribution of the tunneling parameter λ is a superposition of two components that are nearly degenerate in terms of the resultant NPHB yield and represent two tiers of the energy landscape responsible for NPHB. These two components likely burn competitively; we present the first demonstration of modeling a competitive NPHB process. Similar values of the NPHB yield result from distinctly different combinations of barrier heights, shifts along the generalized coordinate d, and/or masses of the entities involved in conformational changes m, with md2 parameter different by a factor of 2.7. Consequently, in cytochrome b6f, the first (at least) 10 h of fixed-temperature recovery preferentially probe different components of the barrier- and λ-distributions encoded into the spectral holes than thermocycling experiments. Both components most likely represent dynamics of the protein and not of the surrounding buffer/glycerol glass.
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Affiliation(s)
- Golia Shafiei
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
| | - Alexander Levenberg
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
| | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005 , 50059 Zaragoza , Spain
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005 , 50059 Zaragoza , Spain
| | - Valter Zazubovich
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
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Levenberg A, Shafiei G, Lujan MA, Giannacopoulos S, Picorel R, Zazubovich V. Probing Energy Landscapes of Cytochrome b 6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent. J Phys Chem B 2017; 121:9848-9858. [PMID: 28956922 DOI: 10.1021/acs.jpcb.7b07686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In non-photochemical spectral hole burning (NPHB) and spectral hole recovery experiments, cytochrome b6f protein exhibits behavior that is almost independent of the deuteration of the buffer/glycerol glassy matrix containing the protein, apart from some differences in heat dissipation. On the other hand, strong dependence of the hole burning properties on sample preparation procedures was observed and attributed to a large increase of the electron-phonon coupling and shortening of the excited-state lifetime occurring when n-dodecyl β-d-maltoside (DM) is used as a detergent instead of n-octyl β-d-glucopyranoside (OGP). The data was analyzed assuming that the tunneling parameter distribution or barrier distribution probed by NPHB and encoded into the spectral holes contains contributions from two nonidentical components with accidentally degenerate excited state λ-distributions. Both components likely reflect protein dynamics, although with some small probability one of them (with larger md2) may still represent the dynamics involving specifically the -OH groups of the water/glycerol solvent. Single proton tunneling in the water/glycerol solvent environment or in the protein can be safely excluded as the origin of observed NPHB and hole recovery dynamics. The intensity dependence of the hole growth kinetics in deuterated samples likely reflects differences in heat dissipation between protonated and deuterated samples. These differences are most probably due to the higher interface thermal resistivity between (still protonated) protein and deuterated water/glycerol outside environment.
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Affiliation(s)
- Alexander Levenberg
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Golia Shafiei
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Steven Giannacopoulos
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Valter Zazubovich
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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Najafi M, Herascu N, Shafiei G, Picorel R, Zazubovich V. Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects. J Phys Chem B 2015; 119:6930-40. [PMID: 25985255 DOI: 10.1021/acs.jpcb.5b02845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mehdi Najafi
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Nicoleta Herascu
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Golia Shafiei
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Valter Zazubovich
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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Najafi M, Herascu N, Seibert M, Picorel R, Jankowiak R, Zazubovich V. Spectral Hole Burning, Recovery, and Thermocycling in Chlorophyll–Protein Complexes: Distributions of Barriers on the Protein Energy Landscape. J Phys Chem B 2012; 116:11780-90. [DOI: 10.1021/jp308055r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mehdi Najafi
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal,
Quebec H4B 1R6 Canada
| | - Nicoleta Herascu
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal,
Quebec H4B 1R6 Canada
| | - Michael Seibert
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC), Avda. Montañana 1005, 50002
Zaragoza, Spain
| | - Ryszard Jankowiak
- Department
of Chemistry, Kansas State University,
Manhattan, Kansas 66505, United
States
| | - Valter Zazubovich
- Department of Physics, Concordia University, 7141 Sherbrooke Str. West, Montreal,
Quebec H4B 1R6 Canada
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Jankowiak R, Reppert M, Zazubovich V, Pieper J, Reinot T. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron–Phonon Coupling of Selected Photosynthetic Complexes. Chem Rev 2011; 111:4546-98. [DOI: 10.1021/cr100234j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B1R6 Quebec, Canada
| | - Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University of Berlin, Germany
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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Herascu N, Najafi M, Amunts A, Pieper J, Irrgang KD, Picorel R, Seibert M, Zazubovich V. Parameters of the protein energy landscapes of several light-harvesting complexes probed via spectral hole growth kinetics measurements. J Phys Chem B 2011; 115:2737-47. [PMID: 21391534 DOI: 10.1021/jp108775y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The parameters of barrier distributions on the protein energy landscape in the excited electronic state of the pigment/protein system have been determined by means of spectral hole burning for the lowest-energy pigments of CP43 core antenna complex and CP29 minor antenna complex of spinach Photosystem II (PS II) as well as of trimeric and monomeric LHCII complexes transiently associated with the pea Photosystem I (PS I) pool. All of these complexes exhibit sixty to several hundred times lower spectral hole burning yields as compared with molecular glassy solids previously probed by means of the hole growth kinetics measurements. Therefore, the entities (groups of atoms), which participate in conformational changes in protein, appear to be significantly larger and heavier than those in molecular glasses. No evidence of a small (∼1 cm(-1)) spectral shift tier of the spectral diffusion dynamics has been observed. Therefore, our data most likely reflect the true barrier distributions of the intact protein and not those related to the interface or surrounding host. Possible applications of the barrier distributions as well as the assignments of low-energy states of CP29 and LHCII are discussed in light of the above results.
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Affiliation(s)
- Nicoleta Herascu
- Department of Physics, Concordia University, Montreal, Quebec, Canada
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Purchase R, Völker S. Spectral hole burning: examples from photosynthesis. PHOTOSYNTHESIS RESEARCH 2009; 101:245-66. [PMID: 19714478 PMCID: PMC2744831 DOI: 10.1007/s11120-009-9484-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/31/2009] [Indexed: 05/14/2023]
Abstract
The optical spectra of photosynthetic pigment-protein complexes usually show broad absorption bands, often consisting of a number of overlapping, "hidden" bands belonging to different species. Spectral hole burning is an ideal technique to unravel the optical and dynamic properties of such hidden species. Here, the principles of spectral hole burning (HB) and the experimental set-up used in its continuous wave (CW) and time-resolved versions are described. Examples from photosynthesis studied with hole burning, obtained in our laboratory, are then presented. These examples have been classified into three groups according to the parameters that were measured: (1) hole widths as a function of temperature, (2) hole widths as a function of delay time and (3) hole depths as a function of wavelength. Two examples from light-harvesting (LH) 2 complexes of purple bacteria are given within the first group: (a) the determination of energy-transfer times from the chromophores in the B800 ring to the B850 ring, and (b) optical dephasing in the B850 absorption band. One example from photosystem II (PSII) sub-core complexes of higher plants is given within the second group: it shows that the size of the complex determines the amount of spectral diffusion measured. Within the third group, two examples from (green) plants and purple bacteria have been chosen for: (a) the identification of "traps" for energy transfer in PSII sub-core complexes of green plants, and (b) the uncovering of the lowest k = 0 exciton-state distribution within the B850 band of LH2 complexes of purple bacteria. The results prove the potential of spectral hole burning measurements for getting quantitative insight into dynamic processes in photosynthetic systems at low temperature, in particular, when individual bands are hidden within broad absorption bands. Because of its high-resolution wavelength selectivity, HB is a technique that is complementary to ultrafast pump-probe methods. In this review, we have provided an extensive bibliography for the benefit of scientists who plan to make use of this valuable technique in their future research.
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Affiliation(s)
- Robin Purchase
- Huygens and Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Silvia Völker
- Huygens and Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
- Department of Biophysics, Faculty of Exact Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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Bonsma S, Purchase R, Jezowski S, Gallus J, Könz F, Völker S. Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning. Chemphyschem 2005; 6:838-49. [PMID: 15884066 DOI: 10.1002/cphc.200500005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Indexed: 11/12/2022]
Abstract
The cloning and expression of autofluorescent proteins in living matter, combined with modern imaging techniques, have thoroughly changed the world of bioscience. In particular, such proteins are widely used as genetically encoded labels to track the movement of proteins as reporters of cellular signals and to study protein-protein interactions by fluorescence resonance energy transfer (FRET). Their optical properties, however, are complex and it is important to understand these for the correct interpretation of imaging data and for the design of new fluorescent mutants. In this Minireview we start with a short survey of the field and then focus on the photo- and thermally induced dynamics of green and red fluorescent proteins. In particular, we show how fluorescence line narrowing and high-resolution spectral hole burning at low temperatures can be used to unravel the photophysics and photochemistry and shed light on the intricate electronic structure of these proteins.
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Affiliation(s)
- S Bonsma
- Huygens and Gorlaeus Laboratories, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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Brüggemann B, Sznee K, Novoderezhkin V, van Grondelle R, May V. From Structure to Dynamics: Modeling Exciton Dynamics in the Photosynthetic Antenna PS1. J Phys Chem B 2004. [DOI: 10.1021/jp0401473] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B. Brüggemann
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany, Division of Physics and Astronomy, Faculty of Sciences and Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - K. Sznee
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany, Division of Physics and Astronomy, Faculty of Sciences and Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - V. Novoderezhkin
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany, Division of Physics and Astronomy, Faculty of Sciences and Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - R. van Grondelle
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany, Division of Physics and Astronomy, Faculty of Sciences and Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - V. May
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany, Division of Physics and Astronomy, Faculty of Sciences and Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
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Borovykh I, Kulik L, Gast P, Dzuba S. Conformation transition in the protein of a photosynthetic reaction center observed at the nanometer range of distances at cryogenic temperatures. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00323-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Creemers TMH, De Caro CA, Visschers RW, van Grondelle R, Völker S. Spectral Hole Burning and Fluorescence Line Narrowing in Subunits of the Light-Harvesting Complex LH1 of Purple Bacteria. J Phys Chem B 1999. [DOI: 10.1021/jp990805x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. M. H. Creemers
- Center for the Study of Excited States of Molecules, Huygens and Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands, Department of Biomolecular Structure and Dynamics, Faculty of Biology, Free University, 1081 HV Amsterdam, The Netherlands, and Department of Biophysics, Faculty of Exact Sciences, Free University, 1081 HV Amsterdam, The Netherlands
| | - C. A. De Caro
- Center for the Study of Excited States of Molecules, Huygens and Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands, Department of Biomolecular Structure and Dynamics, Faculty of Biology, Free University, 1081 HV Amsterdam, The Netherlands, and Department of Biophysics, Faculty of Exact Sciences, Free University, 1081 HV Amsterdam, The Netherlands
| | - R. W. Visschers
- Center for the Study of Excited States of Molecules, Huygens and Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands, Department of Biomolecular Structure and Dynamics, Faculty of Biology, Free University, 1081 HV Amsterdam, The Netherlands, and Department of Biophysics, Faculty of Exact Sciences, Free University, 1081 HV Amsterdam, The Netherlands
| | - R. van Grondelle
- Center for the Study of Excited States of Molecules, Huygens and Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands, Department of Biomolecular Structure and Dynamics, Faculty of Biology, Free University, 1081 HV Amsterdam, The Netherlands, and Department of Biophysics, Faculty of Exact Sciences, Free University, 1081 HV Amsterdam, The Netherlands
| | - S. Völker
- Center for the Study of Excited States of Molecules, Huygens and Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands, Department of Biomolecular Structure and Dynamics, Faculty of Biology, Free University, 1081 HV Amsterdam, The Netherlands, and Department of Biophysics, Faculty of Exact Sciences, Free University, 1081 HV Amsterdam, The Netherlands
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