1
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Sokolov M, Hoffmann DS, Dohmen PM, Krämer M, Höfener S, Kleinekathöfer U, Elstner M. Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex. Phys Chem Chem Phys 2024; 26:19469-19496. [PMID: 38979564 DOI: 10.1039/d4cp02116a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments. Direct simulation of exciton dynamics through light-harvesting complexes on significant time scales is usually challenging due to the coupled motion of nuclear and electronic degrees of freedom in these rather large systems containing several relatively large pigments. In the present approach, however, we are able to evaluate a statistically significant number of non-adiabatic molecular dynamics trajectories with respect to exciton delocalization and exciton paths. The formalism is applied to the Fenna-Matthews-Olson complex of green sulfur bacteria, which transfers energy from the light-harvesting chlorosome to the reaction center with astonishing efficiency. The system has been studied experimentally and theoretically for decades. In total, we were able to simulate non-adiabatically more than 30 ns, sampling also the relevant space of parameters within their uncertainty. Our simulations show that the driving force supplied by the energy landscape resulting from electrostatic tuning is sufficient to funnel the energy towards site 3, from where it can be transferred to the reaction center. However, the high efficiency of transfer within a picosecond timescale can be attributed to the rather unusual properties of the BChl a molecules, resulting in very low inner and outer-sphere reorganization energies, not matched by any other organic molecule, e.g., used in organic electronics. A comparison with electron and exciton transfer in organic materials is particularly illuminating, suggesting a mechanism to explain the comparably high transfer efficiency.
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Affiliation(s)
- Monja Sokolov
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - David S Hoffmann
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Philipp M Dohmen
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Mila Krämer
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Sebastian Höfener
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | | | - Marcus Elstner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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2
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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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3
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Frederiksen A, Gerhards L, Reinholdt P, Kongsted J, Solov’yov IA. Importance of Polarizable Embedding for Absorption Spectrum Calculations of Arabidopsis thaliana Cryptochrome 1. J Phys Chem B 2024; 128:6283-6290. [PMID: 38913544 PMCID: PMC11228989 DOI: 10.1021/acs.jpcb.4c02168] [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: 04/02/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/26/2024]
Abstract
Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH•), characterized through a specific red-light absorption. The absorption spectra of FADH• in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH• absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum, crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process, advancing our understanding of cryptochrome functioning.
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Affiliation(s)
- Anders Frederiksen
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Peter Reinholdt
- Department
of Physics, Chemistry, and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry, and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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4
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Frederiksen A, Aldag M, Solov’yov IA, Gerhards L. Activation of Cryptochrome 4 from Atlantic Herring. BIOLOGY 2024; 13:262. [PMID: 38666874 PMCID: PMC11048568 DOI: 10.3390/biology13040262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.
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Affiliation(s)
- Anders Frederiksen
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Mandus Aldag
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Ilia A. Solov’yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
- Research Centre for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
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5
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Salerno KM, Domenico J, Le NQ, Balakrishnan K, McQuillen RJ, Stiles CD, Solov'yov IA, Martino CF. Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome. J Chem Inf Model 2023; 63:6756-6767. [PMID: 37874902 DOI: 10.1021/acs.jcim.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•- is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide-FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thaliana cryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2-FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.
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Affiliation(s)
- K Michael Salerno
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q Le
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Krithika Balakrishnan
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ryan J McQuillen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D Stiles
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F Martino
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
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6
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Frederiksen A, Langebrake C, Hanić M, Manthey G, Mouritsen H, Liedvogel M, Solov’yov IA. Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a. ACS OMEGA 2023; 8:26425-26436. [PMID: 37521624 PMCID: PMC10373462 DOI: 10.1021/acsomega.3c02963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
The ability of migratory birds to sense magnetic fields has been known for decades, although the understanding of the underlying mechanism is still elusive. Currently, the strongest magnetoreceptor candidate in birds is a protein called cryptochrome 4a. The cryptochrome 4a protein has changed through evolution, apparently endowing some birds with a more pronounced magnetic sensitivity than others. Using phylogenetic tools, we show that a specific tryptophan tetrad and a tyrosine residue predicted to be essential for cryptochrome activation are highly conserved in the avian clade. Through state-of-the-art molecular dynamics simulations and associated analyses, we also studied the role of these specific residues and the associated mutants on the overall dynamics of the protein. The analyses of the single residue mutations were used to judge how far a local change in the protein structure can impact specific dynamics of European robin cryptochrome 4a. We conclude that the replacements of each of the tryptophans one by one with a phenylalanine do not compromise the overall stability of the protein.
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Affiliation(s)
- Anders Frederiksen
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Corinna Langebrake
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Maja Hanić
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Georg Manthey
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Henrik Mouritsen
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Miriam Liedvogel
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- MPRG
Behavioural Genomics, Max Planck Institute
for Evolutionary Biology, August-Thienemann-Str. 2, Plön 24306, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Department
of Physics, Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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7
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Toldo JM, do Casal MT, Ventura E, do Monte SA, Barbatti M. Surface hopping modeling of charge and energy transfer in active environments. Phys Chem Chem Phys 2023; 25:8293-8316. [PMID: 36916738 PMCID: PMC10034598 DOI: 10.1039/d3cp00247k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.
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Affiliation(s)
| | | | - Elizete Ventura
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Silmar A do Monte
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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8
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An ML, Miao JL. Genetic and Molecular Characterization of a Dash Cryptochrome Homologous Gene from Antarctic Diatom Phaeodactylum tricornutum ICE-H. Mol Biol 2022. [DOI: 10.1134/s0026893322060024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Understanding flavin electronic structure and spectra. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Schuhmann F, Kattnig DR, Solov'yov IA. Exploring Post-activation Conformational Changes in Pigeon Cryptochrome 4. J Phys Chem B 2021; 125:9652-9659. [PMID: 34327996 DOI: 10.1021/acs.jpcb.1c02795] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A widespread hypothesis ascribes the ability of migratory birds to navigate over large distances to an inclination compass realized by the protein cryptochrome in the birds' retinae. Cryptochromes are activated by blue light, which induces a radical pair state, the spin dynamics of which may become sensitive to earth's weak magnetic fields. The magnetic information is encoded and passed on to downstream processes by structural rearrangements of the protein, the details of which remain vague. We utilize extensive all-atom molecular dynamics simulations to probe the conformational changes of pigeon cryptochrome 4 upon light activation. The structural dynamics are analyzed based on principal component analysis and with the help of distance matrices, which reveal significant changes in selected inter-residue distances. The results are evaluated and discussed with reference to the protein structure and its putative function as a magnetoreceptor. It is suggested that the phosphate-binding loop could act as a gate controlling the access to the flavin adenine dinucleotide cofactor depending on the redox state of the protein.
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Affiliation(s)
- Fabian Schuhmann
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Rd., Exeter EX4 4QD, U.K
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
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11
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Friis I, Verkhovtsev A, Solov'yov IA, Solov'yov AV. Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field. J Comput Chem 2020; 41:2429-2439. [PMID: 32851682 DOI: 10.1002/jcc.26399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/19/2020] [Accepted: 07/26/2020] [Indexed: 11/06/2022]
Abstract
Ion-induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated how single- and double strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to: (a) quantify the shock wave propagation and (b) describe the dynamics of formation of DNA breaks. The article concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation set-ups.
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Affiliation(s)
- Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | | | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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12
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Sjulstok E, Solov'yov IA. Structural Explanations of Flavin Adenine Dinucleotide Binding in Drosophila melanogaster Cryptochrome. J Phys Chem Lett 2020; 11:3866-3870. [PMID: 32330039 DOI: 10.1021/acs.jpclett.0c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cryptochrome proteins are thought to be involved in light-sensitive magnetoreception in migratory birds triggered by flavin adenine dinucleotide (FAD) light absorption. A recent study, however, calls into question the ability of vertebrate cryptochrome proteins to bind FAD, rendering them unlikely to function as magnetoreceptive proteins. In this Letter, we investigate the structural changes occurring in Drosophila melanogaster cryptochrome, upon key amino acid mutations, which reduce FAD binding. Through computational analysis we have now suggested why some mutations do not preclude FAD binding in all vertebrate cryptochrome proteins.
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Affiliation(s)
- Emil Sjulstok
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Carl von Ossietzky str. 9-11, 26111 Oldenburg, Germany
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13
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Nielsen C, Solov’yov IA. MolSpin—Flexible and extensible general spin dynamics software. J Chem Phys 2019; 151:194105. [DOI: 10.1063/1.5125043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Claus Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ilia A. Solov’yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
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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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Sushko GB, Solov'yov IA, Solov'yov AV. Modeling MesoBioNano systems with MBN Studio made easy. J Mol Graph Model 2019; 88:247-260. [PMID: 30776757 DOI: 10.1016/j.jmgm.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023]
Abstract
This paper introduces MesoBioNano (MBN) Studio - a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization, molecular dynamics, and kinetic Monte Carlo simulations. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner. Employing this plug-in, one can easily construct molecular systems of different geometries (e.g., spherical or ellipsoidal nanoparticles, cubic crystalline samples) with various atomic composition. The paper presents the first public release of MBN Studio and provides an overview of its significant capabilities, as well as the reference point for further extensions.
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Affiliation(s)
- Gennady B Sushko
- MBN Research Center, Altenhöferallee 3, 60438, Frankfurt am Main, Germany.
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
| | - Andrey V Solov'yov
- MBN Research Center, Altenhöferallee 3, 60438, Frankfurt am Main, Germany.
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Applications of molecular modeling to flavoproteins: Insights and challenges. Methods Enzymol 2019; 620:277-314. [DOI: 10.1016/bs.mie.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Goings JJ, Reinhardt CR, Hammes-Schiffer S. Propensity for Proton Relay and Electrostatic Impact of Protein Reorganization in Slr1694 BLUF Photoreceptor. J Am Chem Soc 2018; 140:15241-15251. [DOI: 10.1021/jacs.8b07456] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Joshua J. Goings
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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Nielsen C, Nørby MS, Kongsted J, Solov'yov IA. Absorption Spectra of FAD Embedded in Cryptochromes. J Phys Chem Lett 2018; 9:3618-3623. [PMID: 29905481 DOI: 10.1021/acs.jpclett.8b01528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The magnetic compass sense utilized by migratory birds for long-distance navigation functions only once light of a certain wavelength is present. This piece of evidence fits partially with the popular hypothesis of chemical magnetoreception in cryptochrome proteins, located in the bird retina. According to this hypothesis a magnetosensitive radical pair is produced after photoexcitation of an FAD cofactor inside cryptochrome, and as such the absorption properties of FAD are of crucial importance for cryptochrome activation. However, we reveal that absorption spectra of FAD show very little variation between six different cryptochromes, suggesting that the electronic transitions are barely affected by the chemical differences in the proteins. This conclusion hints on the presence of a secondary photoreceptor or cofactor that could be necessary to explain green-light-activated magnetoreception in birds.
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Affiliation(s)
- Claus Nielsen
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Morten S Nørby
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Jacob Kongsted
- 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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