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Guberman-Pfeffer MJ. To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'. Front Microbiol 2024; 15:1397124. [PMID: 38633696 PMCID: PMC11021709 DOI: 10.3389/fmicb.2024.1397124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.
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2
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Guberman-Pfeffer MJ. Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires. J Phys Chem B 2023; 127:7148-7161. [PMID: 37552847 DOI: 10.1021/acs.jpcb.3c02912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the "nanowires" computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all "nanowires", but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48-0.98 eV. Reaction free energies in all three "nanowires" are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7-1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome "nanowires". Redox currents do not exceed 3.0 × 10-3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the "nanowires" are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.
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Affiliation(s)
- Matthew J Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, Connecticut 06510, United States
- Microbial Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut 06516, United States
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Krupnik T, Zienkiewicz M, Wasilewska-Dębowska W, Drożak A, Kania K. How Light Modulates the Growth of Cyanidioschyzon merolae Cells by Changing the Function of Phycobilisomes. Cells 2023; 12:1480. [PMID: 37296601 PMCID: PMC10252272 DOI: 10.3390/cells12111480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The aim of this study was to examine how light intensity and quality affect the photosynthetic apparatus of Cyanidioschyzon merolae cells by modulating the structure and function of phycobilisomes. Cells were grown in equal amounts of white, blue, red, and yellow light of low (LL) and high (HL) intensity. Biochemical characterization, fluorescence emission, and oxygen exchange were used to investigate selected cellular physiological parameters. It was found that the allophycocyanin content was sensitive only to light intensity, whereas the phycocynin content was also sensitive to light quality. Furthermore, the concentration of the PSI core protein was not affected by the intensity or quality of the growth light, but the concentration of the PSII core D1 protein was. Finally, the amount of ATP and ADP was lower in HL than LL. In our opinion, both light intensity and quality are main factors that play an important regulatory role in acclimatization/adaptation of C. merolae to environmental changes, and this is achieved by balancing the amounts of thylakoid membrane and phycobilisome proteins, the energy level, and the photosynthetic and respiratory activity. This understanding contributes to the development of a mix of cultivation techniques and genetic changes for a future large-scale synthesis of desirable biomolecules.
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Affiliation(s)
- Tomasz Krupnik
- Department of Molecular Plant Physiology, Institute of Environmental Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02096 Warsaw, Poland
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Shaw RA, Manian A, Lyskov I, Russo SP. Efficient enumeration of bosonic configurations with applications to the calculation of non-radiative rates. J Chem Phys 2021; 154:084102. [PMID: 33639737 DOI: 10.1063/5.0039532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This work presents algorithms for the efficient enumeration of configuration spaces following Boltzmann-like statistics, with example applications to the calculation of non-radiative rates, and an open-source implementation. Configuration spaces are found in several areas of physics, particularly wherever there are energy levels that possess variable occupations. In bosonic systems, where there are no upper limits on the occupation of each level, enumeration of all possible configurations is an exceptionally hard problem. We look at the case where the levels need to be filled to satisfy an energy criterion, for example, a target excitation energy, which is a type of knapsack problem as found in combinatorics. We present analyses of the density of configuration spaces in arbitrary dimensions and how particular forms of kernel can be used to envelope the important regions. In this way, we arrive at three new algorithms for enumeration of such spaces that are several orders of magnitude more efficient than the naive brute force approach. Finally, we show how these can be applied to the particular case of internal conversion rates in a selection of molecules and discuss how a stochastic approach can, in principle, reduce the computational complexity to polynomial time.
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Affiliation(s)
- Robert A Shaw
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Anjay Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Igor Lyskov
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Salvy P Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
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5
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Huang X, Vasilev C, Hunter CN. Excitation energy transfer between monomolecular layers of light harvesting LH2 and LH1-reaction centre complexes printed on a glass substrate. LAB ON A CHIP 2020; 20:2529-2538. [PMID: 32662473 DOI: 10.1039/d0lc00156b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Light-harvesting 2 (LH2) and light-harvesting 1 - reaction centre (RCLH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were cross-patterned on glass surfaces for energy transfer studies. Atomic force microscopy (AFM) images of the RCLH1 and LH2 patterns show the deposition of monomolecular layers of complexes on the glass substrate. Spectral imaging and fluorescence life-time imaging microscopy (FLIM) revealed that RCLH1 and LH2 complexes, sealed under physiological conditions, retained their native light-harvesting and energy transfer functions. Measurements of the amplitude and lifetime decay of fluorescence emission from LH2 complexes, the energy transfer donors, and gain of fluorescence emission from acceptor RCLH1 complexes, provide evidence for excitation energy transfer from LH2 to RCLH1. Directional energy transfer on the glass substrate was unequivocally established by using LH2-carotenoid complexes and RCLH1 complexes with genetically removed carotenoids. Specific excitation of carotenoids in donor LH2 complexes elicited fluorescence emission from RCLH1 acceptors. To explore the longevity of this novel nanoprinted photosynthetic unit, RCLH1 and LH2 complexes were cross-patterned on a glass surface and sealed under a protective argon atmosphere. The results show that both complexes retained their individual and collective functions and are capable of directional excitation energy transfer for at least 60 days.
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Affiliation(s)
- Xia Huang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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6
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Makita H, Hastings G. Time-resolved FTIR difference spectroscopy for the study of quinones in the A 1 binding site in photosystem I: Identification of neutral state quinone bands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148173. [PMID: 32059842 DOI: 10.1016/j.bbabio.2020.148173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 11/24/2022]
Abstract
Infrared absorption bands associated with the neutral state of quinones in the A1 binding site in photosystem I (PSI) have been difficult to identify in the past. This problem is addressed here, where time-resolved step-scan FTIR difference spectroscopy at 77 K has been used to study PSI with six different quinones incorporated into the A1 binding site. (P700+A1- - P700A1) and (A1- - A1) FTIR difference spectra (DS) were obtained for PSI with the different quinones incorporated, and several double-difference spectra (DDS) were constructed from the DS. From analysis of the DS and DDS, in combination with density functional theory based vibrational frequency calculations of the quinones, the neutral state bands of the incorporated quinones are identified and assigned. For neutral PhQ in the A1 binding site, infrared absorption bands were identified near 1665 and 1635 cm-1, that are due to the C1O and C4O stretching vibrations of the incorporated PhQ, respectively. These assignments indicate a 30 cm-1 separation between the C1O and C4O modes, considerably less than the ~80 cm-1 found for similar modes of PhQ-. The C4O mode downshifts due to hydrogen bonding, so the suggestion is that hydrogen bonding is weaker for the neutral state compared to the anion state, indicating radical-induced proton dynamics associated with the quinone in the A1 binding site in PSI.
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Affiliation(s)
- Hiroki Makita
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA.
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7
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Cui X, Yan Y, Wei J. Theoretical Study on the Effect of Environment on Excitation Energy Transfer in Photosynthetic Light-Harvesting Systems. J Phys Chem B 2020; 124:2354-2362. [PMID: 32130013 DOI: 10.1021/acs.jpcb.0c00266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, two-dimensional (2D) electronic spectroscopy experiments prove that the excitation energy transfer (EET) in photosynthetic light-harvesting systems presents long-lived electronic quantum beating signals. After being discovered in the light-harvesting system, the quantum coherence effect has aroused widespread discussion. To illustrate the EET process in the Fenna-Matthews-Olson (FMO) and phycocyanin 645 (PC645) complex, the local protein environment is often thought to be the same; however, this is ambivalent to the practical structural analysis of the light-harvesting complex. By adopting the dissipaton equation of motion theory, we present the effect of a heterogeneous protein environment on the energy transfer process with accurate numerical results. We demonstrate that the energy transfer process relies on the local heterogeneous environment for the FMO complex. A similar good agreement is found for the PC645 complex. Furthermore, we discuss the optimal value of different chromophores in the excitation energy transfer process by controlling the environmental characteristics.
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Affiliation(s)
- XueYan Cui
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
| | - YiJing Yan
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - JianHua Wei
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
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8
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Adir N, Bar-Zvi S, Harris D. The amazing phycobilisome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148047. [PMID: 31306623 DOI: 10.1016/j.bbabio.2019.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Cyanobacteria and red-algae share a common light-harvesting complex which is different than all other complexes that serve as photosynthetic antennas - the Phycobilisome (PBS). The PBS is found attached to the stromal side of thylakoid membranes, filling up most of the gap between individual thylakoids. The PBS self assembles from similar homologous protein units that are soluble and contain conserved cysteine residues that covalently bind the light absorbing chromophores, linear tetra-pyrroles. Using similar construction principles, the PBS can be as large as 16.8 MDa (68×45×39nm), as small as 1.2 MDa (24 × 11.5 × 11.5 nm), and in some unique cases smaller still. The PBS can absorb light between 450 nm to 650 nm and in some cases beyond 700 nm, depending on the species, its composition and assembly. In this review, we will present new observations and structures that expand our understanding of the distinctive properties that make the PBS an amazing light harvesting system. At the end we will suggest why the PBS, for all of its excellent properties, was discarded by photosynthetic organisms that arose later in evolution such as green algae and higher plants.
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Affiliation(s)
- Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Shira Bar-Zvi
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dvir Harris
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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9
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Koch F, Stolte M, Zitzler-Kunkel A, Bialas D, Steinbacher A, Brixner T, Würthner F. Unraveling the structure and exciton coupling for multichromophoric merocyanine dye molecules. Phys Chem Chem Phys 2018; 19:6368-6378. [PMID: 28197618 DOI: 10.1039/c7cp00115k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relative orientation of chromophores is a key factor in determining the relationship between the structure and the functionality in molecular multichromophore ensembles. In the case of structurally flexible molecular systems in solution, the task to clarify the relevant effects of accessible chromophore orientations with spectroscopic observations is very demanding. In this study, we address this issue by investigating a series of differently connected multichromophoric systems composed of highly dipolar merocyanine dyes that are systematically varied in their substitution pattern and the number of chromophores attached to a bridging benzene ring. Combining electro-optical absorption (EOA) and UV/Vis spectroscopy with density functional theory (DFT) as well as exciton theory discloses conformational preferences and rationalizes the optical properties of the interacting chromophores. Our findings suggest for all multichromophoric systems there is a relative orientation of the chromophores which compensates for the individual dipole moments of the merocyanine dyes by pointing preferably in opposing directions. These orientations furthermore rationalize the observed spectral properties by partly excitonically-coupled subunits.
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Affiliation(s)
- Federico Koch
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Matthias Stolte
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany and Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - André Zitzler-Kunkel
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - David Bialas
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Andreas Steinbacher
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany. and Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Frank Würthner
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany and Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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10
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Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS. Photophysics of J-Aggregate-Mediated Energy Transfer on DNA. J Phys Chem Lett 2017; 8:5827-5833. [PMID: 29144136 DOI: 10.1021/acs.jpclett.7b01898] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Achieving nanoscale spatial and electronic control over the formation of dye aggregates is a major synthetic challenge due to their typically inhomogeneous self-assembly, which limits control over their higher-order organization. To address these challenges, synthetic DNA-templated pseudoisocyanine (PIC) J-aggregates were recently introduced. However, the dependence of the photophysics of the superradiant exciton on the underlying DNA template length and the impact of static disorder on energy transfer through these PIC J-aggregates remain unknown. We examine the delocalization length progression of superradiant PIC excitons by varying the length of poly-A DNA tracts that template PIC J-aggregates. We then investigate the energy-transfer efficiency from PIC J-aggregates with DNA duplex template length, which we found to be limited by static disorder. Utilizing the self-assembled and selective formation of superradiant excitons on DNA provides a platform to determine the function of delocalized excitons in the context of nanoscale energy transport.
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Affiliation(s)
- James L Banal
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Toru Kondo
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rémi Veneziano
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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11
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Orf GS, Collins AM, Niedzwiedzki DM, Tank M, Thiel V, Kell A, Bryant DA, Montaño GA, Blankenship RE. Polymer-Chlorosome Nanocomposites Consisting of Non-Native Combinations of Self-Assembling Bacteriochlorophylls. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6427-6438. [PMID: 28585832 DOI: 10.1021/acs.langmuir.7b01761] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chlorosomes are one of the characteristic light-harvesting antennas from green sulfur bacteria. These complexes represent a unique paradigm: self-assembly of bacteriochlorophyll pigments within a lipid monolayer without the influence of protein. Because of their large size and reduced complexity, they have been targeted as models for the development of bioinspired light-harvesting arrays. We report the production of biohybrid light-harvesting nanocomposites mimicking chlorosomes, composed of amphiphilic diblock copolymer membrane bodies that incorporate thousands of natural self-assembling bacteriochlorophyll molecules derived from green sulfur bacteria. The driving force behind the assembly of these polymer-chlorosome nanocomposites is the transfer of the mixed raw materials from the organic to the aqueous phase. We incorporated up to five different self-assembling pigment types into single nanocomposites that mimic chlorosome morphology. We establish that the copolymer-BChl self-assembly process works smoothly even when non-native combinations of BChl homologues are included. Spectroscopic characterization revealed that the different types of self-assembling pigments participate in ultrafast energy transfer, expanding beyond single chromophore constraints of the natural chlorosome system. This study further demonstrates the utility of flexible short-chain, diblock copolymers for building scalable, tunable light-harvesting arrays for technological use and allows for an in vitro analysis of the flexibility of natural self-assembling chromophores in unique and controlled combinations.
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Affiliation(s)
| | - Aaron M Collins
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | | | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Biological Sciences, Tokyo Metropolitan University , Tokyo, Japan 192-0397
| | - Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Biological Sciences, Tokyo Metropolitan University , Tokyo, Japan 192-0397
| | - Adam Kell
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Gabriel A Montaño
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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12
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Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol 2017; 14:013001. [DOI: 10.1088/1478-3975/14/1/013001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Kodali G, Mancini JA, Solomon LA, Episova TV, Roach N, Hobbs CJ, Wagner P, Mass OA, Aravindu K, Barnsley JE, Gordon KC, Officer DL, Dutton PL, Moser CC. Design and engineering of water-soluble light-harvesting protein maquettes. Chem Sci 2017; 8:316-324. [PMID: 28261441 PMCID: PMC5330312 DOI: 10.1039/c6sc02417c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/16/2016] [Indexed: 02/04/2023] Open
Abstract
Natural selection in photosynthesis has engineered tetrapyrrole based, nanometer scale, light harvesting and energy capture in light-induced charge separation. By designing and creating nanometer scale artificial light harvesting and charge separating proteins, we have the opportunity to reengineer and overcome the limitations of natural selection to extend energy capture to new wavelengths and to tailor efficient systems that better meet human as opposed to cellular energetic needs. While tetrapyrrole cofactor incorporation in natural proteins is complex and often assisted by accessory proteins for cofactor transport and insertion, artificial protein functionalization relies on a practical understanding of the basic physical chemistry of protein and cofactors that drive nanometer scale self-assembly. Patterning and balancing of hydrophobic and hydrophilic tetrapyrrole substituents is critical to avoid natural or synthetic porphyrin and chlorin aggregation in aqueous media and speed cofactor partitioning into the non-polar core of a man-made water soluble protein designed according to elementary first principles of protein folding. This partitioning is followed by site-specific anchoring of tetrapyrroles to histidine ligands strategically placed for design control of rates and efficiencies of light energy and electron transfer while orienting at least one polar group towards the aqueous phase.
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Affiliation(s)
- Goutham Kodali
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Joshua A. Mancini
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Lee A. Solomon
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Tatiana V. Episova
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Nicholas Roach
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Christopher J. Hobbs
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Pawel Wagner
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Olga A. Mass
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | - Kunche Aravindu
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | | | - Keith C. Gordon
- University of Otago , Department of Chemistry , Dunedin 9016 , New Zealand
| | - David L. Officer
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - P. Leslie Dutton
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Christopher C. Moser
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
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Sener M, Strumpfer J, Singharoy A, Hunter CN, Schulten K. Overall energy conversion efficiency of a photosynthetic vesicle. eLife 2016; 5. [PMID: 27564854 PMCID: PMC5001839 DOI: 10.7554/elife.09541] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/11/2016] [Indexed: 11/25/2022] Open
Abstract
The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytbc1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12–0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination. DOI:http://dx.doi.org/10.7554/eLife.09541.001 Photosynthesis, or the conversion of light energy into chemical energy, is a process that powers almost all life on Earth. Plants and certain bacteria share similar processes to perform photosynthesis, though the purple bacterium Rhodobacter sphaeroides uses a photosynthetic system that is much less complex than that in plants. Light harvesting inside the bacterium takes place in up to hundreds of compartments called chromatophores. Each chromatophore in turn contains hundreds of cooperating proteins that together absorb the energy of sunlight and convert and store it in molecules of ATP, the universal energy currency of all cells. The chromatophore of primitive purple bacteria provides a model for more complex photosynthetic systems in plants. Though researchers had characterized its individual components over the years, less was known about the overall architecture of the chromatophore and how its many components work together to harvest light energy efficiently and robustly. This knowledge would provide insight into the evolutionary pressures that shaped the chromatophore and its ability to work efficiently at different light intensities. Sener et al. now present a highly detailed structural model of the chromatophore of purple bacteria based on the findings of earlier studies. The model features the position of every atom of the constituent proteins and is used to examine how energy is transferred and converted. Sener et al. describe the sequence of energy conversion steps and calculate the overall energy conversion efficiency, namely how much of the light energy arriving at the microorganism is stored as ATP. These calculations show that the chromatophore is optimized to produce chemical energy at low light levels typical of purple bacterial habitats, and dissipate excess energy to avoid being damaged under brighter light. The chromatophore’s architecture also displays robustness against perturbations of its components. In the future, the approach used by Sener et al. to describe light harvesting in this bacterial compartment can be applied to more complex systems, such as those in plants. DOI:http://dx.doi.org/10.7554/eLife.09541.002
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Affiliation(s)
- Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Johan Strumpfer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
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15
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Spenst P, Young RM, Wasielewski MR, Würthner F. Guest and solvent modulated photo-driven charge separation and triplet generation in a perylene bisimide cyclophane. Chem Sci 2016; 7:5428-5434. [PMID: 30034681 PMCID: PMC6021749 DOI: 10.1039/c6sc01574c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 05/06/2016] [Indexed: 01/19/2023] Open
Abstract
Cofacial positioning of two perylene bisimide (PBI) chromophores at a distance of 6.5 Å in a cyclophane structure prohibits the otherwise common excimer formation and directs photoexcited singlet state relaxation towards intramolecular symmetry-breaking charge separation (τCS = 161 ± 4 ps) in polar CH2Cl2, which is thermodynamically favored with a Gibbs free energy of ΔGCS = -0.32 eV. The charges then recombine slowly in τCR = 8.90 ± 0.06 ns to form the PBI triplet excited state, which can be used subsequently to generate singlet oxygen in 27% quantum yield. This sequence of events is eliminated by dissolving the PBI cyclophane in non-polar toluene, where only excited singlet state decay occurs. In contrast, complexation of electron-rich aromatic hydrocarbons by the host PBI cyclophane followed by photoexcitation of PBI results in ultrafast electron transfer (<10 ps) from the guest to the PBI in CH2Cl2. The rate constants for charge separation and recombination increase as the guest molecules become easier to oxidize, demonstrating that charge separation occurs close to the peak of the Marcus curve and the recombination lies far into the Marcus inverted region.
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Affiliation(s)
- Peter Spenst
- Institut für Organische Chemie and Center for Nanosystems Chemistry , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Ryan M Young
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - Michael R Wasielewski
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - Frank Würthner
- Institut für Organische Chemie and Center for Nanosystems Chemistry , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany .
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16
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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17
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Zhang Q, Zhang C, Cao L, Wang Z, An B, Lin Z, Huang R, Zhang Z, Wang C, Lin W. Förster Energy Transport in Metal–Organic Frameworks Is Beyond Step-by-Step Hopping. J Am Chem Soc 2016; 138:5308-15. [DOI: 10.1021/jacs.6b01345] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Qiongqiong Zhang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Cankun Zhang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Lingyun Cao
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zi Wang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Bing An
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zekai Lin
- Department
of Chemistry, University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Ruiyun Huang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zhiming Zhang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Cheng Wang
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Wenbin Lin
- Collaborative
Innovation Center of Chemistry for Energy Materials, State Key Laboratory
of Physical Chemistry of Solid Surfaces, Department of Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
- Department
of Chemistry, University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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18
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Plumeré N, Nowaczyk MM. Biophotoelectrochemistry of Photosynthetic Proteins. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 158:111-136. [DOI: 10.1007/10_2016_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Kandemir B, Chakraborty S, Guo Y, Bren KL. Semisynthetic and Biomolecular Hydrogen Evolution Catalysts. Inorg Chem 2015; 55:467-77. [DOI: 10.1021/acs.inorgchem.5b02054] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Banu Kandemir
- Department of Chemistry, University of Rochester, Rochester New York 14627-0216, United States
| | - Saikat Chakraborty
- Department of Chemistry, University of Rochester, Rochester New York 14627-0216, United States
| | - Yixing Guo
- Department of Chemistry, University of Rochester, Rochester New York 14627-0216, United States
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester New York 14627-0216, United States
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20
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Berstis L, Beckham GT, Crowley MF. Electronic coupling through natural amino acids. J Chem Phys 2015; 143:225102. [PMID: 26671404 DOI: 10.1063/1.4936588] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Laura Berstis
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Gregg T. Beckham
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Michael F. Crowley
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
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21
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Matyushov DV. Protein electron transfer: is biology (thermo)dynamic? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:473001. [PMID: 26558324 DOI: 10.1088/0953-8984/27/47/473001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated kinetics, which extends the transition-state theory to dynamically dispersive media. Releasing the grip of thermodynamics in kinetic calculations through nonergodicity provides the mechanism for an efficient optimization between reaction rates and the spectrum of relaxation times of the protein-water thermal bath. Bath dynamics, it appears, play as important role as the free energy in optimizing biology's performance.
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Affiliation(s)
- Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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22
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Mukherjee P, Biswas S, Sen P. Real Time Quantification of Ultrafast Photoinduced Bimolecular Electron Transfer Rate: Direct Probing of the Transient Intermediate. J Phys Chem B 2015; 119:11253-61. [DOI: 10.1021/acs.jpcb.5b03105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Puspal Mukherjee
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Somnath Biswas
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
| | - Pratik Sen
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, Uttar Pradesh, India
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23
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de la Lande A, Gillet N, Chen S, Salahub DR. Progress and challenges in simulating and understanding electron transfer in proteins. Arch Biochem Biophys 2015; 582:28-41. [PMID: 26116376 DOI: 10.1016/j.abb.2015.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/15/2015] [Accepted: 06/22/2015] [Indexed: 11/19/2022]
Abstract
This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France.
| | - Natacha Gillet
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Shufeng Chen
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris Sud. 15, av. Jean Perrin, 91405 Orsay, France
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation and IQST - Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada.
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24
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Purchase RL, de Groot HJM. Biosolar cells: global artificial photosynthesis needs responsive matrices with quantum coherent kinetic control for high yield. Interface Focus 2015; 5:20150014. [PMID: 26052428 PMCID: PMC4410567 DOI: 10.1098/rsfs.2015.0014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This contribution discusses why we should consider developing artificial photosynthesis with the tandem approach followed by the Dutch BioSolar Cells consortium, a current operational paradigm for a global artificial photosynthesis project. We weigh the advantages and disadvantages of a tandem converter against other approaches, including biomass. Owing to the low density of solar energy per unit area, artificial photosynthetic systems must operate at high efficiency to minimize the land (or sea) area required. In particular, tandem converters are a much better option than biomass for densely populated countries and use two photons per electron extracted from water as the raw material into chemical conversion to hydrogen, or carbon-based fuel when CO2 is also used. For the average total light sum of 40 mol m−2 d−1 for The Netherlands, the upper limits are many tons of hydrogen or carbon-based fuel per hectare per year. A principal challenge is to forge materials for quantitative conversion of photons to chemical products within the physical limitation of an internal potential of ca 2.9 V. When going from electric charge in the tandem to hydrogen and back to electricity, only the energy equivalent to 1.23 V can be stored in the fuel and regained. A critical step is then to learn from nature how to use the remaining difference of ca 1.7 V effectively by triple use of one overpotential for preventing recombination, kinetic stabilization of catalytic intermediates and finally generating targeted heat for the release of oxygen. Probably the only way to achieve this is by using bioinspired responsive matrices that have quantum–classical pathways for a coherent conversion of photons to fuels, similar to what has been achieved by natural selection in evolution. In appendix A for the expert, we derive a propagator that describes how catalytic reactions can proceed coherently by a convergence of time scales of quantum electron dynamics and classical nuclear dynamics. We propose that synergy gains by such processes form a basis for further progress towards high efficiency and yield for a global project on artificial photosynthesis. Finally, we look at artificial photosynthesis research in The Netherlands and use this as an example of how an interdisciplinary approach is beneficial to artificial photosynthesis research. We conclude with some of the potential societal consequences of a large-scale roll out of artificial photosynthesis.
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Affiliation(s)
- R L Purchase
- Biophysical Organic Chemistry/Solid State NMR , Leiden Institute of Chemistry , PO Box 9502, 2300 RA Leiden , The Netherlands
| | - H J M de Groot
- Biophysical Organic Chemistry/Solid State NMR , Leiden Institute of Chemistry , PO Box 9502, 2300 RA Leiden , The Netherlands
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25
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Adams PG, Collins AM, Sahin T, Subramanian V, Urban VS, Vairaprakash P, Tian Y, Evans DG, Shreve AP, Montaño GA. Diblock copolymer micelles and supported films with noncovalently incorporated chromophores: a modular platform for efficient energy transfer. NANO LETTERS 2015; 15:2422-2428. [PMID: 25719733 DOI: 10.1021/nl504814x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report generation of modular, artificial light-harvesting assemblies where an amphiphilic diblock copolymer, poly(ethylene oxide)-block-poly(butadiene), serves as the framework for noncovalent organization of BODIPY-based energy donor and bacteriochlorin-based energy acceptor chromophores. The assemblies are adaptive and form well-defined micelles in aqueous solution and high-quality monolayer and bilayer films on solid supports, with the latter showing greater than 90% energy transfer efficiency. This study lays the groundwork for further development of modular, polymer-based materials for light harvesting and other photonic applications.
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Affiliation(s)
- Peter G Adams
- †Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
| | - Aaron M Collins
- †Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
| | - Tuba Sahin
- ‡Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Vijaya Subramanian
- §Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Volker S Urban
- ⊥Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Pothiappan Vairaprakash
- ‡Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yongming Tian
- †Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
- ¶Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, New Mexico 87801, United States
| | - Deborah G Evans
- §Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Andrew P Shreve
- §Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Gabriel A Montaño
- †Center for Integrated Nanotechnologies, Los Alamos National Laboratories, Los Alamos, New Mexico 87545, United States
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Abstract
Technical progress in laser-sources and detectors has allowed the temporal and spatial resolution of chemical reactions down to femtoseconds and Å-units. In photon-excitable systems the key to chemical kinetics, trajectories across the vibrational saddle landscape, are experimentally accessible. Simple and thus well-defined chemical compounds are preferred objects for calibrating new methodologies and carving out paradigms of chemical dynamics, as shown in several contributions to this Faraday Discussion. Aerobic life on earth is powered by solar energy, which is captured by microorganisms and plants. Oxygenic photosynthesis relies on a three billion year old molecular machinery which is as well defined as simpler chemical constructs. It has been analysed to a very high precision. The transfer of excitation between pigments in antennae proteins, of electrons between redox-cofactors in reaction centres, and the oxidation of water by a Mn4Ca-cluster are solid state reactions. ATP, the general energy currency of the cell, is synthesized by a most agile, rotary molecular machine. While the efficiency of photosynthesis competes well with photovoltaics at the time scale of nanoseconds, it is lower by an order of magnitude for crops and again lower for bio-fuels. The enormous energy demand of mankind calls for engineered (bio-mimetic or bio-inspired) solar-electric and solar-fuel devices.
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Affiliation(s)
- Wolfgang Junge
- Dept. Biology & Chemistry, University of Osnabrück, R. 35/E42 Barbarastrasse 11, 49076 Osnabrück, Germany.
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27
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Abstract
Oxygenic photosynthesis is the principal converter of sunlight into chemical energy on Earth. Cyanobacteria and plants provide the oxygen, food, fuel, fibers, and platform chemicals for life on Earth. The conversion of solar energy into chemical energy is catalyzed by two multisubunit membrane protein complexes, photosystem I (PSI) and photosystem II (PSII). Light is absorbed by the pigment cofactors, and excitation energy is transferred among the antennae pigments and converted into chemical energy at very high efficiency. Oxygenic photosynthesis has existed for more than three billion years, during which its molecular machinery was perfected to minimize wasteful reactions. Light excitation transfer and singlet trapping won over fluorescence, radiation-less decay, and triplet formation. Photosynthetic reaction centers operate in organisms ranging from bacteria to higher plants. They are all evolutionarily linked. The crystal structure determination of photosynthetic protein complexes sheds light on the various partial reactions and explains how they are protected against wasteful pathways and why their function is robust. This review discusses the efficiency of photosynthetic solar energy conversion.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
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28
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Natural strategies for photosynthetic light harvesting. Nat Chem Biol 2014; 10:492-501. [PMID: 24937067 DOI: 10.1038/nchembio.1555] [Citation(s) in RCA: 586] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/15/2014] [Indexed: 12/13/2022]
Abstract
Photosynthetic organisms are crucial for life on Earth as they provide food and oxygen and are at the basis of most energy resources. They have a large variety of light-harvesting strategies that allow them to live nearly everywhere where sunlight can penetrate. They have adapted their pigmentation to the spectral composition of light in their habitat, they acclimate to slowly varying light intensities and they rapidly respond to fast changes in light quality and quantity. This is particularly important for oxygen-producing organisms because an overdose of light in combination with oxygen can be lethal. Rapid progress is being made in understanding how different organisms maximize light harvesting and minimize deleterious effects. Here we summarize the latest findings and explain the main design principles used in nature. The available knowledge can be used for optimizing light harvesting in both natural and artificial photosynthesis to improve light-driven production processes.
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DePaoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3381-93. [PMID: 24567493 DOI: 10.1093/jxb/eru038] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To meet future food and energy security needs, which are amplified by increasing population growth and reduced natural resource availability, metabolic engineering efforts have moved from manipulating single genes/proteins to introducing multiple genes and novel pathways to improve photosynthetic efficiency in a more comprehensive manner. Biochemical carbon-concentrating mechanisms such as crassulacean acid metabolism (CAM), which improves photosynthetic, water-use, and possibly nutrient-use efficiency, represent a strategic target for synthetic biology to engineer more productive C3 crops for a warmer and drier world. One key challenge for introducing multigene traits like CAM onto a background of C3 photosynthesis is to gain a better understanding of the dynamic spatial and temporal regulatory events that underpin photosynthetic metabolism. With the aid of systems and computational biology, vast amounts of experimental data encompassing transcriptomics, proteomics, and metabolomics can be related in a network to create dynamic models. Such models can undergo simulations to discover key regulatory elements in metabolism and suggest strategic substitution or augmentation by synthetic components to improve photosynthetic performance and water-use efficiency in C3 crops. Another key challenge in the application of synthetic biology to photosynthesis research is to develop efficient systems for multigene assembly and stacking. Here, we review recent progress in computational modelling as applied to plant photosynthesis, with attention to the requirements for CAM, and recent advances in synthetic biology tool development. Lastly, we discuss possible options for multigene pathway construction in plants with an emphasis on CAM-into-C3 engineering.
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Affiliation(s)
- Henrique C DePaoli
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Anne M Borland
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA School of Biology, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Xiaohan Yang
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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30
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Cartron ML, Olsen JD, Sener M, Jackson PJ, Brindley AA, Qian P, Dickman MJ, Leggett GJ, Schulten K, Neil Hunter C. Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1769-80. [PMID: 24530865 DOI: 10.1016/j.bbabio.2014.02.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 02/03/2014] [Accepted: 02/05/2014] [Indexed: 02/04/2023]
Abstract
Photosynthesis converts absorbed solar energy to a protonmotive force, which drives ATP synthesis. The membrane network of chlorophyll-protein complexes responsible for light absorption, photochemistry and quinol (QH2) production has been mapped in the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides using atomic force microscopy (AFM), but the membrane location of the cytochrome bc1 (cytbc1) complexes that oxidise QH2 to quinone (Q) to generate a protonmotive force is unknown. We labelled cytbc1 complexes with gold nanobeads, each attached by a Histidine10 (His10)-tag to the C-terminus of cytc1. Electron microscopy (EM) of negatively stained chromatophore vesicles showed that the majority of the cytbc1 complexes occur as dimers in the membrane. The cytbc1 complexes appeared to be adjacent to reaction centre light-harvesting 1-PufX (RC-LH1-PufX) complexes, consistent with AFM topographs of a gold-labelled membrane. His-tagged cytbc1 complexes were retrieved from chromatophores partially solubilised by detergent; RC-LH1-PufX complexes tended to co-purify with cytbc1 whereas LH2 complexes became detached, consistent with clusters of cytbc1 complexes close to RC-LH1-PufX arrays, but not with a fixed, stoichiometric cytbc1-RC-LH1-PufX supercomplex. This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1-RC-PufX dimers & 2 RC-LH1-PufX monomers, 4 cytbc1 dimers and 2 ATP synthases. Simulation of the interconnected energy, electron and proton transfer processes showed a half-maximal ATP turnover rate for a light intensity equivalent to only 1% of bright sunlight. Thus, the photosystem architecture of the chromatophore is optimised for growth at low light intensities.
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Affiliation(s)
- Michaël L Cartron
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - John D Olsen
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Melih Sener
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK; ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Graham J Leggett
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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31
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Abstract
Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies establishes the parameter by which the energetic efficiency of protein electron transfer is increased relative to the standard expectations, thus minimizing losses of energy to heat. Energetically efficient electron transfer occurs in a chain of conformationally quenched cofactors and is characterized by flattened free energy surfaces, reminiscent of the flat and rugged landscape at the stability basin of a folded protein.
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Affiliation(s)
- Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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32
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Varejao JO, Barbosa LC, Maltha CR, Lage MR, Lanznaster M, Carneiro JW, Forlani G. Voltammetric and Theoretical Study of the Redox Properties of Rubrolide Analogues. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.12.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Crofts AR, Hong S, Wilson C, Burton R, Victoria D, Harrison C, Schulten K. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1362-77. [PMID: 23396004 PMCID: PMC3995752 DOI: 10.1016/j.bbabio.2013.01.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/12/2012] [Accepted: 01/18/2013] [Indexed: 01/04/2023]
Abstract
1. Recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. The bifurcated reaction at the Qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (SQ) intermediate, and a rapid second electron transfer in which the SQ is oxidized by the low potential chain. 3. The rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a Marcus-Brønsted treatment in which a rapid electron transfer is convoluted with a weak occupancy of the proton configuration needed for electron transfer. 4. A rapid second electron transfer pulls the overall reaction over. Mutation of Glu-295 of cyt b shows it to be a key player. 5. In more crippled mutants, electron transfer is severely inhibited and the bell-shaped pH dependence of wildtype is replaced by a dependence on a single pK at ~8.5 favoring electron transfer. Loss of a pK ~6.5 is explained by a change in the rate limiting step from the first to the second electron transfer; the pK ~8.5 may reflect dissociation of QH. 6. A rate constant (<10(3)s(-1)) for oxidation of SQ in the distal domain by heme bL has been determined, which precludes mechanisms for normal flux in which SQ is constrained there. 7. Glu-295 catalyzes proton exit through H(+) transfer from QH, and rotational displacement to deliver the H(+) to exit channel(s). This opens a volume into which Q(-) can move closer to the heme to speed electron transfer. 8. A kinetic model accounts well for the observations, but leaves open the question of gating mechanisms. For the first step we suggest a molecular "escapement"; for the second a molecular ballet choreographed through coulombic interactions. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Antony R Crofts
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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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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35
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Sumino A, Dewa T, Noji T, Nakano Y, Watanabe N, Hildner R, Bösch N, Köhler J, Nango M. Influence of Phospholipid Composition on Self-Assembly and Energy-Transfer Efficiency in Networks of Light-Harvesting 2 Complexes. J Phys Chem B 2013; 117:10395-404. [DOI: 10.1021/jp4047819] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ayumi Sumino
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Takehisa Dewa
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Tomoyasu Noji
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yuki Nakano
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Natsuko Watanabe
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Richard Hildner
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Nils Bösch
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Jürgen Köhler
- Experimental
Physics IV and BIMF, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Mamoru Nango
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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36
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Jiang N, Kuznetsov A, Nocek JM, Hoffman BM, Crane BR, Hu X, Beratan DN. Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies. J Phys Chem B 2013; 117:9129-41. [PMID: 23895339 PMCID: PMC3809023 DOI: 10.1021/jp401551t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and in complexes with four mutants of the Cc protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:Cc interface for the F82Y(I) mutants compared to that the WT and F82S(W) complexes are predicted to change the reorganization energies for the CcP:Cc ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor-acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET.
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Affiliation(s)
- Nan Jiang
- Department of Chemistry, Duke University, Durham, NC 27708
| | | | - Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, NC 27708
- Department of Biochemistry, Duke University, Durham, NC 27708
- Department of Physics, Duke University, Durham, NC 27708
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37
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Leiger K, Reisberg L, Freiberg A. Fluorescence Micro-Spectroscopy Study of Individual Photosynthetic Membrane Vesicles and Light-Harvesting Complexes. J Phys Chem B 2013; 117:9315-26. [DOI: 10.1021/jp4014509] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristjan Leiger
- Institute
of Physics, University of Tartu, Riia 142,
Tartu 51014, Estonia
| | - Liis Reisberg
- Institute
of Physics, University of Tartu, Riia 142,
Tartu 51014, Estonia
| | - Arvi Freiberg
- Institute
of Physics, University of Tartu, Riia 142,
Tartu 51014, Estonia
- Institute
of Molecular and Cell
Biology, University of Tartu, Riia 23,
Tartu 51010, Estonia
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38
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Sai Sankar Gupta KB, Alia A, de Groot HJ, Matysik J. Symmetry Break of Special Pair: Photochemically Induced Dynamic Nuclear Polarization NMR Confirms Control by Nonaromatic Substituents. J Am Chem Soc 2013; 135:10382-7. [DOI: 10.1021/ja402238w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - A. Alia
- Institute
of Chemistry, Leiden University, P.O. Box
9502, 2300 RA Leiden, The
Netherlands
- Institut für Medizinische
Physik und Biophysik, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Huub J.M. de Groot
- Institute
of Chemistry, Leiden University, P.O. Box
9502, 2300 RA Leiden, The
Netherlands
| | - Jörg Matysik
- Institute
of Chemistry, Leiden University, P.O. Box
9502, 2300 RA Leiden, The
Netherlands
- Institut für
Analytische
Chemie, Universität Leipzig, Linnèstr.
3, 04104 Leipzig, Germany
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39
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Alia A, Buda F, de Groot HJ, Matysik J. Solid-State NMR of Nanomachines Involved in Photosynthetic Energy Conversion. Annu Rev Biophys 2013; 42:675-99. [DOI: 10.1146/annurev-biophys-083012-130415] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Magic-angle spinning NMR, often in combination with photo-CIDNP, is applied to determine how photosynthetic antennae and reaction centers are activated in the ground state to perform their biological function upon excitation by light. Molecular modeling resolves molecular mechanisms by way of computational integration of NMR data with other structure-function analyses. By taking evolutionary historical contingency into account, a better biophysical understanding is achieved. Chlorophyll cofactors and proteins go through self-assembly trajectories that are engineered during evolution and lead to highly homogeneous protein complexes optimized for exciton or charge transfer. Histidine-cofactor interactions allow biological nanomachines to lower energy barriers for light harvesting and charge separation in photosynthetic energy conversion. In contrast, in primordial chlorophyll antenna aggregates, excessive heterogeneity is paired with much less specific characteristics, and both exciton and charge-transfer character are encoded in the ground state.
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Affiliation(s)
- A. Alia
- Solid State NMR, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RB, The Netherlands;, , ,
| | - Francesco Buda
- Solid State NMR, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RB, The Netherlands;, , ,
| | - Huub J.M. de Groot
- Solid State NMR, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RB, The Netherlands;, , ,
| | - Jörg Matysik
- Solid State NMR, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RB, The Netherlands;, , ,
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40
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van den Bosch B, Chen HC, van der Vlugt JI, Brouwer AM, Reek JNH. A noble-metal-free system for photodriven catalytic proton reduction. CHEMSUSCHEM 2013; 6:790-793. [PMID: 23512840 DOI: 10.1002/cssc.201200960] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 06/01/2023]
Abstract
Who needs the nobles? Ideally, devices to harvest solar energy into fuels would, in addition to having very high turnover numbers, make use of earth-abundant materials. In this Highlight we focus on a recent example in which a copper-based photosensitizer is used, in combination with an iron-based catalyst for light-driven proton reduction.
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Affiliation(s)
- Bart van den Bosch
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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41
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Sai Sankar Gupta KB, Alia A, Buda F, de Groot HJM, Matysik J. Bacteriopheophytin a in the active branch of the reaction center of rhodobacter sphaeroides is not disturbed by the protein matrix as shown by 13C photo-CIDNP MAS NMR. J Phys Chem B 2013; 117:3287-97. [PMID: 23452037 DOI: 10.1021/jp3121319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic structure of bacteriopheophytin a (BPhe a), the primary electron acceptor (ΦA) in photosynthetic reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides, is investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) magic-angle spinning (MAS) NMR spectroscopy at atomic resolution. By using various isotope labeling systems, introduced by adding different (13)C selectively labeled δ-aminolevulinic acid precursors in the growing medium of R. sphaeroides wild type (WT), we were able to extract light-induced (13)C NMR signals originating from the primary electron acceptor. The assignments are backed by theoretical calculations. By comparison of these chemical shifts to those obtained from monomeric BPhe a in solution, it is demonstrated that ΦA in the active branch appears to be electronically close to free bacteriopheophytin. Hence, there is little effect of the protein surrounding on the cofactor functionally which contributes with its standard redox potential to the electron transfer process that is asymmetric.
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42
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Joya KS, Vallés-Pardo JL, Joya YF, Eisenmayer T, Thomas B, Buda F, de Groot HJM. Molecular Catalytic Assemblies for Electrodriven Water Splitting. Chempluschem 2012. [DOI: 10.1002/cplu.201200161] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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43
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Wilker MB, Schnitzenbaumer KJ, Dukovic G. Recent Progress in Photocatalysis Mediated by Colloidal II-VI Nanocrystals. Isr J Chem 2012; 52:1002-1015. [PMID: 24115781 PMCID: PMC3791552 DOI: 10.1002/ijch.201200073] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/29/2012] [Indexed: 12/14/2022]
Abstract
The use of photoexcited electrons and holes in semiconductor nanocrystals as reduction and oxidation reagents is an intriguing way of harvesting photon energy to drive chemical reactions. This review focuses on recent research efforts to understand and control the photocatalytic processes mediated by colloidal II-VI nanocrystalline materials, such as cadmium and zinc chalcogenides. First, we highlight how nanocrystal properties govern the rates and efficiencies of charge-transfer processes relevant to photocatalysis. We then describe the use of nanocrystal catalyst heterostructures for fuel-forming reactions, most commonly H2 generation. Finally, we review the use of nanocrystal photocatalysis as a synthetic tool for metal-semiconductor nano-heterostructures.
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Affiliation(s)
- Molly B Wilker
- Department of Chemistry and Biochemistry, University of Colorado BoulderBoulder, CO 80309, USA
| | - Kyle J Schnitzenbaumer
- Department of Chemistry and Biochemistry, University of Colorado BoulderBoulder, CO 80309, USA
| | - Gordana Dukovic
- Department of Chemistry and Biochemistry, University of Colorado BoulderBoulder, CO 80309, USA
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44
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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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45
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Liu X, Li J, Dong J, Hu C, Gong W, Wang J. Genetic Incorporation of a Metal-Chelating Amino Acid as a Probe for Protein Electron Transfer. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Liu X, Li J, Dong J, Hu C, Gong W, Wang J. Genetic incorporation of a metal-chelating amino acid as a probe for protein electron transfer. Angew Chem Int Ed Engl 2012; 51:10261-5. [PMID: 22936654 DOI: 10.1002/anie.201204962] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 07/26/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Xiaohong Liu
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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Hong S, Victoria D, Crofts AR. Inter-monomer electron transfer is too slow to compete with monomeric turnover in bc(1) complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1053-62. [PMID: 22465023 DOI: 10.1016/j.bbabio.2012.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 03/08/2012] [Accepted: 03/11/2012] [Indexed: 11/30/2022]
Abstract
The homodimeric bc(1) complexes are membrane proteins essential in respiration and photosynthesis. The ~11Å distance between the two b(L)-hemes of the dimer opens the possibility of electron transfer between them, but contradictory reports make such inter-monomer electron transfer controversial. We have constructed in Rhodobacter sphaeroides a heterodimeric expression system similar to those used before, in which the bc(1) complex can be mutated differentially in the two copies of cyt b to test for inter-monomer electron transfer, but found that genetic recombination by cross-over then occurs to produce wild-type homodimer. Selection pressure under photosynthetic growth always favored the homodimer over heterodimeric variants enforcing inter-monomer electron transfer, showing that the latter are not competitive. These results, together with kinetic analysis of myxothiazol titrations, demonstrate that inter-monomer electron transfer does not occur at rates competitive with monomeric turnover. We examine the results from other groups interpreted as demonstrating rapid inter-monomer electron transfer, conclude that similar mechanisms are likely to be in play, and suggest that such claims might need to be re-examined.
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Affiliation(s)
- Sangjin Hong
- Departments of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Abstract
This paper presents an overview of the prospects for bio-solar energy conversion. The Global Artificial Photosynthesis meeting at Lord Howe Island (14–18 August 2011) underscored the dependence that the world has placed on non-renewable energy supplies, particularly for transport fuels, and highlighted the potential of solar energy. Biology has used solar energy for free energy gain to drive chemical reactions for billions of years. The principal conduits for energy conversion on earth are photosynthetic reaction centres – but can they be harnessed, copied and emulated? In this communication, we initially discuss algal-based biofuels before investigating bio-inspired solar energy conversion in artificial and engineered systems. We show that the basic design and engineering principles for assembling photocatalytic proteins can be used to assemble nanocatalysts for solar fuel production.
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Fleming GR, Schlau-Cohen GS, Amarnath K, Zaks J. Design principles of photosynthetic light-harvesting. Faraday Discuss 2012; 155:27-41; discussion 103-14. [DOI: 10.1039/c1fd00078k] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Schlau-Cohen GS, Fleming GR. Structure, Dynamics, and Function in the Major Light-Harvesting Complex of Photosystem II. Aust J Chem 2012. [DOI: 10.1071/ch12022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In natural light-harvesting systems, pigment-protein complexes (PPC) convert sunlight to chemical energy with near unity quantum efficiency. PPCs exhibit emergent properties that cannot be simply extrapolated from knowledge of their component parts. In this Perspective, we examine the design principles of PPCs, focussing on the major light-harvesting complex of Photosystem II (LHCII), the most abundant PPC in green plants. Studies using two-dimensional electronic spectroscopy (2DES) provide an incisive tool to probe the electronic, energetic, and spatial landscapes that enable the efficiency observed in photosynthetic light-harvesting. Using the information about energy transfer pathways, quantum effects, and excited state geometry contained within 2D spectra, the excited state properties can be linked back to the molecular structure. This understanding of the structure-function relationships of natural systems constitutes a step towards a blueprint for the construction of artificial light-harvesting devices that can reproduce the efficacy of natural systems.
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