1
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Dodia M, Rouxel JR, Cho D, Zhang Y, Keefer D, Bonn M, Nagata Y, Mukamel S. Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer. J Chem Theory Comput 2024. [PMID: 38727197 DOI: 10.1021/acs.jctc.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.
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Affiliation(s)
- Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Jérémy R Rouxel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Daeheum Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yu Zhang
- Ames National Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Daniel Keefer
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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2
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Coppola F, Cimino P, Petrone A, Rega N. Evidence of Excited-State Vibrational Mode Governing the Photorelaxation of a Charge-Transfer Complex. J Phys Chem A 2024; 128:1620-1633. [PMID: 38381887 DOI: 10.1021/acs.jpca.3c08366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical-computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation. Our protocol provides an accurate description that facilitates a direct comparison between transient vibrational analysis and time-resolved spectroscopic signals. This molecular level perspective enhances our understanding of photorelaxation processes confined in the adiabatic regime and offers an improved interpretation of vibrational spectra. Furthermore, it enables the quantification of anharmonic vibrational couplings between high- and low-frequency modes, specifically the TCNQ "rocking" and "bending" modes. Additionally, it identifies the primary vibrational mode that governs the adiabaticity between the ground state and the CT state. This comprehensive understanding of photorelaxation processes holds significant importance in the rational design and precise control of more efficient photovoltaic and sensor devices.
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Affiliation(s)
- Federico Coppola
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Paola Cimino
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Istituto Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italia
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3
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Hamada M, Iwata T, Fuki M, Kandori H, Weber S, Kobori Y. Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome. Commun Chem 2021; 4:141. [PMID: 36697801 PMCID: PMC9814139 DOI: 10.1038/s42004-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/02/2021] [Indexed: 01/28/2023] Open
Abstract
In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, WA(H), WB(H) and WC(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD-•) and radical cation WB(H)+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.
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Affiliation(s)
- Misato Hamada
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Tatsuya Iwata
- grid.265050.40000 0000 9290 9879Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274‒8510 Japan
| | - Masaaki Fuki
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Hideki Kandori
- grid.47716.330000 0001 0656 7591Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan ,grid.47716.330000 0001 0656 7591OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan
| | - Stefan Weber
- grid.5963.9Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Yasuhiro Kobori
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
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4
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Lacombat F, Espagne A, Dozova N, Plaza P, Müller P, Emmerich HJ, Saft M, Essen LO. Ultrafast photoreduction dynamics of a new class of CPD photolyases. Photochem Photobiol Sci 2021; 20:733-746. [PMID: 33977513 DOI: 10.1007/s43630-021-00048-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/22/2021] [Indexed: 01/09/2023]
Abstract
NewPHL is a recently discovered subgroup of ancestral DNA photolyases. Its domain architecture displays pronounced differences from that of canonical photolyases, in particular at the level of the characteristic electron transfer chain, which is limited to merely two tryptophans, instead of the "classical" three or four. Using transient absorption spectroscopy, we show that the dynamics of photoreduction of the oxidized FAD cofactor in the NewPHL begins similarly as that in canonical photolyases, i.e., with a sub-ps primary reduction of the excited FAD cofactor by an adjacent tryptophan, followed by migration of the electron hole towards the second tryptophan in the tens of ps regime. However, the resulting tryptophanyl radical then undergoes an unprecedentedly fast deprotonation in less than 100 ps in the NewPHL. In spite of the stabilization effect of this deprotonation, almost complete charge recombination follows in two phases of ~ 950 ps and ~ 50 ns. Such a rapid recombination of the radical pair implies that the first FAD photoreduction step, i.e., conversion of the fully oxidized to the semi-quinone state, should be rather difficult in vivo. We hence suggest that the flavin chromophore likely switches only between its semi-reduced and fully reduced form in NewPHL under physiological conditions.
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Affiliation(s)
- Fabien Lacombat
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Agathe Espagne
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Nadia Dozova
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France
| | - Pascal Plaza
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, CNRS, Sorbonne Université, 75005, Paris, France.
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - Hans-Joachim Emmerich
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany
| | - Martin Saft
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Center for Synthetic Microbiology, Philipps University, 35032, Marburg, Germany.
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5
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Miles JA, Davies TA, Hayman RD, Lorenzen G, Taylor J, Anjarwalla M, Allen SJR, Graham JWD, Taylor PC. A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins. J Mol Evol 2020; 88:662-673. [PMID: 32979052 PMCID: PMC7560933 DOI: 10.1007/s00239-020-09965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/05/2020] [Indexed: 11/23/2022]
Abstract
Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.
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Affiliation(s)
- Jennifer A Miles
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Thomas A Davies
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Robert D Hayman
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Georgia Lorenzen
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Jamie Taylor
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Mubeena Anjarwalla
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Sammie J R Allen
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - John W D Graham
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Paul C Taylor
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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6
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Abstract
Cryptochromes are blue-light receptors that mediate photoresponses in plants. The genomes of most land plants encode two clades of cryptochromes, CRY1 and CRY2, which mediate distinct and overlapping photoresponses within the same species and between different plant species. Photoresponsive protein-protein interaction is the primary mode of signal transduction of cryptochromes. Cryptochromes exist as physiologically inactive monomers in the dark; the absorption of photons leads to conformational change and cryptochrome homooligomerization, which alters the affinity of cryptochromes interacting with cryptochrome-interacting proteins to form various cryptochrome complexes. These cryptochrome complexes, collectively referred to as the cryptochrome complexome, regulate transcription or stability of photoresponsive proteins to modulate plant growth and development. The activity of cryptochromes is regulated by photooligomerization; dark monomerization; cryptochrome regulatory proteins; and cryptochrome phosphorylation, ubiquitination, and degradation. Most of the more than 30 presently known cryptochrome-interacting proteins are either regulated by other photoreceptors or physically interactingwith the protein complexes of other photoreceptors. Some cryptochrome-interacting proteins are also hormonal signaling or regulatory proteins. These two mechanisms enable cryptochromes to integrate blue-light signals with other internal and external signals to optimize plant growth and development.
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Affiliation(s)
- Qin Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095, USA;
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7
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Affiliation(s)
- Chadsley Atkins
- Institute and Department of Physics, University of Exeter, North Park Road, Exeter EX4 4QL, United Kingdom
| | - Kieran Bajpai
- Institute and Department of Physics, University of Exeter, North Park Road, Exeter EX4 4QL, United Kingdom
| | - Jeremy Rumball
- Institute and Department of Physics, University of Exeter, North Park Road, Exeter EX4 4QL, United Kingdom
| | - Daniel R. Kattnig
- Institute and Department of Physics, University of Exeter, North Park Road, Exeter EX4 4QL, United Kingdom
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
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8
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Abstract
Flavin semiquinone redox states are important intermediates in a broad variety of reactions catalyzed by flavoproteins. As paramagnetic states they can be favorably probed by EPR spectroscopy in all its flavors. This review summarizes recent results in the characterization of flavin radicals. On the one hand, flavin radical states, e.g., trapped as reaction intermediates, can be characterized using modern pulsed EPR methods to unravel their electronic structure and to gain information about the surrounding environment and its changes on protein action. On the other hand, short-lived intermediate flavin radical states generated, e.g., photochemically, can be followed by time-resolved EPR, which allows a direct tracking of flavin-dependent reactions with a temporal resolution reaching nanoseconds.
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Affiliation(s)
- Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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9
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10
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Worster SB, Hore PJ. Proposal to use superparamagnetic nanoparticles to test the role of cryptochrome in magnetoreception. J R Soc Interface 2018; 15:20180587. [PMID: 30381345 PMCID: PMC6228473 DOI: 10.1098/rsif.2018.0587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/08/2018] [Indexed: 11/12/2022] Open
Abstract
Evidence is accumulating to support the hypothesis that some animals use light-induced radical pairs to detect the direction of the Earth's magnetic field. Cryptochrome proteins seem to be involved in the sensory pathway but it is not yet clear if they are the magnetic sensors: they could, instead, play a non-magnetic role as signal transducers downstream of the primary sensor. Here we propose an experiment with the potential to distinguish these functions. The principle is to use superparamagnetic nanoparticles to disable any magnetic sensing role by enhancing the electron spin relaxation of the radicals so as to destroy their spin correlation. We use spin dynamics simulations to show that magnetoferritin, a synthetic, protein-based nanoparticle, has the required properties. If cryptochrome is the primary sensor, then it should be inactivated by a magnetoferritin particle placed 12-16 nm away. This would prevent a bird from using its magnetic compass in behavioural tests and abolish magnetically sensitive neuronal firing in the retina. The key advantage of such an experiment is that any signal transduction role should be completely unaffected by the tiny magnetic interactions (≪kBT) required to enhance the spin relaxation of the radical pair.
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Affiliation(s)
- Susannah Bourne Worster
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, UK
| | - P J Hore
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, UK
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11
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Nielsen C, Kattnig DR, Sjulstok E, Hore PJ, Solov'yov IA. Ascorbic acid may not be involved in cryptochrome-based magnetoreception. J R Soc Interface 2018; 14:rsif.2017.0657. [PMID: 29263128 DOI: 10.1098/rsif.2017.0657] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/28/2017] [Indexed: 01/13/2023] Open
Abstract
Seventeen years after it was originally suggested, the photoreceptor protein cryptochrome remains the most probable host for the radical pair intermediates that are thought to be the sensors in the avian magnetic compass. Although evidence in favour of this hypothesis is accumulating, the intracellular interaction partners of the sensory protein are still unknown. It has been suggested that ascorbate ions could interact with surface-exposed tryptophan radicals in photoactivated cryptochromes, and so lead to the formation of a radical pair comprised of the reduced form of the flavin adenine dinucleotide cofactor, FAD•-, and the ascorbate radical, Asc•- This species could provide a more sensitive compass than a FAD-tryptophan radical pair. In this study of Drosophila melanogaster cryptochrome and Erithacus rubecula (European robin) cryptochrome 1a, we use molecular dynamics simulations to characterize the transient encounters of ascorbate ions with tryptophan radicals in cryptochrome in order to assess the likelihood of the [FAD•- Asc•-]-pathway. It is shown that ascorbate ions are expected to bind near the tryptophan radicals for periods of a few nanoseconds. The rate at which these encounters happen is low, and it is therefore concluded that ascorbate ions are unlikely to be involved in magnetoreception if the ascorbate concentration is only of the order of 1 mM or less.
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Affiliation(s)
- Claus Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - P J Hore
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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12
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Abstract
The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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13
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Magerl K, Stambolic I, Dick B. Switching from adduct formation to electron transfer in a light-oxygen-voltage domain containing the reactive cysteine. Phys Chem Chem Phys 2018; 19:10808-10819. [PMID: 28271102 DOI: 10.1039/c6cp08370f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.
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Affiliation(s)
- Kathrin Magerl
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany.
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14
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Affiliation(s)
- Daniel R. Kattnig
- Living Systems Institute
and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
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15
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Friis I, Sjulstok E, Solov'yov IA. Computational reconstruction reveals a candidate magnetic biocompass to be likely irrelevant for magnetoreception. Sci Rep 2017; 7:13908. [PMID: 29066765 PMCID: PMC5654753 DOI: 10.1038/s41598-017-13258-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/20/2017] [Indexed: 11/30/2022] Open
Abstract
Birds use the magnetic field of the Earth to navigate during their annual migratory travel. The possible mechanism to explain the biophysics of this compass sense involves electron transfers within the photoreceptive protein cryptochrome. The magnetoreceptive functioning of cryptochromes is supposedly facilitated through an iron rich polymer complex which couples to multiple cryptochromes. The present investigation aims to independently reconstruct this complex and describe its interaction with Drosophila melanogaster cryptochromes. The polymer complex consists of ISCA1 protein monomers with internally bound iron sulphur clusters and simultaneously binds ten cryptochromes. Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. It is found that the cryptochrome binding to the ISCA1 polymer is not uniform and that the binding affinity depends on its placement along the ISCA1 polymer. This finding supports the claim that the individual ISCA1 monomer acts as possible intracellular interaction partner of cryptochrome, but the proposed existence of an elongated ISCA1 polymer with multiple attached cryptochromes appears to be questionable.
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Affiliation(s)
- Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230, Odense M, Denmark.
| | - Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230, Odense M, Denmark.
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16
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Kopka B, Magerl K, Savitsky A, Davari MD, Röllen K, Bocola M, Dick B, Schwaneberg U, Jaeger KE, Krauss U. Electron transfer pathways in a light, oxygen, voltage (LOV) protein devoid of the photoactive cysteine. Sci Rep 2017; 7:13346. [PMID: 29042655 PMCID: PMC5645311 DOI: 10.1038/s41598-017-13420-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Blue-light absorption by the flavin chromophore in light, oxygen, voltage (LOV) photoreceptors triggers photochemical reactions that lead to the formation of a flavin-cysteine adduct. While it has long been assumed that adduct formation is essential for signaling, it was recently shown that LOV photoreceptor variants devoid of the photoactive cysteine can elicit a functional response and that flavin photoreduction to the neutral semiquinone radical is sufficient for signal transduction. Currently, the mechanistic basis of the underlying electron- (eT) and proton-transfer (pT) reactions is not well understood. We here reengineered pT into the naturally not photoreducible iLOV protein, a fluorescent reporter protein derived from the Arabidopsis thaliana phototropin-2 LOV2 domain. A single amino-acid substitution (Q489D) enabled efficient photoreduction, suggesting that an eT pathway is naturally present in the protein. By using a combination of site-directed mutagenesis, steady-state UV/Vis, transient absorption and electron paramagnetic resonance spectroscopy, we investigate the underlying eT and pT reactions. Our study provides strong evidence that several Tyr and Trp residues, highly conserved in all LOV proteins, constitute the eT pathway for flavin photoreduction, suggesting that the propensity for photoreduction is evolutionary imprinted in all LOV domains, while efficient pT is needed to stabilize the neutral semiquinone radical.
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Affiliation(s)
- Benita Kopka
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Kathrin Magerl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, 45470, Mülheim an der Ruhr, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Bernhard Dick
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.,IBG-1: Biotechnologie, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
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17
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Kottke T, Oldemeyer S, Wenzel S, Zou Y, Mittag M. Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions. J Plant Physiol 2017; 217:4-14. [PMID: 28619534 DOI: 10.1016/j.jplph.2017.05.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.
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Affiliation(s)
- Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Yong Zou
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
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18
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Yamamoto J, Shimizu K, Kanda T, Hosokawa Y, Iwai S, Plaza P, Müller P. Loss of Fourth Electron-Transferring Tryptophan in Animal (6–4) Photolyase Impairs DNA Repair Activity in Bacterial Cells. Biochemistry 2017; 56:5356-5364. [DOI: 10.1021/acs.biochem.7b00366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junpei Yamamoto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kohei Shimizu
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Takahiro Kanda
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yuhei Hosokawa
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Pascal Plaza
- PASTEUR,
Département de chimie, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, CNRS, PASTEUR, 75005 Paris, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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19
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Nohr D, Paulus B, Rodriguez R, Okafuji A, Bittl R, Schleicher E, Weber S. Bestimmung des Radikal-Radikal-Abstands in lichtaktiven Proteinen im angeregten Zustand und dessen Bedeutung für die biologische Magnetorezeption. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Nohr
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
| | - Bernd Paulus
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
| | - Ryan Rodriguez
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
| | - Asako Okafuji
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
| | - Robert Bittl
- Fachbereich Physik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Deutschland
| | - Erik Schleicher
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
| | - Stefan Weber
- Institut für Physikalische Chemie; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg Deutschland
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20
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Nohr D, Paulus B, Rodriguez R, Okafuji A, Bittl R, Schleicher E, Weber S. Determination of Radical-Radical Distances in Light-Active Proteins and Their Implication for Biological Magnetoreception. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201700389] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Nohr
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
| | - Bernd Paulus
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
| | - Ryan Rodriguez
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
| | - Asako Okafuji
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
| | - Robert Bittl
- Department of Physics; Freie Universität Berlin; Arnimallee 14 14195 Berlin Germany
| | - Erik Schleicher
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
| | - Stefan Weber
- Institute of Physical Chemistry; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg Germany
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21
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Nohr D, Franz S, Rodriguez R, Paulus B, Essen LO, Weber S, Schleicher E. Extended Electron-Transfer in Animal Cryptochromes Mediated by a Tetrad of Aromatic Amino Acids. Biophys J 2017; 111:301-311. [PMID: 27463133 DOI: 10.1016/j.bpj.2016.06.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/24/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
The cryptochrome/photolyase protein family possesses a conserved triad of tryptophans that may act as a molecular wire to transport electrons from the protein surface to the FAD cofactor for activation and/or signaling-state formation. Members from the animal (and animal-like) cryptochrome subclade use this process in a light-induced fashion in a number of exciting responses, such as the (re-)setting of circadian rhythms or magnetoreception; however, electron-transfer pathways have not been explored in detail yet. Therefore, we present an in-depth time-resolved optical and electron-paramagnetic resonance spectroscopic study of two cryptochromes from Chlamydomonas reinhardtii and Drosophila melanogaster. The results do not only reveal the existence of a fourth, more distant aromatic amino acid that serves as a terminal electron donor in both proteins, but also show that a tyrosine is able to fulfill this very role in Chlamydomonas reinhardtii cryptochrome. Additionally, exchange of the respective fourth aromatic amino acid to redox-inactive phenylalanines still leads to light-induced radical pair formation; however, the lifetimes of these species are drastically reduced from the ms- to the μs-range. The results presented in this study open up a new chapter, to our knowledge, in the diversity of electron-transfer pathways in cryptochromes. Moreover, they could explain unique functions of animal cryptochromes, in particular their potential roles in magnetoreception because magnetic-field effects of light-induced radical pairs strongly depend on distance and orientation parameters.
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Affiliation(s)
- Daniel Nohr
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | | | - Ryan Rodriguez
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Bernd Paulus
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | | | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
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22
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Affiliation(s)
- P. J. Hore
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Henrik Mouritsen
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, DE-26111 Oldenburg, Germany;
- Research Centre for Neurosensory Sciences, University of Oldenburg, DE-26111 Oldenburg, Germany
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23
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Abstract
The magnetic compass sense of migratory birds is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the retina. An important requirement of this hypothesis is that electron spin relaxation is slow enough for the Earth's magnetic field to have a significant effect on the coherent spin dynamics of the radicals. It is generally assumed that evolutionary pressure has led to protection of the electron spins from irreversible loss of coherence in order that the underlying quantum dynamics can survive in a noisy biological environment. Here, we address this question for a structurally characterized model cryptochrome expected to share many properties with the putative avian receptor protein. To this end we combine all-atom molecular dynamics simulations, Bloch-Redfield relaxation theory and spin dynamics calculations to assess the effects of spin relaxation on the performance of the protein as a compass sensor. Both flavin-tryptophan and flavin-Z˙ radical pairs are studied (Z˙ is a radical with no hyperfine interactions). Relaxation is considered to arise from modulation of hyperfine interactions by librational motions of the radicals and fluctuations in certain dihedral angles. For Arabidopsis thaliana cryptochrome 1 (AtCry1) we find that spin relaxation implies optimal radical pair lifetimes of the order of microseconds, and that flavin-Z˙ pairs are less affected by relaxation than flavin-tryptophan pairs. Our results also demonstrate that spin relaxation in isolated AtCry1 is incompatible with the long coherence times that have been postulated to explain the disruption of the avian magnetic compass sense by weak radiofrequency magnetic fields. We conclude that a cryptochrome sensor in vivo would have to differ dynamically, if not structurally, from isolated AtCry1. Our results clearly mark the limits of the current hypothesis and lead to a better understanding of the operation of radical pair magnetic sensors in noisy biological environments.
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Affiliation(s)
- Daniel R Kattnig
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, OX1 3QZ, UK.
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24
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Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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25
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Nohr D, Rodriguez R, Weber S, Schleicher E. How can EPR spectroscopy help to unravel molecular mechanisms of flavin-dependent photoreceptors? Front Mol Biosci 2015; 2:49. [PMID: 26389123 PMCID: PMC4555020 DOI: 10.3389/fmolb.2015.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a well-established spectroscopic method for the examination of paramagnetic molecules. Proteins can contain paramagnetic moieties in form of stable cofactors, transiently formed intermediates, or spin labels artificially introduced to cysteine sites. The focus of this review is to evaluate potential scopes of application of EPR to the emerging field of optogenetics. The main objective for EPR spectroscopy in this context is to unravel the complex mechanisms of light-active proteins, from their primary photoreaction to downstream signal transduction. An overview of recent results from the family of flavin-containing, blue-light dependent photoreceptors is given. In detail, mechanistic similarities and differences are condensed from the three classes of flavoproteins, the cryptochromes, LOV (Light-oxygen-voltage), and BLUF (blue-light using FAD) domains. Additionally, a concept that includes spin-labeled proteins and examination using modern pulsed EPR is introduced, which allows for a precise mapping of light-induced conformational changes.
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Affiliation(s)
- Daniel Nohr
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Ryan Rodriguez
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Stefan Weber
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Erik Schleicher
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
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26
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Thöing C, Oldemeyer S, Kottke T. Microsecond Deprotonation of Aspartic Acid and Response of the α/β Subdomain Precede C-Terminal Signaling in the Blue Light Sensor Plant Cryptochrome. J Am Chem Soc 2015; 137:5990-9. [PMID: 25909499 DOI: 10.1021/jacs.5b01404] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plant cryptochromes are photosensory receptors that regulate various central aspects of plant growth and development. These receptors consist of a photolyase homology region (PHR) carrying the oxidized flavin adenine dinucleotide (FAD) cofactor, and a cryptochrome C-terminal extension (CCT), which is essential for signaling. Absorption of blue/UVA light leads to formation of the FAD neutral radical as the likely signaling state, and ultimately activates the CCT. Little is known about the signal transfer from the flavin to the CCT. Here, we investigated the photoreaction of the PHR by time-resolved step-scan FT-IR spectroscopy complemented by UV-vis spectroscopy. The first spectrum at 500 ns shows major contributions from the FAD anion radical, which is demonstrated to then be protonated by aspartic acid 396 to the neutral radical within 3.5 μs. The analysis revealed the existence of three intermediates characterized by changes in secondary structure. A marked loss of β-sheet structure is observed in the second intermediate evolving with a time constant of 500 μs. This change is accompanied by a conversion of a tyrosine residue, which is identified as the formation of a tyrosine radical in the UV-vis. The only β-sheet in the PHR is located within the α/β subdomain, ∼25 Å away from the flavin. This subdomain has been previously attributed a role as a putative antenna binding site, but is now suggested to have evolved to a component in the signaling of plant cryptochromes by mediating the interaction with the CCT.
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Affiliation(s)
- Christian Thöing
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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27
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Paulus B, Bajzath C, Melin F, Heidinger L, Kromm V, Herkersdorf C, Benz U, Mann L, Stehle P, Hellwig P, Weber S, Schleicher E. Spectroscopic characterization of radicals and radical pairs in fruit fly cryptochrome - protonated and nonprotonated flavin radical-states. FEBS J 2015; 282:3175-89. [PMID: 25879256 DOI: 10.1111/febs.13299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/21/2015] [Accepted: 04/14/2015] [Indexed: 01/05/2023]
Abstract
Drosophila melanogaster cryptochrome is one of the model proteins for animal blue-light photoreceptors. Using time-resolved and steady-state optical spectroscopy, we studied the mechanism of light-induced radical-pair formation and decay, and the photoreduction of the FAD cofactor. Exact kinetics on a microsecond to minutes timescale could be extracted for the wild-type protein using global analysis. The wild-type exhibits a fast photoreduction reaction from the oxidized FAD to the FAD(•-) state with a very positive midpoint potential of ~ +125 mV, although no further reduction could be observed. We could also demonstrate that the terminal tryptophan of the conserved triad, W342, is directly involved in electron transfer; however, photoreduction could not be completely inhibited in a W342F mutant. The investigation of another mutation close to the FAD cofactor, C416N, rather unexpectedly reveals accumulation of a protonated flavin radical on a timescale of several seconds. The obtained data are critically discussed with the ones obtained from another protein, Escherichia coli photolyase, and we conclude that the amino acid opposite N(5) of the isoalloxazine moiety of FAD is able to (de)stabilize the protonated FAD radical but not to significantly modulate the kinetics of any light-inducted reactions.
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Affiliation(s)
- Bernd Paulus
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Csaba Bajzath
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Viktoria Kromm
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Ulrike Benz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Lisa Mann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Patricia Stehle
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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28
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Hense A, Herman E, Oldemeyer S, Kottke T. Proton transfer to flavin stabilizes the signaling state of the blue light receptor plant cryptochrome. J Biol Chem 2014; 290:1743-51. [PMID: 25471375 DOI: 10.1074/jbc.m114.606327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant cryptochromes regulate the circadian rhythm, flowering time, and photomorphogenesis in higher plants as responses to blue light. In the dark, these photoreceptors bind oxidized FAD in the photolyase homology region (PHR). Upon blue light absorption, FAD is converted to the neutral radical state, the likely signaling state, by electron transfer via a conserved tryptophan triad and proton transfer from a nearby aspartic acid. Here we demonstrate, by infrared and time-resolved UV-visible spectroscopy on the PHR domain, that replacement of the aspartic acid Asp-396 with cysteine prevents proton transfer. The lifetime of the radical is decreased by 6 orders of magnitude. This short lifetime does not permit to drive conformational changes in the C-terminal extension that have been associated with signal transduction. Only in the presence of ATP do both the wild type and mutant form a long-lived radical state. However, in the mutant, an anion radical is formed instead of the neutral radical, as found previously in animal type I cryptochromes. Infrared spectroscopic experiments demonstrate that the light-induced conformational changes of the PHR domain are conserved in the mutant despite the lack of proton transfer. These changes are not detected in the photoreduction of the non-photosensory d-amino acid oxidase to the anion radical. In conclusion, formation of the anion radical is sufficient to generate a protein response in plant cryptochromes. Moreover, the intrinsic proton transfer is required for stabilization of the signaling state in the absence of ATP.
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Affiliation(s)
- Anika Hense
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Elena Herman
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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29
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Engelhard C, Wang X, Robles D, Moldt J, Essen LO, Batschauer A, Bittl R, Ahmad M. Cellular metabolites enhance the light sensitivity of Arabidopsis cryptochrome through alternate electron transfer pathways. Plant Cell 2014; 26:4519-31. [PMID: 25428980 PMCID: PMC4277212 DOI: 10.1105/tpc.114.129809] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cryptochromes are blue light receptors with multiple signaling roles in plants and animals. Plant cryptochrome (cry1 and cry2) biological activity has been linked to flavin photoreduction via an electron transport chain comprising three evolutionarily conserved tryptophan residues known as the Trp triad. Recently, it has been reported that cry2 Trp triad mutants, which fail to undergo photoreduction in vitro, nonetheless show biological activity in vivo, raising the possibility of alternate signaling pathways. Here, we show that Arabidopsis thaliana cry2 proteins containing Trp triad mutations indeed undergo robust photoreduction in living cultured insect cells. UV/Vis and electron paramagnetic resonance spectroscopy resolves the discrepancy between in vivo and in vitro photochemical activity, as small metabolites, including NADPH, NADH, and ATP, were found to promote cry photoreduction even in mutants lacking the classic Trp triad electron transfer chain. These metabolites facilitate alternate electron transfer pathways and increase light-induced radical pair formation. We conclude that cryptochrome activation is consistent with a mechanism of light-induced electron transfer followed by flavin photoreduction in vivo. We further conclude that in vivo modulation by cellular compounds represents a feature of the cryptochrome signaling mechanism that has important consequences for light responsivity and activation.
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Affiliation(s)
| | - Xuecong Wang
- University of Paris VI, UMR 8256 (B2A), IBPS, 75005 Paris, France
| | - David Robles
- University of Paris VI, UMR 8256 (B2A), IBPS, 75005 Paris, France
| | - Julia Moldt
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Biomedical Research Centre/Faculty of Chemistry, Philipps-University, 35032 Marburg, Germany
| | - Alfred Batschauer
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University, 35032 Marburg, Germany
| | - Robert Bittl
- Fachbereich Physik, Free University, 14195 Berlin, Germany
| | - Margaret Ahmad
- University of Paris VI, UMR 8256 (B2A), IBPS, 75005 Paris, France Xavier University, Cincinatti, Ohio 45207
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30
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Cailliez F, Müller P, Gallois M, de la Lande A. ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome. J Am Chem Soc 2014; 136:12974-86. [PMID: 25157750 DOI: 10.1021/ja506084f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°(-)). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud and CNRS , Orsay F-91405, France
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Solov'yov IA, Domratcheva T, Schulten K. Separation of photo-induced radical pair in cryptochrome to a functionally critical distance. Sci Rep 2014; 4:3845. [PMID: 24457842 PMCID: PMC4894384 DOI: 10.1038/srep03845] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/27/2013] [Indexed: 11/09/2022] Open
Abstract
Cryptochrome is a blue light receptor that acts as a sensor for the geomagnetic field and assists many animals in long-range navigation. The magnetoreceptor function arises from light-induced formation of a radical pair through electron transfer between a flavin cofactor (FAD) and a triad of tryptophan residues. Here, this electron transfer is investigated by quantum chemical and classical molecular dynamics calculations. The results reveal how sequential electron transfer, assisted by rearrangement of polar side groups in the cryptochrome interior, can yield a FAD-Trp radical pair state with the FAD and Trp partners separated beyond a critical distance. The large radical pair separation reached establishes cryptochrome's sensitivity to the geomagnetic field through weakening of distance-dependent exchange and dipole-dipole interactions. It is estimated that the key secondary electron transfer step can overcome in speed both recombination (electron back-transfer) and proton transfer involving the radical pair reached after primary electron transfer.
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Affiliation(s)
- Ilia A Solov'yov
- 1] Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana Illinois 61801, USA [2] Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Klaus Schulten
- 1] Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana Illinois 61801, USA [2] Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, Illinois 61801, USA
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Burggraf F, Koslowski T. Charge transfer through a cytochrome multiheme chain: Theory and simulation. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2014; 1837:186-92. [DOI: 10.1016/j.bbabio.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
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Abstract
Flavoproteins often employ radical mechanisms in their enzymatic reactions. This involves paramagnetic species, which can ideally be investigated with electron paramagnetic resonance (EPR) spectroscopy. In this chapter we focus on the example of flavin-based photoreceptors and discuss, how different EPR methods have been used to extract information about the flavin radical's electronic state, its binding pocket, electron-transfer pathways, and about the protein's tertiary and quaternary structure.
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Affiliation(s)
- Richard Brosi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany,
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Abstract
Within the framework of the radical pair mechanism, magnetic fields may alter the rate and yields of chemical reactions involving spin-correlated radical pairs as intermediates. Such effects have been studied in detail in a variety of chemical systems both experimentally and theoretically. In recent years, there has been growing interest in whether such magnetic field effects (MFEs) also occur in biological systems, a question driven most notably by the increasing body of evidence for the involvement of such effects in the magnetic compass sense of animals. The blue-light photoreceptor cryptochrome is placed at the centre of this debate and photoexcitation of its bound flavin cofactor has indeed been shown to result in the formation of radical pairs. Here, we review studies of MFEs on free flavins in model systems as well as in blue-light photoreceptor proteins and discuss the properties that are crucial in determining the magnetosensitivity of these systems.
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Affiliation(s)
- Emrys W. Evans
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Charlotte A. Dodson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Kiminori Maeda
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Till Biskup
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - C. J. Wedge
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
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36
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Biskup T, Paulus B, Okafuji A, Hitomi K, Getzoff ED, Weber S, Schleicher E. Variable electron transfer pathways in an amphibian cryptochrome: tryptophan versus tyrosine-based radical pairs. J Biol Chem 2013; 288:9249-60. [PMID: 23430261 DOI: 10.1074/jbc.m112.417725] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Electron transfer reactions play vital roles in many biological processes. Very often the transfer of charge(s) proceeds stepwise over large distances involving several amino acid residues. By using time-resolved electron paramagnetic resonance and optical spectroscopy, we have studied the mechanism of light-induced reduction of the FAD cofactor of cryptochrome/photolyase family proteins. In this study, we demonstrate that electron abstraction from a nearby amino acid by the excited FAD triggers further electron transfer steps even if the conserved chain of three tryptophans, known to be an effective electron transfer pathway in these proteins, is blocked. Furthermore, we were able to characterize this secondary electron transfer pathway and identify the amino acid partner of the resulting flavin-amino acid radical pair as a tyrosine located at the protein surface. This alternative electron transfer pathway could explain why interrupting the conserved tryptophan triad does not necessarily alter photoreactions of cryptochromes in vivo. Taken together, our results demonstrate that light-induced electron transfer is a robust property of cryptochromes and more intricate than commonly anticipated.
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Affiliation(s)
- Till Biskup
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
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37
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Lau JCS, Rodgers CT, Hore PJ. Compass magnetoreception in birds arising from photo-induced radical pairs in rotationally disordered cryptochromes. J R Soc Interface 2012; 9:3329-37. [PMID: 22977104 PMCID: PMC3481564 DOI: 10.1098/rsif.2012.0374] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/21/2012] [Indexed: 01/14/2023] Open
Abstract
According to the radical pair model, the magnetic compass sense of migratory birds relies on photochemical transformations in the eye to detect the direction of the geomagnetic field. Magnetically sensitive radical pairs are thought to be generated in cryptochrome proteins contained in magnetoreceptor cells in the retina. A prerequisite of the current model is for some degree of rotational ordering of both the cryptochromes within the cells and of the cells within the retina so that the directional responses of individual molecules do not average to zero. Here, it is argued that anisotropic distributions of radical pairs can be generated by the photoselection effects that arise from the directionality of the light entering the eye. Light-induced rotational order among the transient radical pairs rather than intrinsic ordering of their molecular precursors is seen as the fundamental condition for a magnetoreceptor cell to exhibit an anisotropic response. A theoretical analysis shows that a viable compass magnetoreceptor could result from randomly oriented cryptochromes contained in randomly oriented cells distributed around the retina.
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Affiliation(s)
| | | | - P. J. Hore
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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38
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Hogben HJ, Biskup T, Hore PJ. Entanglement and sources of magnetic anisotropy in radical pair-based avian magnetoreceptors. Phys Rev Lett 2012; 109:220501. [PMID: 23368109 DOI: 10.1103/physrevlett.109.220501] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Indexed: 06/01/2023]
Abstract
One of the principal models of magnetic sensing in migratory birds rests on the quantum spin dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyperfine-anisotropy model. This property offers new and more flexible opportunities for the design of biologically inspired magnetic compass sensors.
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Affiliation(s)
- Hannah J Hogben
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
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39
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Fedin MV, Bagryanskaya EG, Matsuoka H, Yamauchi S, Veber SL, Maryunina KY, Tretyakov EV, Ovcharenko VI, Sagdeev RZ. W-Band Time-Resolved Electron Paramagnetic Resonance Study of Light-Induced Spin Dynamics in Copper–Nitroxide-Based Switchable Molecular Magnets. J Am Chem Soc 2012; 134:16319-26. [DOI: 10.1021/ja306467e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Matvey V. Fedin
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
| | - Elena G. Bagryanskaya
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva
9, 630090 Novosibirsk, Russia
| | - Hideto Matsuoka
- Institute of Multidisciplinary
Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Seigo Yamauchi
- Institute of Multidisciplinary
Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sergey L. Veber
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
| | - Ksenia Yu. Maryunina
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
| | - Evgeny V. Tretyakov
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
| | - Victor I. Ovcharenko
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
| | - Renad Z. Sagdeev
- International Tomography Center SB RAS, Institutskaya str. 3a, 630090 Novosibirsk,
Russia
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40
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Koslowski T, Burggraf F, Krapf S, Steinbrecher T, Wittekindt C. Recent progress in biological charge transfer: theory and simulation. Biochim Biophys Acta 2012; 1817:1955-7. [PMID: 22395149 DOI: 10.1016/j.bbabio.2012.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 02/15/2012] [Accepted: 02/21/2012] [Indexed: 11/19/2022]
Abstract
In this contribution, we discuss three recent developments in atomistic biological charge transfer theory. First, in the context of Marcus' classical theory of charge transfer, key quantities of the theory such as driving forces and reorganization enthalpies are now accessible by thermodynamic integration schemes within standard molecular dynamics simulations at high accuracy. Second, direct simulations of charge transfer enable the computation of fast charge transfer reaction rates without having to resort to Marcus' theory. Finally, exploring the electronic structure beyond that of hitherto presumed centers of localization helps to identify new stepping stones of charge transfer reactions. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Thorsten Koslowski
- Institut für Physikalische Chemie, Universität Freiburg, Freiburg im Breisgau, Germany.
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41
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Krapf S, Weber S, Koslowski T. The road not taken: a theoretical view of an unexpected cryptochrome charge transfer path. Phys Chem Chem Phys 2012; 14:11518-24. [DOI: 10.1039/c2cp40793k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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