51
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Oba T, Tamiaki H. Asymmetry of chlorophylls in photosynthetic proteins: from the viewpoint of coordination chemistry. J PORPHYR PHTHALOCYA 2014. [DOI: 10.1142/s1088424614500710] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We conducted a meta-analysis of (bacterio)chlorophyll [(B)Chl] molecules in photosynthetic pigment-protein complexes from the viewpoint of coordination chemistry. We surveyed the ligand species and site in the axial coordination of 146 Chl and 21 BChl molecules in 42 reported crystal structures of 12-type proteins. The imidazolyl moiety of histidine (His) is the most abundant ligand, and the second is water, a much weaker ligand. We focused on the positions, the circumstances, and the macrocycle sides for the coordination of the 31 hydrated (B)Chl molecules found in these proteins. A ligand water molecule of a hydrated (B)Chl is not necessarily hydrogen-bonded to the surrounding protein residues. A hydrated (B)Chl seems to occupy the redundant space where more strongly coupled His-Chl complexes cannot be formed. It is noted that 28 of 31 hydrated (B)Chl molecules (90) were coordinated from the α-side of the (bacterio)chlorin macrocycle, the opposite side from which the C 17-propionic ester protrudes. Among them, all five hydrated Chl molecules at the edges of the proteins were coordinated from the α-side, suggesting that (B)Chl molecules prefer this side for the coordination bondings to the β-side. The analysis also revealed that each (B)Chl binding site was composed of both the protein residues and the neighboring pigment molecules contributing roughly equally. It can be safely said that the cofactor pigments aggregated even in the proteins. Penta-coordination is advantageous to flexible adjustment of intermolecular orientations of (B)Chl molecules in the aggregates.
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Affiliation(s)
- Toru Oba
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, Utsunomiya, Tochigi 321-8585, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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52
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Dutta PK, Levenberg S, Loskutov A, Jun D, Saer R, Beatty JT, Lin S, Liu Y, Woodbury NW, Yan H. A DNA-Directed Light-Harvesting/Reaction Center System. J Am Chem Soc 2014; 136:16618-25. [DOI: 10.1021/ja509018g] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | - Daniel Jun
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rafael Saer
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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53
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Saggu M, Carter B, Zhou X, Faries K, Cegelski L, Holten D, Boxer SG, Kirmaier C. Putative hydrogen bond to tyrosine M208 in photosynthetic reaction centers from Rhodobacter capsulatus significantly slows primary charge separation. J Phys Chem B 2014; 118:6721-32. [PMID: 24902471 PMCID: PMC4064694 DOI: 10.1021/jp503422c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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Slow, ∼50
ps, P* → P+HA– electron
transfer is observed in Rhodobacter
capsulatus reaction centers (RCs) bearing the native
Tyr residue at M208 and the single amino acid change of isoleucine
at M204 to glutamic acid. The P* decay kinetics are unusually homogeneous
(single exponential) at room temperature. Comparative solid-state
NMR of [4′-13C]Tyr labeled wild-type and M204E RCs
show that the chemical shift of Tyr M208 is significantly altered
in the M204E mutant and in a manner consistent with formation of a
hydrogen bond to the Tyr M208 hydroxyl group. Models based on RC crystal
structure coordinates indicate that if such a hydrogen bond is formed
between the Glu at M204 and the M208 Tyr hydroxyl group, the −OH
would be oriented in a fashion expected (based on the calculations
by Alden et al., J. Phys. Chem.1996, 100, 16761–16770) to destabilize P+BA– in free energy. Alteration
of the environment of Tyr M208 and BA by Glu M204 via this
putative hydrogen bond has a powerful influence on primary charge
separation.
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Affiliation(s)
- Miguel Saggu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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54
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The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:301-15. [PMID: 24824111 DOI: 10.1007/s00249-014-0963-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/07/2014] [Accepted: 04/25/2014] [Indexed: 12/29/2022]
Abstract
Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.
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55
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Marchanka A, Lubitz W, Plato M, van Gastel M. Comparative ENDOR study at 34 GHz of the triplet state of the primary donor in bacterial reaction centers of Rb. sphaeroides and Bl. viridis. PHOTOSYNTHESIS RESEARCH 2014; 120:99-111. [PMID: 23184403 DOI: 10.1007/s11120-012-9786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/07/2012] [Indexed: 05/22/2023]
Abstract
The primary electron donor (P) in the photosynthetic bacterial reaction center of Rhodobacter sphaeroides and Blastochloris viridis consists of a dimer of bacteriochlorophyll a and b cofactors, respectively. Its photoexcited triplet state in frozen solution has been investigated by time resolved ENDOR spectroscopy at 34 GHz. The observed ENDOR spectra for (3)P865 and (3)P960 are essentially the same, indicating very similar spin density distributions. Exceptions are the ethylidene groups unique to the bacteriochlorophyll b dimer in (3)P960. Strikingly, the observed hyperfine coupling constants of the ethylidene groups are larger than in the monomer, which speaks for an asymmetrically delocalized wave function over both monomer halves in the dimer. The latter observation corroborates previous findings of the spin density in the radical cation states P 865 (•+) (Lendzian et al. in Biochim Biophys Acta 1183:139-160, 1993) and P 960 (•+) (Lendzian et al. in Chem Phys Lett 148:377-385, 1988). As compared to the bacteriochlorophyll monomer, the hyperfine coupling constants of the methyl groups 2(1) and 12(1) are reduced by at least a factor of two, and quantitative analysis of these couplings gives rise to a ratio of approximately 3:1 for the spin density on the halves PL:PM. Our findings are discussed in light of the large difference in photosynthetic activity of the two branches of cofactors present in the bacterial reaction center proteins.
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Affiliation(s)
- Aliaksandr Marchanka
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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56
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Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:366-74. [DOI: 10.1016/j.bbabio.2013.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/21/2013] [Accepted: 11/26/2013] [Indexed: 11/22/2022]
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57
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Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Nuclear hyperfine and quadrupole tensor characterization of the nitrogen hydrogen bond donors to the semiquinone of the QB site in bacterial reaction centers: a combined X- and S-band (14,15)N ESEEM and DFT study. J Phys Chem B 2014; 118:1501-9. [PMID: 24437652 PMCID: PMC3983398 DOI: 10.1021/jp411023k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
secondary quinone anion radical QB– (SQB) in reaction centers of Rhodobacter
sphaeroides interacts with Nδ of
His-L190 and Np (peptide nitrogen) of Gly-L225 involved
in hydrogen bonds to the QB carbonyls. In this work, S-band
(∼3.6 GHz) ESEEM was used with the aim of obtaining a complete
characterization of the nuclear quadrupole interaction (nqi) tensors
for both nitrogens by approaching the cancelation condition between
the isotropic hyperfine coupling and 14N Zeeman frequency
at lower microwave frequencies than traditional X-band (9.5 GHz).
By performing measurements at S-band, we found a dominating contribution
of Nδ in the form of a zero-field nqi triplet at
0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e2qQ/4h = 0.4 MHz and associated asymmetry parameter η =
0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of
1D and 2D 14,15N X-band and three-pulse 14N
S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the
contribution of Np to the S-band spectrum is suppressed
by its strong nqi and weak isotropic hfi comparable to the level of
hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations
and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to
full tensor characterizations.
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Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, ‡Department of Biochemistry, §Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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58
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Linke K, Ho FM. Water in Photosystem II: Structural, functional and mechanistic considerations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:14-32. [DOI: 10.1016/j.bbabio.2013.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 12/30/2022]
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59
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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60
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Qian P, Papiz MZ, Jackson PJ, Brindley AA, Ng IW, Olsen JD, Dickman MJ, Bullough PA, Hunter CN. Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX. Biochemistry 2013; 52:7575-85. [DOI: 10.1021/bi4011946] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pu Qian
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Miroslav Z. Papiz
- Institute
of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Philip J. Jackson
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Amanda A. Brindley
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Irene W. Ng
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - John D. Olsen
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - Mark J. Dickman
- ChELSI
Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Per A. Bullough
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, United Kingdom
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61
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Müh F, Zouni A. The nonheme iron in photosystem II. PHOTOSYNTHESIS RESEARCH 2013; 116:295-314. [PMID: 24077892 DOI: 10.1007/s11120-013-9926-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/17/2013] [Indexed: 06/02/2023]
Abstract
Photosystem II (PSII), the light-driven water:plastoquinone (PQ) oxidoreductase of oxygenic photosynthesis, contains a nonheme iron (NHI) at its electron acceptor side. The NHI is situated between the two PQs QA and QB that serve as one-electron transmitter and substrate of the reductase part of PSII, respectively. Among the ligands of the NHI is a (bi)carbonate originating from CO2, the substrate of the dark reactions of oxygenic photosynthesis. Based on recent advances in the crystallography of PSII, we review the structure of the NHI in PSII and discuss ideas concerning its function and the role of bicarbonate along with a comparison to the reaction center of purple bacteria and other enzymes containing a mononuclear NHI site.
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62
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Pan J, Saer RG, Lin S, Guo Z, Beatty JT, Woodbury NW. The Protein Environment of the Bacteriopheophytin Anion Modulates Charge Separation and Charge Recombination in Bacterial Reaction Centers. J Phys Chem B 2013; 117:7179-89. [DOI: 10.1021/jp400132k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Pan
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - Rafael G. Saer
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Su Lin
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
| | - Zhi Guo
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
| | - J. Thomas Beatty
- Department of Microbiology and
Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada
V6T 1Z3
| | - Neal W. Woodbury
- The Biodesign
Institute at Arizona
State University, Arizona State University, Tempe, Arizona 85287-5201, United States
- Department of Chemistry and
Biochemistry, Arizona State University,
Tempe, Arizona 85287-1604, United States
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63
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Onidas D, Sipka G, Asztalos E, Maróti P. Mutational control of bioenergetics of bacterial reaction center probed by delayed fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1191-9. [PMID: 23685111 DOI: 10.1016/j.bbabio.2013.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/01/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
The free energy gap between the metastable charge separated state P(+)QA(-) and the excited bacteriochlorophyll dimer P* was measured by delayed fluorescence of the dimer in mutant reaction center proteins of the photosynthetic bacterium Rhodobacter sphaeroides. The mutations were engineered both at the donor (L131L, M160L, M197F and M202H) and acceptor (M265I and M234E) sides. While the donor side mutations changed systematically the number of H-bonds to P, the acceptor side mutations modified the energetics of QA by altering the van-der-Waals and electronic interactions (M265IT) and H-bond network to the acidic cluster around QB (M234EH, M234EL, M234EA and M234ER). All mutants decreased the free energy gap of the wild type RC (~890meV), i.e. destabilized the P(+)QA(-) charge pair by 60-110meV at pH8. Multiple modifications in the hydrogen bonding pattern to P resulted in systematic changes of the free energy gap. The destabilization showed no pH-dependence (M234 mutants) or slight increase (WT, donor-side mutants and M265IT above pH8) with average slope of 10-15meV/pH unit over the 6-10.5pH range. In wild type and donor-side mutants, the free energy change of the charge separation consisted of mainly enthalpic term but the acceptor side mutants showed increased entropic (even above that of enthalpic) contributions. This could include softening the structure of the iron ligand (M234EH) and the QA binding pocket (M265IT) and/or increase of the multiplicity of the electron transfer of charge separation in the acceptor side upon mutation.
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Affiliation(s)
- Delphine Onidas
- Laboratoire de Chimie Physique UMR 8000, Batiment 350, Orsay-Cedex, Université de Paris-Sud, 91405, France
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64
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Harris MA, Luehr CA, Faries KM, Wander M, Kressel L, Holten D, Hanson DK, Laible PD, Kirmaier C. Protein Influence on Charge-Asymmetry of the Primary Donor in Photosynthetic Bacterial Reaction Centers Containing a Heterodimer: Effects on Photophysical Properties and Electron Transfer. J Phys Chem B 2013; 117:4028-41. [DOI: 10.1021/jp401138h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michelle A. Harris
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Craig A. Luehr
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Kaitlyn M. Faries
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Marc Wander
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Lucas Kressel
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Deborah K. Hanson
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Philip D. Laible
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,
United States
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
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65
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Chernev P, Zaharieva I, Dau H, Haumann M. Coordination Changes of Carboxyl Ligands at the QAFeQB Triad in Photosynthetic Reaction Centers Studied by Density-Functional Theory. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-642-32034-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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66
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Dikanov SA. Resolving protein-semiquinone interactions by two-dimensional ESEEM spectroscopy. ELECTRON PARAMAGNETIC RESONANCE 2012. [DOI: 10.1039/9781849734837-00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S. A. Dikanov
- University of Illinois at Urbana-Champaign, Department of Veterinary Clinical Medicine 190 MSB, 506 S. Mathews Ave., Urbana IL 61801 USA
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67
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Martin E, Baldansuren A, Lin TJ, Samoilova RI, Wraight CA, Dikanov SA, O'Malley PJ. Hydrogen bonding between the Q(B) site ubisemiquinone and Ser-L223 in the bacterial reaction center: a combined spectroscopic and computational perspective. Biochemistry 2012; 51:9086-93. [PMID: 23016832 DOI: 10.1021/bi300834w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the Q(B) site of the Rhodobacter sphaeroides photosynthetic reaction center, the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study, we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM, and HYSCORE spectroscopic differences between mutant L223SA and the wild-type sample (WT) are negligible, indicating only minor perturbations in the ubisemiquinone spin density for the mutant sample. Qualitatively, this suggests that a strong hydrogen bond does not exist in the WT between the Ser-L223 hydroxyl group and the semiquinone O(1) atom, as removal of this hydrogen bond in the mutant should cause a significant redistribution of spin density in the semiquinone. We show quantitatively, using QM/MM calculations, that a WT model in which the Ser-L223 hydroxyl group is rotated to prevent hydrogen bond formation with the O(1) atom of the semiquinone predicts negligible change for the L223SA mutant. This, together with the better agreement between key QM/MM calculated and experimental hyperfine couplings for the non-hydrogen-bonded model, leads us to conclude that no strong hydrogen bond is formed between the Ser-L223 hydroxyl group and the semiquinone O(1) atom after the first flash. The implications of this finding for quinone reduction in photosynthetic reaction centers are discussed.
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Affiliation(s)
- Erik Martin
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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68
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Effects of dehydration on light-induced conformational changes in bacterial photosynthetic reaction centers probed by optical and differential FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:328-39. [PMID: 23103449 DOI: 10.1016/j.bbabio.2012.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 11/22/2022]
Abstract
Following light-induced electron transfer between the primary donor (P) and quinone acceptor (Q(A)) the bacterial photosynthetic reaction center (RC) undergoes conformational relaxations which stabilize the primary charge separated state P(+)Q(A)(-). Dehydration of RCs from Rhodobacter sphaeroides hinders these conformational dynamics, leading to acceleration of P(+)Q(A)(-) recombination kinetics [Malferrari et al., J. Phys. Chem. B 115 (2011) 14732-14750]. To clarify the structural basis of the conformational relaxations and the involvement of bound water molecules, we analyzed light-induced P(+)Q(A)(-)/PQ(A) difference FTIR spectra of RC films at two hydration levels (relative humidity r=76% and r=11%). Dehydration reduced the amplitude of bands in the 3700-3550cm(-1) region, attributed to water molecules hydrogen bonded to the RC, previously proposed to stabilize the charge separation by dielectric screening [Iwata et al., Biochemistry 48 (2009) 1220-1229]. Other features of the FTIR difference spectrum were affected by partial depletion of the hydration shell (r=11%), including contributions from modes of P (9-keto groups), and from NH or OH stretching modes of amino acidic residues, absorbing in the 3550-3150cm(-1) range, a region so far not examined in detail for bacterial RCs. To probe in parallel the effects of dehydration on the RC conformational relaxations, we analyzed by optical absorption spectroscopy the kinetics of P(+)Q(A)(-) recombination following the same photoexcitation used in FTIR measurements (20s continuous illumination). The results suggest a correlation between the observed FTIR spectral changes and the conformational rearrangements which, in the hydrated system, strongly stabilize the P(+)Q(A)(-) charge separated state over the second time scale.
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69
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Hałas A, Orzechowska A, Derrien V, Chumakov AI, Sebban P, Fiedor J, Lipińska M, Zając M, Ślęzak T, Strzałka K, Matlak K, Korecki J, Fiedor L, Burda K. The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:2095-102. [PMID: 22921693 DOI: 10.1016/j.bbabio.2012.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 08/06/2012] [Accepted: 08/09/2012] [Indexed: 11/28/2022]
Abstract
We investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θ(D0)~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c(2), and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe.
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Affiliation(s)
- A Hałas
- AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, 30-059 Kraków, Poland
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70
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Carter B, Boxer SG, Holten D, Kirmaier C. Photochemistry of a Bacterial Photosynthetic Reaction Center Missing the Initial Bacteriochlorophyll Electron Acceptor. J Phys Chem B 2012; 116:9971-82. [DOI: 10.1021/jp305276m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brett Carter
- Department of Chemistry, Stanford University, Stanford, California
94305-5080, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California
94305-5080, United States
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri
63130-4899, United States
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri
63130-4899, United States
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71
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Saito K, Umena Y, Kawakami K, Shen JR, Kamiya N, Ishikita H. Deformation of Chlorin Rings in the Photosystem II Crystal Structure. Biochemistry 2012; 51:4290-9. [DOI: 10.1021/bi300428s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Keisuke Saito
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
| | - Yasufumi Umena
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
| | - Keisuke Kawakami
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Jian-Ren Shen
- Division of Bioscience,
Graduate
School of Natural Science and Technology/Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Nobuo Kamiya
- The OCU
Advanced Research Institute
for Natural Science and Technology (OCARINA)/Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
- Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan
| | - Hiroshi Ishikita
- 202 Building E, Career-Path
Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto
606-8501, Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic
Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
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72
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Ullmann RT, Ullmann GM. GMCT : a Monte Carlo simulation package for macromolecular receptors. J Comput Chem 2012; 33:887-900. [PMID: 22278916 DOI: 10.1002/jcc.22919] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/21/2011] [Accepted: 12/02/2011] [Indexed: 11/08/2022]
Abstract
Generalized Monte Carlo titration (GMCT) is a versatile suite of computer programs for the efficient simulation of complex macromolecular receptor systems as for example proteins. The computational model of the system is based on a microstate description of the receptor and an average description of its surroundings in terms of chemical potentials. The receptor can be modeled in great detail including conformational flexibility and many binding sites with multiple different forms that can bind different ligand types. Membrane embedded systems can be modeled including electrochemical potential gradients. Overall properties of the receptor as well as properties of individual sites can be studied with a variety of different Monte Carlo (MC) simulation methods. Metropolis MC, Wang-Landau MC and efficient free energy calculation methods are included. GMCT is distributed as free open source software at www.bisb.uni-bayreuth.de under the terms of the GNU Affero General Public License.
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Affiliation(s)
- R Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, Bayreuth 95447, Germany.
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73
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Leonova MM, Fufina TY, Vasilieva LG, Shuvalov VA. Structure-function investigations of bacterial photosynthetic reaction centers. BIOCHEMISTRY (MOSCOW) 2012; 76:1465-83. [DOI: 10.1134/s0006297911130074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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74
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Abstract
In this paper, we describe a new method to obtain D2O/H2O exchange in photosynthetic reaction centres fromRhodobacter sphaeroides. The method is characterized by: (i) a very high efficiency of the isotopic replacement; (ii) an extremely low amount of D2O needed; (iii) the short time required for dehydration and D2O rehydration; (iv) the possibility of controlling concomitantly the hydration state of the sample. The proposed method can be applied to other proteins.
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75
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Khatypov RA, Khmelnitskiy AY, Khristin AM, Fufina TY, Vasilieva LG, Shuvalov VA. Primary charge separation within P870* in wild type and heterodimer mutants in femtosecond time domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:1392-8. [PMID: 22209778 DOI: 10.1016/j.bbabio.2011.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/09/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
Abstract
Primary charge separation dynamics in the reaction center (RC) of purple bacterium Rhodobacter sphaeroides and its P870 heterodimer mutants have been studied using femtosecond time-resolved spectroscopy with 20 and 40fs excitation at 870nm at 293K. Absorbance increase in the 1060-1130nm region that is presumably attributed to P(A)(δ+) cation radical molecule as a part of mixed state with a charge transfer character P*(P(A)(δ+)P(B)(δ-)) was found. This state appears at 120-180fs time delay in the wild type RC and even faster in H(L173)L and H(M202)L heterodimer mutants and precedes electron transfer (ET) to B(A) bacteriochlorophyll with absorption band at 1020nm in WT. The formation of the P(A)(δ+)B(A)(δ-) state is a result of the electron transfer from P*(P(A)(δ+)P(B)(δ-)) to the primary electron acceptor B(A) (still mixed with P*) with the apparent time delay of ~1.1ps. Next step of ET is accompanied by the 3-ps appearance of bacteriopheophytin a(-) (H(A)(-)) band at 960nm. The study of the wave packet formation upon 20-fs illumination has shown that the vibration energy of the wave packet promotes reversible overcoming of an energy barrier between two potential energy surfaces P* and P*(P(A)(δ+)B(A)(δ-)) at ~500fs. For longer excitation pulses (40fs) this promotion is absent and tunneling through an energy barrier takes about 3ps. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- R A Khatypov
- Russian Academy of Sciences, Moscow, Russian Federation
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76
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Kargul J, Barber J. Structure and Function of Photosynthetic Reaction Centres. MOLECULAR SOLAR FUELS 2011. [DOI: 10.1039/9781849733038-00107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Extensive biochemical, biophysical, molecular biological and structural studies on a wide range of prokaryotic and eukaryotic photosynthetic organisms has revealed common features of their reaction centres where light induced charge separation and stabilization occurs. There is little doubt that all reaction centres have evolved from a common ancestor and have been optimized to maximum efficiency. As such they provide principles that can be used as a blueprint for developing artificial photo-electrochemical catalytic systems to generate solar fuels. This chapter summarises the common features of the organization of cofactors, electron transfer pathways and protein environments of reaction centres of anoxygenic and oxygenic phototrophs. In particular, the latest molecular details derived from X-ray crystallography are discussed in context of the specific catalytic functions of the Type I and Type II reaction centres.
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Affiliation(s)
- Joanna Kargul
- Division of Molecular Biosciences, Faculty of Natural Sciences Imperial College London, London, SW7 2AZ UK
| | - James Barber
- Division of Molecular Biosciences, Faculty of Natural Sciences Imperial College London, London, SW7 2AZ UK
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77
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Malferrari M, Francia F, Venturoli G. Coupling between Electron Transfer and Protein–Solvent Dynamics: FTIR and Laser-Flash Spectroscopy Studies in Photosynthetic Reaction Center Films at Different Hydration Levels. J Phys Chem B 2011; 115:14732-50. [DOI: 10.1021/jp2057767] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
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78
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Deshmukh SS, Tang K, Kálmán L. Lipid binding to the carotenoid binding site in photosynthetic reaction centers. J Am Chem Soc 2011; 133:16309-16. [PMID: 21894992 DOI: 10.1021/ja207750z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S.; Williams, J. C.; Allen, J. P.; Kalman, L. Biochemistry 2011, 50, 340). Here in the R-26 reaction centers, the combination of light-induced structural changes and lipid binding resulted in a 5 orders of magnitude increase in the lifetime of the charge-separated state involving the oxidized dimer and the reduced primary quinone in proteoliposomes. Only saturated phospholipids with fatty acid chains of 12 and 14 carbon atoms long were bound successfully at 8 °C by cooling the reaction center protein slowly from room temperature. In addition to reporting a dramatic increase of the lifetime of the charge-separated state at physiologically relevant temperatures, this study reveals a novel lipid binding site in photosynthetic reaction center. These results shed light on a new potential application of the reaction center in energy storage as a light-driven biocapacitor since the charges separated by ∼30 Å in a low-dielectric medium can be prevented from recombination for hours.
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Affiliation(s)
- Sasmit S Deshmukh
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
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79
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Zabelin AA, Shkuropatova VA, Shuvalov VA, Shkuropatov AY. FTIR spectroscopy of the reaction center of Chloroflexus aurantiacus: Photoreduction of the bacteriopheophytin electron acceptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1013-21. [DOI: 10.1016/j.bbabio.2011.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 11/25/2022]
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80
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Wientjes E, van Stokkum IHM, van Amerongen H, Croce R. Excitation-energy transfer dynamics of higher plant photosystem I light-harvesting complexes. Biophys J 2011; 100:1372-80. [PMID: 21354411 DOI: 10.1016/j.bpj.2011.01.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 01/19/2011] [Indexed: 11/15/2022] Open
Abstract
Photosystem I (PSI) plays a major role in the light reactions of photosynthesis. In higher plants, PSI is composed of a core complex and four outer antennas that are assembled as two dimers, Lhca1/4 and Lhca2/3. Time-resolved fluorescence measurements on the isolated dimers show very similar kinetics. The intermonomer transfer processes are resolved using target analysis. They occur at rates similar to those observed in transfer to the PSI core, suggesting competition between the two transfer pathways. It appears that each dimer is adopting various conformations that correspond to different lifetimes and emission spectra. A special feature of the Lhca complexes is the presence of an absorption band at low energy, originating from an excitonic state of a chlorophyll dimer, mixed with a charge-transfer state. These low-energy bands have high oscillator strengths and they are superradiant in both Lhca1/4 and Lhca2/3. This challenges the view that the low-energy charge-transfer state always functions as a quencher in plant Lhc's and it also challenges previous interpretations of PSI kinetics. The very similar properties of the low-energy states of both dimers indicate that the organization of the involved chlorophylls should also be similar, in disagreement with the available structural data.
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Affiliation(s)
- Emilie Wientjes
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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81
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Müh F, Glöckner C, Hellmich J, Zouni A. Light-induced quinone reduction in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:44-65. [PMID: 21679684 DOI: 10.1016/j.bbabio.2011.05.021] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 05/20/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022]
Abstract
The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.
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Affiliation(s)
- Frank Müh
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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82
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Martin E, Samoilova RI, Narasimhulu KV, Lin TJ, O'Malley PJ, Wraight CA, Dikanov SA. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site. J Am Chem Soc 2011; 133:5525-37. [PMID: 21417328 DOI: 10.1021/ja2001538] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.
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Affiliation(s)
- Erik Martin
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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83
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Chernev P, Zaharieva I, Dau H, Haumann M. Carboxylate shifts steer interquinone electron transfer in photosynthesis. J Biol Chem 2011; 286:5368-74. [PMID: 21169354 PMCID: PMC3037649 DOI: 10.1074/jbc.m110.202879] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/10/2010] [Indexed: 11/06/2022] Open
Abstract
Understanding the mechanisms of electron transfer (ET) in photosynthetic reaction centers (RCs) may inspire novel catalysts for sunlight-driven fuel production. The electron exit pathway of type II RCs comprises two quinone molecules working in series and in between a non-heme iron atom with a carboxyl ligand (bicarbonate in photosystem II (PSII), glutamate in bacterial RCs). For decades, the functional role of the iron has remained enigmatic. We tracked the iron site using microsecond-resolution x-ray absorption spectroscopy after laser-flash excitation of PSII. After formation of the reduced primary quinone, Q(A)(-), the x-ray spectral changes revealed a transition (t½ ≈ 150 μs) from a bidentate to a monodentate coordination of the bicarbonate at the Fe(II) (carboxylate shift), which reverted concomitantly with the slower ET to the secondary quinone Q(B). A redox change of the iron during the ET was excluded. Density-functional theory calculations corroborated the carboxylate shift both in PSII and bacterial RCs and disclosed underlying changes in electronic configuration. We propose that the iron-carboxyl complex facilitates the first interquinone ET by optimizing charge distribution and hydrogen bonding within the Q(A)FeQ(B) triad for high yield Q(B) reduction. Formation of a specific priming intermediate by nuclear rearrangements, setting the stage for subsequent ET, may be a common motif in reactions of biological redox cofactors.
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Affiliation(s)
- Petko Chernev
- From the Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Ivelina Zaharieva
- From the Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Holger Dau
- From the Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Michael Haumann
- From the Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
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84
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Rea G, Lambreva M, Polticelli F, Bertalan I, Antonacci A, Pastorelli S, Damasso M, Johanningmeier U, Giardi MT. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure. PLoS One 2011; 6:e16216. [PMID: 21249156 PMCID: PMC3020971 DOI: 10.1371/journal.pone.0016216] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/15/2010] [Indexed: 11/18/2022] Open
Abstract
Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to oxidative damage in the eukaryotic/cyanobacterial proteins compared to their bacterial orthologs. These results led us to hypothesize an archaean atmosphere less challenging in terms of ionizing radiation than the present one.
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Affiliation(s)
- Giuseppina Rea
- Institute of Crystallography, National Research Council, Monterotondo, Italy.
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85
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Krammer EM, Bernad S, Ullmann GM, Hickman A, Sebban P. Chemical Evidence for the Dawn of Life on Earth. Aust J Chem 2011. [DOI: 10.1071/ch10427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The dating of the dawn of life on Earth is a difficult task, requiring an accumulation of evidences from many different research fields. Here we shall summarize findings from the molecular scale (proteins) to cells and photosynthesis-related-fossils (stromatolites from the early and the late Archaean Eon), which indicate that life emerged on Earth 4.2–3.8 Ga (i.e. 4.2–3.8 × 109 years) ago. Among the data supporting this age, the isotopic and palaeontological fingerprints of photosynthesis provide some of the strongest evidence. The reason for this is that photosynthesis, carried out in particular by cyanobacteria, was responsible for massive changes to the Earth’s environment, i.e. the oxygenation of the Earth’s atmosphere and seawater, and the fixation of carbon from atmospheric CO2 in organic material. The possibility of a very early (>3.8 Ga ago) appearance of complex autotrophic organisms, such as cyanobacteria, is a major change in our view of life’s origins.
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86
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Martin E, Samoilova RI, Narasimhulu KV, Wraight CA, Dikanov SA. Hydrogen bonds between nitrogen donors and the semiquinone in the Q(B) site of bacterial reaction centers. J Am Chem Soc 2010; 132:11671-7. [PMID: 20672818 DOI: 10.1021/ja104134e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (Q(A)) and secondary (Q(B)) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the Q(B) site semiquinone with nitrogens from the local protein environment in natural and (15)N uniformly labeled reactions centers. (14)N and (15)N HYSCORE spectra of the Q(B) semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from (14)N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. (15)N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the Q(B) semiquinone forms hydrogen bonds with two nitrogens and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the Q(B) site. On the basis of the quadrupole coupling constant, one nitrogen can only be assigned to N(delta) of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen.
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Affiliation(s)
- Erik Martin
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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87
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Histidine is involved in coupling proton uptake to electron transfer in photosynthetic proteins. Eur J Cell Biol 2010; 89:983-9. [DOI: 10.1016/j.ejcb.2010.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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88
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Zheng Z, Dutton PL, Gunner MR. The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers. Proteins 2010; 78:2638-54. [PMID: 20607696 DOI: 10.1002/prot.22779] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quinones play important roles in mitochondrial and photosynthetic energy conversion acting as intramembrane, mobile electron, and proton carriers between catalytic sites in various electron transfer proteins. They display different affinity, selectivity, functionality, and exchange dynamics in different binding sites. The computational analysis of quinone binding sheds light on the requirements for quinone affinity and specificity. The affinities of 10 oxidized, neutral benzoquinones were measured for the high affinity Q(A) site in the detergent-solubilized Rhodobacter sphaeroides bacterial photosynthetic reaction center. Multiconformation Continuum Electrostatics was then used to calculate their relative binding free energies by grand canonical Monte Carlo sampling with a rigid protein backbone, flexible ligand, and side chain positions and protonation states. Van der Waals and torsion energies, Poisson-Boltzmann continuum electrostatics, and accessible surface area-dependent ligand-solvent interactions are considered. An initial, single cycle of GROMACS backbone optimization improves the match with experiment as do coupled-ligand and side-chain motions. The calculations match experiment with an root mean square deviation (RMSD) of 2.29 and a slope of 1.28. The affinities are dominated by favorable protein-ligand van der Waals rather than electrostatic interactions. Each quinone appears in a closely clustered set of positions. Methyl and methoxy groups move into the same positions as found for the native quinone. Difficulties putting methyls into methoxy sites are observed. Calculations using a solvent-accessible surface area-dependent implicit van der Waals interaction smoothed out small clashes, providing a better match to experiment with a RMSD of 0.77 and a slope of 0.97.
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Affiliation(s)
- Zhong Zheng
- Department of Physics, City College of New York, New York, New York 10031, USA
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89
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Mezzetti A, Blanchet L, de Juan A, Leibl W, Ruckebusch C. Ubiquinol formation in isolated photosynthetic reaction centres monitored by time-resolved differential FTIR in combination with 2D correlation spectroscopy and multivariate curve resolution. Anal Bioanal Chem 2010; 399:1999-2014. [DOI: 10.1007/s00216-010-4325-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/07/2010] [Accepted: 10/10/2010] [Indexed: 11/24/2022]
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90
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Orzechowska A, Lipińska M, Fiedor J, Chumakov A, Zając M, Ślęzak T, Matlak K, Strzałka K, Korecki J, Fiedor L, Burda K. Coupling of collective motions of the protein matrix to vibrations of the non-heme iron in bacterial photosynthetic reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1696-704. [DOI: 10.1016/j.bbabio.2010.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 06/23/2010] [Accepted: 06/26/2010] [Indexed: 10/19/2022]
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91
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Savitsky A, Malferrari M, Francia F, Venturoli G, Möbius K. Bacterial Photosynthetic Reaction Centers in Trehalose Glasses: Coupling between Protein Conformational Dynamics and Electron-Transfer Kinetics as Studied by Laser-Flash and High-Field EPR Spectroscopies. J Phys Chem B 2010; 114:12729-43. [DOI: 10.1021/jp105801q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Savitsky
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Marco Malferrari
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Francesco Francia
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Giovanni Venturoli
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Klaus Möbius
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany, Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy, and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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92
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Engineering of an alternative electron transfer path in photosystem II. Proc Natl Acad Sci U S A 2010; 107:9650-5. [PMID: 20457933 DOI: 10.1073/pnas.1000187107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The initial steps of oxygenic photosynthetic electron transfer occur within photosystem II, an intricate pigment/protein transmembrane complex. Light-driven electron transfer occurs within a multistep pathway that is efficiently insulated from competing electron transfer pathways. The heart of the electron transfer system, composed of six linearly coupled redox active cofactors that enable electron transfer from water to the secondary quinone acceptor Q(B), is mainly embedded within two proteins called D1 and D2. We have identified a site in silico, poised in the vicinity of the Q(A) intermediate quinone acceptor, which could serve as a potential binding site for redox active proteins. Here we show that modification of Lysine 238 of the D1 protein to glutamic acid (Glu) in the cyanobacterium Synechocystis sp. PCC 6803, results in a strain that grows photautotrophically. The Glu thylakoid membranes are able to perform light-dependent reduction of exogenous cytochrome c with water as the electron donor. Cytochrome c photoreduction by the Glu mutant was also shown to significantly protect the D1 protein from photodamage when isolated thylakoid membranes were illuminated. We have therefore engineered a novel electron transfer pathway from water to a soluble protein electron carrier without harming the normal function of photosystem II.
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93
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Wöhri AB, Wahlgren WY, Malmerberg E, Johansson LC, Neutze R, Katona G. Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface. Biochemistry 2009; 48:9831-8. [PMID: 19743880 DOI: 10.1021/bi900545e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins are embedded in a lipid bilayer and maintain strong interactions with lipid molecules. Tightly bound lipids are responsible for vertical positioning and integration of proteins in the membrane and for assembly of multisubunit complexes and occasionally act as substrates. In this work we present the lipidic sponge phase crystal structure of the reaction center from Blastochloris viridis to 1.86 A, which reveals lipid molecules interacting with the protein surface. A diacylglycerol molecule is bound, through a thioether bond, to the N-terminus of the tetraheme cytochrome c subunit. From the electron density recovered at the Q(B) site and the observed change in recombination kinetics in lipidic sponge phase-grown crystals, the mobile ubiquinone appears to be displaced by a monoolein molecule. A 36 A long electron density feature is observed at the interface of transmembrane helices belonging to the H- and M-subunits, probably arising from an unidentified lipid.
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Affiliation(s)
- Annemarie B Wöhri
- Department of Chemical and Biological Engineering, Molecular Biotechnology, Chalmers University of Technology, SE-405 30 Gothenburg, Sweden
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94
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The local electric field within phospholipid membranes modulates the charge transfer reactions in reaction centres. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1039-49. [DOI: 10.1016/j.bbabio.2009.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 03/03/2009] [Accepted: 03/05/2009] [Indexed: 11/19/2022]
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95
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Cheap H, Bernad S, Derrien V, Gerencsér L, Tandori J, de Oliveira P, Hanson DK, Maróti P, Sebban P. M234Glu is a component of the proton sponge in the reaction center from photosynthetic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1505-15. [PMID: 19632193 DOI: 10.1016/j.bbabio.2009.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
Abstract
Bacterial reaction centers use light energy to couple the uptake of protons to the successive semi-reduction of two quinones, namely Q(A) and Q(B). These molecules are situated symmetrically in regard to a non-heme iron atom. Four histidines and one glutamic acid, M234Glu, constitute the five ligands of this atom. By flash-induced absorption spectroscopy and delayed fluorescence we have studied in the M234EH and M234EL variants the role played by this acidic residue on the energetic balance between the two quinones as well as in proton uptake. Delayed fluorescence from the P(+)Q(A)(-) state (P is the primary electron donor) and temperature dependence of the rate of P(+)Q(A)(-) charge recombination that are in good agreement show that in the two RC variants, both Q(A)(-) and Q(B)(-) are destabilized by about the same free energy amount: respectively approximately 100 +/- 5 meV and 90 +/- 5 meV for the M234EH and M234EL variants, as compared to the WT. Importantly, in the M234EH and M234EL variants we observe a collapse of the high pH band (present in the wild-type reaction center) of the proton uptake amplitudes associated with formation of Q(A)(-) and Q(B)(-). This band has recently been shown to be a signature of a collective behaviour of an extended, multi-entry, proton uptake network. M234Glu seems to play a central role in the proton sponge-like system formed by the RC protein.
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Affiliation(s)
- Hélène Cheap
- Laboratoire de Chimie Physique, UMR 8000, University of Paris-Sud 11/CNRS, 91405 cedex, France
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96
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McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J Mol Model 2009; 16:419-29. [PMID: 19626353 DOI: 10.1007/s00894-009-0541-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 05/23/2009] [Indexed: 10/20/2022]
Abstract
In this paper, we describe a Monte Carlo method for determining the volume of a molecule. A molecule is considered to consist of hard, overlapping spheres. The surface of the molecule is defined by rolling a probe sphere over the surface of the spheres. To determine the volume of the molecule, random points are placed in a three-dimensional box, which encloses the whole molecule. The volume of the molecule in relation to the volume of the box is estimated by calculating the ratio of the random points placed inside the molecule and the total number of random points that were placed. For computational efficiency, we use a grid-cell based neighbor list to determine whether a random point is placed inside the molecule or not. This method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules. Since cavities and clefts are potential water binding sites, we place water molecules in the cavities. The potential water positions can be used in molecular dynamics calculations as well as in other molecular calculations. We apply this method to several proteins and demonstrate the usefulness of the program. The described methods are all implemented in the program McVol, which is available free of charge from our website at http://www.bisb.uni-bayreuth.de/software.html .
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97
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Francia F, Malferrari M, Sacquin-Mora S, Venturoli G. Charge Recombination Kinetics and Protein Dynamics in Wild Type and Carotenoid-less Bacterial Reaction Centers: Studies in Trehalose Glasses. J Phys Chem B 2009; 113:10389-98. [DOI: 10.1021/jp902287y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Francia
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France, and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Bologna, Italy
| | - Marco Malferrari
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France, and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Bologna, Italy
| | - Sophie Sacquin-Mora
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France, and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France, and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Bologna, Italy
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98
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Kaneko Y, Hayashi S, Ohmine I. Proton-Transfer Reactions in Reaction Center of Photosynthetic Bacteria Rhodobacter sphaeroides. J Phys Chem B 2009; 113:8993-9003. [DOI: 10.1021/jp9008898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Kaneko
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Iwao Ohmine
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
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99
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Krammer EM, Till MS, Sebban P, Ullmann GM. Proton-transfer pathways in photosynthetic reaction centers analyzed by profile hidden markov models and network calculations. J Mol Biol 2009; 388:631-43. [PMID: 19285988 DOI: 10.1016/j.jmb.2009.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/05/2009] [Accepted: 03/08/2009] [Indexed: 11/28/2022]
Abstract
In the bacterial reaction center (bRC) of Rhodobacter sphaeroides, the key residues of proton transfer to the secondary quinone (Q(B)) are known. Also, several possible proton entry points and proton-transfer pathways have been proposed. However, the mechanism of the proton transfer to Q(B) remains unclear. The proton transfer to Q(B) in the bRC of Blastochloris viridis is less explored. To analyze whether the bRCs of different species use the same key residues for proton transfer to Q(B), we determined the conservation of these residues. We performed a multiple-sequence alignment based on profile hidden Markov models. Residues involved in proton transfer but not located at the protein surface are conserved or are only exchanged to functionally similar amino acids, whereas potential proton entry points are not conserved to the same extent. The analysis of the hydrogen-bond network of the bRC from R. sphaeroides and that from B. viridis showed that a large network connects Q(B) with the cytoplasmic region in both bRCs. For both species, all non-surface key residues are part of the network. However, not all proton entry points proposed for the bRC of R. sphaeroides are included in the network in the bRC of B. viridis. From our analysis, we could identify possible proton entry points. These proton entry points differ between the two bRCs. Together, the results of the conservation analysis and the hydrogen-bond network analysis make it likely that the proton transfer to Q(B) is not mediated by distinct pathways but by a large hydrogen-bond network.
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Affiliation(s)
- Eva-Maria Krammer
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, Bayreuth, Germany
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100
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Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol 2009; 388:356-80. [PMID: 19265704 DOI: 10.1016/j.jmb.2009.02.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
Abstract
In metalloproteins, the protein environment modulates metal properties to achieve the required goal, which can be protein stabilization or function. The analysis of metal sites at the atomic level of detail provided by protein structures can thus be of benefit in functional and evolutionary studies of proteins. In this work, we propose a structural bioinformatics approach to the study of metalloproteins based on structural templates of metal sites that include the PDB coordinates of protein residues forming the first and the second coordination sphere of the metal. We have applied this approach to non-heme iron sites, which have been analyzed at various levels. Templates of sites located in different protein domains have been compared, showing that similar sites can be found in unrelated proteins as the result of convergent evolution. Templates of sites located in proteins of a large superfamily have been compared, showing possible mechanisms of divergent evolution of proteins to achieve different functions. Furthermore, template comparisons have been used to predict the function of uncharacterized proteins, showing that similarity searches focused on metal sites can be advantageously combined with typical whole-domain comparisons. Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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