1
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Cellini A, Shankar MK, Nimmrich A, Hunt LA, Monrroy L, Mutisya J, Furrer A, Beale EV, Carrillo M, Malla TN, Maj P, Vrhovac L, Dworkowski F, Cirelli C, Johnson PJM, Ozerov D, Stojković EA, Hammarström L, Bacellar C, Standfuss J, Maj M, Schmidt M, Weinert T, Ihalainen JA, Wahlgren WY, Westenhoff S. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Nat Chem 2024; 16:624-632. [PMID: 38225270 PMCID: PMC10997514 DOI: 10.1038/s41557-023-01413-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024]
Abstract
Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Leigh Anna Hunt
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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2
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Melčák M, Šebesta F, Heyda J, Gray HB, Záliš S, Vlček A. Tryptophan to Tryptophan Hole Hopping in an Azurin Construct. J Phys Chem B 2024; 128:96-108. [PMID: 38145895 PMCID: PMC10788906 DOI: 10.1021/acs.jpcb.3c06568] [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] [Received: 10/02/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
Electron transfer (ET) between neutral and cationic tryptophan residues in the azurin construct [ReI(H126)(CO)3(dmp)](W124)(W122)CuI (dmp = 4,7-Me2-1,10-phenanthroline) was investigated by Born-Oppenheimer quantum-mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) simulations. We focused on W124•+ ← W122 ET, which is the middle step of the photochemical hole-hopping process *ReII(CO)3(dmp•-) ← W124 ← W122 ← CuI, where sequential hopping amounts to nearly 10,000-fold acceleration over single-step tunneling (ACS Cent. Sci. 2019, 5, 192-200). In accordance with experiments, UKS-DFT QM/MM/MD simulations identified forward and reverse steps of W124•+ ↔ W122 ET equilibrium, as well as back ET ReI(CO)3(dmp•-) → W124•+ that restores *ReII(CO)3(dmp•-). Strong electronic coupling between the two indoles (≥40 meV in the crossing region) makes the productive W124•+ ← W122 ET adiabatic. Energies of the two redox states are driven to degeneracy by fluctuations of the electrostatic potential at the two indoles, mainly caused by water solvation, with contributions from the protein dynamics in the W122 vicinity. ET probability depends on the orientation of Re(CO)3(dmp) relative to W124 and its rotation diminishes the hopping yield. Comparison with hole hopping in natural systems reveals structural and dynamics factors that are important for designing efficient hole-hopping processes.
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Affiliation(s)
- Martin Melčák
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Filip Šebesta
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, CZ-121 16 Prague, Czech Republic
| | - Jan Heyda
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Harry B. Gray
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Stanislav Záliš
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Antonín Vlček
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Department
of Chemistry, Queen Mary University of London, London E1 4NS, U.K.
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3
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Sarimov RM, Serov DA, Gudkov SV. Hypomagnetic Conditions and Their Biological Action (Review). BIOLOGY 2023; 12:1513. [PMID: 38132339 PMCID: PMC10740674 DOI: 10.3390/biology12121513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic field interaction with living systems. The applied significance is improving the training of astronauts for long-term space expeditions. This review describes the effects of HMC on animals and plants, manifested at the cellular and organismal levels. General information is given about the probable mechanisms of HMC and geomagnetic field action on living systems. The main experimental approaches are described. We attempted to systematize quantitative data from various studies and identify general dependencies of the magnetobiology effects' value on HMC characteristics (induction, exposure duration) and the biological parameter under study. The most pronounced effects were found at the cellular level compared to the organismal level. Gene expression and protein activity appeared to be the most sensitive to HMC among the molecular cellular processes. The nervous system was found to be the most sensitive in the case of the organism level. The review may be of interest to biologists, physicians, physicists, and specialists in interdisciplinary fields.
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Affiliation(s)
| | | | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilove St. 38, 119991 Moscow, Russia; (R.M.S.); (D.A.S.)
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4
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Skinner KC, Kammeraad JA, Wymore T, Narayan ARH, Zimmerman PM. Simulating Electron Transfer Reactions in Solution: Radical-Polar Crossover. J Phys Chem B 2023; 127:10097-10107. [PMID: 37976536 PMCID: PMC11135460 DOI: 10.1021/acs.jpcb.3c06120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Single-electron transfer (SET) promotes a wide variety of interesting chemical transformations, but modeling of SET requires a careful treatment of electronic and solvent effects to give meaningful insight. Therefore, a combined constrained density functional theory and molecular mechanics (CDFT/MM) tool is introduced specifically for SET-initiated reactions. Mechanisms for two radical-polar crossover reactions involving the organic electron donors tetrakis(dimethylamino)ethylene (TDAE) and tetrathiafulvalene (TTF) were studied with the new tool. An unexpected tertiary radical intermediate within the TDAE system was identified, relationships between kinetics and substitution in the TTF system were explained, and the impact of the solvent environments on the TDAE and TTF reactions were examined. The results highlight the need for including solvent dynamics when quantifying SET kinetics and thermodynamics, as a free energy difference of >20 kcal/mol was observed. Overall, the new method informs mechanistic analysis of SET-initiated reactions and therefore is envisioned to be useful for studying reactions in the condensed phase.
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Affiliation(s)
- Kevin C Skinner
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Josh A Kammeraad
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Troy Wymore
- Laufer Center, Stony Brook University, Stony Brook, New York 11794, United States
| | - Alison R H Narayan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Krishnan S, Aksimentiev A, Lindsay S, Matyushov D. Long-Range Conductivity in Proteins Mediated by Aromatic Residues. ACS PHYSICAL CHEMISTRY AU 2023; 3:444-455. [PMID: 37780537 PMCID: PMC10540285 DOI: 10.1021/acsphyschemau.3c00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 09/30/2023]
Abstract
Single-molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen over 10 nm distances, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1 V. This is puzzling because, for fast transport (i.e., a free energy barrier of zero), the hopping rate is determined by the reorganization energy of approximately 0.8 eV, and this sets the time scale of a single hop to at least 1 μs. Furthermore, the Fermi energies of typical metal electrodes are far removed from the energies required for sequential oxidation and reduction of the aromatic residues of the protein, which should further reduce the hopping current. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox-active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transport. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the non-ergodic sampling of molecular configurations by the protein results in reaction-reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ∼0.2 eV, which is small enough to enable long-range conductivity, without invoking quantum coherent transport. Using the MD values of the reorganization energies, we calculate a current decay with distance that is in agreement with experiment.
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Affiliation(s)
- Siddharth Krishnan
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stuart Lindsay
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Dmitry Matyushov
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
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6
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Mostajabi Sarhangi S, Matyushov DV. Electron Tunneling in Biology: When Does it Matter? ACS OMEGA 2023; 8:27355-27365. [PMID: 37546584 PMCID: PMC10399179 DOI: 10.1021/acsomega.3c02719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport. In addition, universal charge-transport properties are assigned to all proteins, making protein identity, flexibility, and dynamics insignificant. This paradigm is challenged by dynamical models of electron transfer, showing that the electron hopping rate is constant within the crossover distance R* ≃ 12 Å, followed with an exponential falloff at longer distances. If this hypothesis is fully confirmed, natural and man-made energy chains for electron transport should be best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover distance. Changes in protein flexibility between forward and backward transitions contribute to vectorial charge transport. For biological energy chains, charge transport through proteins is not defined by universal parameters, and protein identity matters.
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7
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Mostajabi Sarhangi S, Matyushov DV. Effect of Water Deuteration on Protein Electron Transfer. J Phys Chem Lett 2023; 14:723-729. [PMID: 36648391 DOI: 10.1021/acs.jpclett.2c03690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration. H/D substitution changes the rate constant pre-exponential factor in the regime of electron transfer controlled by medium dynamics. Switching from light to heavy water increases the effective medium relaxation time. The effect is caused by both a global change in the flexibility of the protein backbone and locally stronger hydrogen bonds to charged residues.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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8
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Zadeh-Haghighi H, Simon C. Magnetic field effects in biology from the perspective of the radical pair mechanism. J R Soc Interface 2022; 19:20220325. [PMID: 35919980 PMCID: PMC9346374 DOI: 10.1098/rsif.2022.0325] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/14/2022] [Indexed: 04/07/2023] Open
Abstract
Hundreds of studies have found that weak magnetic fields can significantly influence various biological systems. However, the underlying mechanisms behind these phenomena remain elusive. Remarkably, the magnetic energies implicated in these effects are much smaller than thermal energies. Here, we review these observations, and we suggest an explanation based on the radical pair mechanism, which involves the quantum dynamics of the electron and nuclear spins of transient radical molecules. While the radical pair mechanism has been studied in detail in the context of avian magnetoreception, the studies reviewed here show that magnetosensitivity is widespread throughout biology. We review magnetic field effects on various physiological functions, discussing static, hypomagnetic and oscillating magnetic fields, as well as isotope effects. We then review the radical pair mechanism as a potential unifying model for the described magnetic field effects, and we discuss plausible candidate molecules for the radical pairs. We review recent studies proposing that the radical pair mechanism provides explanations for isotope effects in xenon anaesthesia and lithium treatment of hyperactivity, magnetic field effects on the circadian clock, and hypomagnetic field effects on neurogenesis and microtubule assembly. We conclude by discussing future lines of investigation in this exciting new area of quantum biology.
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Affiliation(s)
- Hadi Zadeh-Haghighi
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Institute for Quantum Science and Technology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Christoph Simon
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Institute for Quantum Science and Technology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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9
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López-Ortiz M, Zamora RA, Giannotti MI, Hu C, Croce R, Gorostiza P. Distance and Potential Dependence of Charge Transport Through the Reaction Center of Individual Photosynthetic Complexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104366. [PMID: 34874621 DOI: 10.1002/smll.202104366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Charge separation and transport through the reaction center of photosystem I (PSI) is an essential part of the photosynthetic electron transport chain. A strategy is developed to immobilize and orient PSI complexes on gold electrodes allowing to probe the complex's electron acceptor side, the chlorophyll special pair P700. Electrochemical scanning tunneling microscopy (ECSTM) imaging and current-distance spectroscopy of single protein complex shows lateral size in agreement with its known dimensions, and a PSI apparent height that depends on the probe potential revealing a gating effect in protein conductance. In current-distance spectroscopy, it is observed that the distance-decay constant of the current between PSI and the ECSTM probe depends on the sample and probe electrode potentials. The longest charge exchange distance (lowest distance-decay constant β) is observed at sample potential 0 mV/SSC (SSC: reference electrode silver/silver chloride) and probe potential 400 mV/SSC. These potentials correspond to hole injection into an electronic state that is available in the absence of illumination. It is proposed that a pair of tryptophan residues located at the interface between P700 and the solution and known to support the hydrophobic recognition of the PSI redox partner plastocyanin, may have an additional role as hole exchange mediator in charge transport through PSI.
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Affiliation(s)
- Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Marina Inés Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- Department of Materials Science and Physical Chemistry, University of Barcelona, Martí i Franquès 1-11, Barcelona, 08028, Spain
| | - Chen Hu
- Biophysics of PhotosynthesisDepartment of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Roberta Croce
- Biophysics of PhotosynthesisDepartment of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
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10
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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Anisotropic magnetic field effects in the re-oxidation of cryptochrome in the presence of scavenger radicals. J Chem Phys 2022; 156:025101. [PMID: 35032990 DOI: 10.1063/5.0078115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The avian compass and many other of nature's magnetoreceptive traits are widely ascribed to the protein cryptochrome. There, magnetosensitivity is thought to emerge as the spin dynamics of radicals in the applied magnetic field enters in competition with their recombination. The first and dominant model makes use of a radical pair. However, recent studies have suggested that magnetosensitivity could be markedly enhanced for a radical triad, the primary radical pair of which undergoes a spin-selective recombination reaction with a third radical. Here, we test the practicality of this supposition for the reoxidation reaction of the reduced FAD cofactor in cryptochrome, which has been implicated with light-independent magnetoreception but appears irreconcilable with the classical radical pair mechanism (RPM). Based on the available realistic cryptochrome structures, we predict the magnetosensitivity of radical triad systems comprising the flavin semiquinone, the superoxide, and a tyrosine or ascorbyl scavenger radical. We consider many hyperfine-coupled nuclear spins, the relative orientation and placement of the radicals, their coupling by the electron-electron dipolar interaction, and spin relaxation in the superoxide radical in the limit of instantaneous decoherence, which have not been comprehensively considered before. We demonstrate that these systems can provide superior magnetosensitivity under realistic conditions, with implications for dark-state cryptochrome magnetoreception and other biological magneto- and isotope-sensitive radical recombination reactions.
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Affiliation(s)
- Jean Deviers
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Fabien Cailliez
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Daniel R Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
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11
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Abstract
Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)3(dmp)+, and one or two tryptophans (W1, W2). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from CuI to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of ReI(His)(CO)3(dmp)+-W1(-W2) exhibited crossings between sensitizer-localized (*Re) and charge-separated [ReI(His)(CO)3(dmp•-)/(W1 •+ or W2 •+)] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)3(dmp)+←W1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)3(dmp)+(W1); and CS1 is stabilized by Re(dmp•-)/W1 •+ electron/hole interaction and enhanced W1 •+ solvation. The second hop, W1 •+←W2, is facilitated by water fluctuations near the W1/W2 unit, taking place when the electrostatic potential at W2 drops well below that at W1 •+ Insufficient solvation and reorganization around W2 make W1 •+←W2 ET endergonic, shifting the equilibrium toward W1 •+ and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds.
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12
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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] [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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13
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Duan HD, Khan SA, Miller AF. Photogeneration and reactivity of flavin anionic semiquinone in a bifurcating electron transfer flavoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148415. [PMID: 33727071 DOI: 10.1016/j.bbabio.2021.148415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 02/04/2023]
Abstract
Electron transfer bifurcation allows production of a strongly reducing carrier at the expense of a weaker one, by redistributing energy among a pair of electrons. Thus, two weakly-reducing electrons from NADH are consumed to produce a strongly reducing ferredoxin or flavodoxin, paid for by reduction of an oxidizing acceptor. The prevailing mechanism calls for participation of a strongly reducing flavin semiquinone which has been difficult to observe with site-certainly in multi-flavin systems. Using blue light (450 nm) to photoexcite the flavins of bifurcating electron transfer flavoprotein (ETF), we demonstrate accumulation of anionic flavin semiquinone in excess of what is observed in equilibrium titrations, and establish its ability to reduce the low-potential electron acceptor benzyl viologen. This must occur at the bifurcating flavin because the midpoint potentials of the electron transfer (ET) flavin are not sufficiently negative. We show that bis-tris propane buffer is an effective electron donor to the flavin photoreduction, but that if the system is prepared with the ET flavin chemically reduced, so that only the bifurcating flavin is oxidized and photochemically active, flavin anionic semiquinone is formed more rapidly. Thus, excited bifurcating flavin is able to draw on an electron stored at the ET flavin. Flavin semiquinone photogenerated at the bifurcation site must therefore be accompanied by additional semiquinone formation by oxidation of the ET flavin. Consistent with the expected instability of bifurcating flavin semiquinone, it subsides immediately upon cessation of illumination. However comparison with yields of semiquinone in equilibrium titrations suggest that during continuous illumination at pH 9 a steady state population of 0.3 equivalents of bifurcating flavin semiquinone accumulates, and then undergoes further photoreduction to the hydroquinone. Although transient, the population of bifurcating flavin semiquinone explains the system's ability to conduct light-driven electron transfer from bis-tris propane to benzyl viologen, in effect trapping energy from light.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Sharique A Khan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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14
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Zhuang B, Seo D, Aleksandrov A, Vos MH. Characterization of Light-Induced, Short-Lived Interacting Radicals in the Active Site of Flavoprotein Ferredoxin-NADP + Oxidoreductase. J Am Chem Soc 2021; 143:2757-2768. [PMID: 33591179 DOI: 10.1021/jacs.0c09627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radicals of flavin adenine dinucleotide (FAD), as well as tyrosine and tryptophan, are widely involved as key reactive intermediates during electron-transfer (ET) reactions in flavoproteins. Due to the high reactivity of these species and their corresponding short lifetime, characterization of these intermediates in functional processes of flavoproteins is usually challenging but can be achieved by ultrafast spectroscopic studies of light-activatable flavoproteins. In ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (BsFNR), fluorescence of the FAD cofactor that very closely interacts with a neighboring tyrosine residue (Tyr50) is strongly quenched. Here we study short-lived photoproducts of this enzyme and its variants, with Tyr50 replaced by tryptophan or glycine. Using time-resolved fluorescence and absorption spectroscopies, we show that, upon the excitation of WT BsFNR, ultrafast ET from Tyr50 to the excited FAD cofactor occurs in ∼260 fs, an order of magnitude faster than the decay by charge recombination, facilitating the characterization of the reaction intermediates in the charge-separated state with respect to other recently studied systems. These studies are corroborated by experiments on the Y50W mutant protein, which yield photoproducts qualitatively similar to those observed in other tryptophan-bearing flavoproteins. By combining the experimental results with molecular dynamics simulations and quantum mechanics calculations, we investigate in detail the effects of protein environment and relaxations on the spectral properties of those radical intermediates and demonstrate that the spectral features of radical anionic FAD are highly sensitive to its environment, and in particular to the dynamics and nature of the counterions formed in the photoproducts. Altogether, comprehensive characterizations are provided for important radical intermediates that are generally involved in functional processes of flavoproteins.
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Affiliation(s)
- Bo Zhuang
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, 920-1192 Kanazawa, Ishikawa, Japan
| | - Alexey Aleksandrov
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Marten H Vos
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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15
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Wong SY, Solov'yov IA, Hore PJ, Kattnig DR. Nuclear polarization effects in cryptochrome-based magnetoreception. J Chem Phys 2021; 154:035102. [PMID: 33499614 DOI: 10.1063/5.0038947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mechanism of the magnetic compass sense of migratory songbirds is thought to involve magnetically sensitive chemical reactions of light-induced radical pairs in cryptochrome proteins located in the birds' eyes. However, it is not yet clear whether this mechanism would be sensitive enough to form the basis of a viable compass. In the present work, we report spin dynamics simulations of models of cryptochrome-based radical pairs to assess whether accumulation of nuclear spin polarization in multiple photocycles could lead to significant enhancements in the sensitivity with which the proteins respond to the direction of the geomagnetic field. Although buildup of nuclear polarization appears to offer sensitivity advantages in the more idealized model systems studied, we find that these enhancements do not carry over to conditions that more closely resemble the situation thought to exist in vivo. On the basis of these simulations, we conclude that buildup of nuclear polarization seems unlikely to be a source of significant improvements in the performance of cryptochrome-based radical pair magnetoreceptors.
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Affiliation(s)
- Siu Ying Wong
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A Solov'yov
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany
| | - P J Hore
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Exeter EX4 4QD, United Kingdom
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16
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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] [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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17
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Atkins C, Bajpai K, Rumball J, Kattnig DR. On the optimal relative orientation of radicals in the cryptochrome magnetic compass. J Chem Phys 2019. [DOI: 10.1063/1.5115445] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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18
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Holub D, Lamparter T, Elstner M, Gillet N. Biological relevance of charge transfer branching pathways in photolyases. Phys Chem Chem Phys 2019; 21:17072-17081. [PMID: 31313765 DOI: 10.1039/c9cp01609k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The repair of sun-induced DNA lesions by photolyases is driven by a photoinduced electron transfer from a fully reduced FAD to the damaged DNA. A chain of several aromatic residues connecting FAD to solvent ensures the prior photoreduction of the FAD cofactor. In PhrA, a class III CPD photolyase, two branching tryptophan charge transfer pathways have been characterized. According to previous experiments, both pathways play a role in the FAD photoreduction. To provide a molecular insight to the charge transfer abilities of both pathways, we perform multiscales simulations where the protein motion and the positive charge are simultaneously propagated. Our computational approach reveals that one pathway drives a very fast charge transfer whereas the other pathway provides a very good thermodynamic stabilization of the positive charge. During the simulations, the positive charge firstly moves on the fast triad, while a reorganization of the close FAD˙- environment occurs. Then, backward transfers can lead to the propagation of the positive charge on the second pathway. After one nanosecond, we observe a nearly equal probability to find the charge at ending tryptophan of either pathway; eventually the charge distribution will likely evolve towards a charge stabilization on the last tryptophan of the slowest pathway. Our results highlight the role the protein environment, which manages the association of a kinetic and a thermodynamic pathways to trigger a fast and efficient FAD photoreduction.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Fritz Haber Weg 4, 76131, Karlsruhe, Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany. and Institute of Biological Interfaces (IBG2), Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
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19
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Hosokawa Y, Sato R, Iwai S, Yamamoto J. Implications of a Water Molecule for Photoactivation of Plant (6-4) Photolyase. J Phys Chem B 2019; 123:5059-5068. [PMID: 31117614 DOI: 10.1021/acs.jpcb.9b03030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photolyases (PLs) are flavoproteins able to repair cross-links formed between adjacent pyrimidine bases in DNA in a light-dependent manner via an electron transfer. The catalytically active redox state of the flavin chromophore for the DNA repair is a fully reduced form of flavin adenine dinucleotide (FADH-). PLs and their relative, cryptochromes (CRYs), share a physicochemical process attributable to the light-dependent reduction of the chromophore via an ultrafast successive electron transfer through exclusively conserved three tryptophan side chains. In some (6-4) PLs and animal CRYs, an additional tryptophan participates in this photoactivation process. In a search for the intrinsic difference between the Trp triad and tetrad, a water molecule proximal to the second and third Trp was found in the reported crystal structure of Arabidopsis thaliana (6-4) PL. Here, we investigated the involvement of the water molecule in photoactivation. Molecular dynamics simulations indicated that the water molecule is stably captured in the binding site, while mutation of S412 increased water displacement from the binding site. Photochemical analysis of recombinant proteins revealed that the S412A mutation significantly decelerated the FAD photoreduction as compared to the wild type. The hydrogen-bonding network including the water molecule would play a key role in the stabilization of the FAD-Trp radical pair.
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Affiliation(s)
- Yuhei Hosokawa
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Ryuma Sato
- Center for Biosystems Dynamics Research , RIKEN , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science , Osaka University , 1-3 Machikaneyama , Toyonaka , Osaka 560-8531 , Japan
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20
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de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia Iriepa C, Salahub DR, Köster AM. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules 2019; 24:molecules24091653. [PMID: 31035516 PMCID: PMC6539060 DOI: 10.3390/molecules24091653] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Karim Hasnaoui
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Fabien Cailliez
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, 75005 Paris, France.
| | - Tzonka Mineva
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, France.
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Luis López-Sosa
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Gerald Geudtner
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Cristina Garcia Iriepa
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Dennis R Salahub
- Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, Canada.
- College of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, China.
| | - Andreas M Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
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21
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Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. J Phys Chem Lett 2019; 10:1450-1456. [PMID: 30855973 DOI: 10.1021/acs.jpclett.9b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Redox proteins and enzymes are at risk of irreversible oxidative damage from highly oxidizing intermediates generated in the active site in the case of unsuccessful functional reaction. Chains of tyrosine and/or tryptophan residues have been recently proposed to provide protection to the active site and the whole protein by delivering oxidizing equivalents (holes) out of the protein via a multistep hopping mechanism. In the present work we use a hybrid quantum/classical theoretical-computational methodology based on the perturbed matrix method and on molecular dynamics simulations to calculate the oxidation potential difference along a chain of tyrosine and tryptophan residues in a human redox enzyme of major importance, a superoxide dismutase, which acts as antioxidant defense. We show that the hole hopping is thermodynamically favored along such a chain and that the hopping propensity is strongly affected by the protein environment and in particular by the active site and its second coordination sphere.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Stefano Corni
- Department of Chemical Sciences , University of Padova , I-35131 Padova , Italy
- Center S3 , CNR-Institute of Nanoscience , Via Campi 213/A , 41125 Modena , Italy
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22
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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23
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Zeng Z, Wei J, Liu Y, Zhang W, Mabe T. Magnetoreception of Photoactivated Cryptochrome 1 in Electrochemistry and Electron Transfer. ACS OMEGA 2018; 3:4752-4759. [PMID: 31458694 PMCID: PMC6641772 DOI: 10.1021/acsomega.8b00645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 04/23/2018] [Indexed: 06/10/2023]
Abstract
Cryptochromes are flavoproteins whose photochemistry is important for crucial functions associated with phototropism and circadian clocks. In this report, we, for the first time, observed a magnetic response of the cryptochrome 1 (CRY1) immobilized at a gold electrode with illumination of blue light. These results present the magnetic field-enhanced photoinduced electron transfer of CRY1 to the electrode by voltammetry, exhibiting magnetic responsive rate constant and electrical current changes. A mechanism of the electron transfer, which involves photoinduced radicals in the CRY, is sensitive to the weak magnetic field; and the long-lived free radical FAD•- is responsible for the detected electrochemical Faradaic current. As a photoreceptor, the finding of a 5.7% rate constant change in electron transfer corresponding to a 50 μT magnetic field may be meaningful in regulation of magnetic field signaling and circadian clock function under an electromagnetic field.
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24
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Piechota EJ, Troian-Gautier L, Sampaio RN, Brennaman MK, Hu K, Berlinguette CP, Meyer GJ. Optical Intramolecular Electron Transfer in Opposite Directions through the Same Bridge That Follows Different Pathways. J Am Chem Soc 2018; 140:7176-7186. [DOI: 10.1021/jacs.8b02715] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Eric J. Piechota
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
| | - Ludovic Troian-Gautier
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
| | - Renato N. Sampaio
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
| | - M. Kyle Brennaman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
| | - Ke Hu
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
| | - Curtis P. Berlinguette
- Departments of Chemistry and Chemical & Biological Engineering, and the Stewart Blusson Quantum Matter Institute, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Gerald J. Meyer
- Department of Chemistry, The University of North Carolina at Chapel Hill, Murray Hall 2202B, Chapel Hill, North Carolina 27599, United States
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25
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Gupta S, Kumar A, Joshi KB. Study of electron transfer process in aqueous methanol system by using tryptophan based short peptide – Amino acid pairs. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.01.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Mendive-Tapia D, Mangaud E, Firmino T, de la Lande A, Desouter-Lecomte M, Meyer HD, Gatti F. Multidimensional Quantum Mechanical Modeling of Electron Transfer and Electronic Coherence in Plant Cryptochromes: The Role of Initial Bath Conditions. J Phys Chem B 2017; 122:126-136. [DOI: 10.1021/acs.jpcb.7b10412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Mendive-Tapia
- Institut
Charles Gerhardt Montpellier, UMR 5253, CNRS-UM-ENSCM, CTMM, Université Montpellier, CC 15001, Place Eugène Bataillon, 34095 Montpellier, France
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Etienne Mangaud
- Laboratoire
Collisions Agrégats Réactivité, UMR 5589, IRSAMC, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Michèle Desouter-Lecomte
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Hans-Dieter Meyer
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Fabien Gatti
- Institut
des Sciences Moléculaires d’Orsay, UMR-CNRS 8214, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
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27
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Holub D, Ma H, Krauß N, Lamparter T, Elstner M, Gillet N. Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase. Chem Sci 2017; 9:1259-1272. [PMID: 29675172 PMCID: PMC5887102 DOI: 10.1039/c7sc03386a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/09/2017] [Indexed: 11/21/2022] Open
Abstract
Cryptochromes and photolyases form a flavoprotein family in which the FAD chromophore undergoes light induced changes of its redox state. During this process, termed photoreduction, electrons flow from the surface via conserved amino acid residues to FAD. The bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Mutagenesis studies have identified Trp342 and Trp390 as essential for charge transfer. Trp342 is located at the periphery of PhrB while Trp390 connects Trp342 and Tyr391. The role of Tyr391, which lies between Trp390 and FAD, is however unclear as its replacement by phenylalanine did not block photoreduction. Experiments reported here, which replace Tyr391 by Ala, show that photoreduction is blocked, underlining the relevance of Tyr/Phe at position 391 and indicating that charge transfer occurs via the triad 391-390-342. This raises the question, why PhrB positions a tyrosine at this location, having a less favourable ionisation potential than tryptophan, which occurs at this position in many proteins of the photolyase/cryptochrome family. Tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings. Since replacement of Tyr391 by Trp resulted in loss of FAD and DMRL chromophores, electron transfer cannot be studied experimentally in this mutant, but calculations on a mutant model suggest that Trp might participate in the electron transfer cascade. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad. Our results suggest that evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
| | - Hongju Ma
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Norbert Krauß
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Tilman Lamparter
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany . .,Institute of Biological Interfaces (IGB2) , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
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28
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Kattnig DR. Radical-Pair-Based Magnetoreception Amplified by Radical Scavenging: Resilience to Spin Relaxation. J Phys Chem B 2017; 121:10215-10227. [DOI: 10.1021/acs.jpcb.7b07672] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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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29
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Essen LO, Franz S, Banerjee A. Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:27-37. [PMID: 28756992 DOI: 10.1016/j.jplph.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Blue-light reception plays a pivotal role for algae to adapt to changing environmental conditions. In this review we summarize the current structural and mechanistic knowledge about flavin-dependent algal photoreceptors. We especially focus on the cryptochrome and aureochrome type photoreceptors in the context of their evolutionary divergence. Despite similar photochemical characteristics to orthologous photoreceptors from higher plants and animals the algal blue-light photoreceptors have developed a set of unique structural and mechanistic features that are summarized below.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology, Philipps-University, 35043 Marburg, Germany.
| | - Sophie Franz
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| | - Ankan Banerjee
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
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30
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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] [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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31
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The sensitivity of a radical pair compass magnetoreceptor can be significantly amplified by radical scavengers. Sci Rep 2017; 7:11640. [PMID: 28912470 PMCID: PMC5599710 DOI: 10.1038/s41598-017-09914-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/31/2017] [Indexed: 11/08/2022] Open
Abstract
Birds have a remarkable ability to obtain navigational information from the Earth's magnetic field. The primary detection mechanism of this compass sense is uncertain but appears to involve the quantum spin dynamics of radical pairs formed transiently in cryptochrome proteins. We propose here a new version of the current model in which spin-selective recombination of the radical pair is not essential. One of the two radicals is imagined to react with a paramagnetic scavenger via spin-selective electron transfer. By means of simulations of the spin dynamics of cryptochrome-inspired radical pairs, we show that the new scheme offers two clear and important benefits. The sensitivity to a 50 μT magnetic field is greatly enhanced and, unlike the current model, the radicals can be more than 2 nm apart in the magnetoreceptor protein. The latter means that animal cryptochromes that have a tetrad (rather than a triad) of tryptophan electron donors can still be expected to be viable as magnetic compass sensors. Lifting the restriction on the rate of the spin-selective recombination reaction also means that the detrimental effects of inter-radical exchange and dipolar interactions can be minimised by placing the radicals much further apart than in the current model.
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32
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Sheppard DMW, Li J, Henbest KB, Neil SRT, Maeda K, Storey J, Schleicher E, Biskup T, Rodriguez R, Weber S, Hore PJ, Timmel CR, Mackenzie SR. Millitesla magnetic field effects on the photocycle of an animal cryptochrome. Sci Rep 2017; 7:42228. [PMID: 28176875 PMCID: PMC5296725 DOI: 10.1038/srep42228] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/06/2017] [Indexed: 11/09/2022] Open
Abstract
Drosophila have been used as model organisms to explore both the biophysical mechanisms of animal magnetoreception and the possibility that weak, low-frequency anthropogenic electromagnetic fields may have biological consequences. In both cases, the presumed receptor is cryptochrome, a protein thought to be responsible for magnetic compass sensing in migratory birds and a variety of magnetic behavioural responses in insects. Here, we demonstrate that photo-induced electron transfer reactions in Drosophila melanogaster cryptochrome are indeed influenced by magnetic fields of a few millitesla. The form of the protein containing flavin and tryptophan radicals shows kinetics that differ markedly from those of closely related members of the cryptochrome-photolyase family. These differences and the magnetic sensitivity of Drosophila cryptochrome are interpreted in terms of the radical pair mechanism and a photocycle involving the recently discovered fourth tryptophan electron donor.
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Affiliation(s)
- Dean M. W. Sheppard
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Jing Li
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kevin B. Henbest
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Simon R. T. Neil
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kiminori Maeda
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Jonathan Storey
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Erik Schleicher
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Till Biskup
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Ryan Rodriguez
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - P. J. Hore
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Christiane R. Timmel
- Department of Chemistry, University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Stuart R. Mackenzie
- Department of Chemistry, University of Oxford, Physical & Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
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33
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Martin R, Lacombat F, Espagne A, Dozova N, Plaza P, Yamamoto J, Müller P, Brettel K, de la Lande A. Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad. Phys Chem Chem Phys 2017; 19:24493-24504. [DOI: 10.1039/c7cp04555g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast photoreduction of animal (6-4) photolyase: delocalized oxidation hole reaches fourth tryptophan in less than 40 ps.
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Affiliation(s)
- Ryan Martin
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Fabien Lacombat
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Agathe Espagne
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Nadia Dozova
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Pascal Plaza
- PASTEUR
- Département de chimie
- École normale supérieure
- UPMC Univ. Paris 06
- CNRS
| | - Junpei Yamamoto
- Division of Chemistry
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC)
- Joliot
- CEA
- CNRS
- Univ. Paris-Sud
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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34
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Gillet N, Berstis L, Wu X, Gajdos F, Heck A, de la Lande A, Blumberger J, Elstner M. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level. J Chem Theory Comput 2016; 12:4793-4805. [DOI: 10.1021/acs.jctc.6b00564] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natacha Gillet
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Laura Berstis
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Xiaojing Wu
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Alexander Heck
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
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35
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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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36
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Dinpajooh M, Martin DR, Matyushov DV. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer. Sci Rep 2016; 6:28152. [PMID: 27306204 PMCID: PMC4910110 DOI: 10.1038/srep28152] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/27/2016] [Indexed: 11/12/2022] Open
Abstract
Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.
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Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - Daniel R Martin
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
| | - 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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37
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Firmino T, Mangaud E, Cailliez F, Devolder A, Mendive-Tapia D, Gatti F, Meier C, Desouter-Lecomte M, de la Lande A. Quantum effects in ultrafast electron transfers within cryptochromes. Phys Chem Chem Phys 2016; 18:21442-57. [DOI: 10.1039/c6cp02809h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors.
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Affiliation(s)
- Thiago Firmino
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Etienne Mangaud
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Fabien Cailliez
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Adrien Devolder
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | | | - Fabien Gatti
- CTMM
- Institut Charles Gerhardt UMR 5253
- CNRS/Université de Montpellier
- France
| | - Christoph Meier
- Laboratoire Collisions Agrégats Réactivité
- UMR 5589
- IRSAMC
- Université Toulouse III Paul Sabatier
- Toulouse
| | | | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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