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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Avian cryptochrome 4 binds superoxide. Comput Struct Biotechnol J 2024; 26:11-21. [PMID: 38204818 PMCID: PMC10776438 DOI: 10.1016/j.csbj.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2 • - ) is generated in the re-oxidation with molecular oxygen. The resulting O2 • - -containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged "crypt" region that leads to the flavin binding pocket transiently binds O2 • - at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - 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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2
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Tandiana R, Omar KA, Luppi E, Cailliez F, Van-Oanh NT, Clavaguéra C, de la Lande A. Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7740-7752. [PMID: 37874960 DOI: 10.1021/acs.jctc.3c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.
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Affiliation(s)
- Rika Tandiana
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Karwan Ali Omar
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
- Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Eleonora Luppi
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
| | - Fabien Cailliez
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Nguyen-Thi Van-Oanh
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
| | - Aurélien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, F-91405 Orsay, France
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3
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Deviers J, Cailliez F, Gutiérrez BZ, Kattnig DR, de la Lande A. Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome. Phys Chem Chem Phys 2022; 24:16784-16798. [PMID: 35775941 DOI: 10.1039/d1cp05804e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.,Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Bernardo Zúñiga Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C. P. 44430, Guadalajara Jal, Mexico
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Wu X, Hénin J, Baciou L, Baaden M, Cailliez F, de la Lande A. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations. Front Chem 2021; 9:650651. [PMID: 34017816 PMCID: PMC8129163 DOI: 10.3389/fchem.2021.650651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. −0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the μeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected O2−binding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O2 binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.
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Affiliation(s)
- Xiaojing Wu
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Jérôme Hénin
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Laura Baciou
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, Paris, France
| | - Fabien Cailliez
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), Orsay, France
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput 2017; 13:3985-4002. [DOI: 10.1021/acs.jctc.7b00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaojing Wu
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Jean-Marie Teuler
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Fabien Cailliez
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Carine Clavaguéra
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, 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 NW, Calgary, Alberta, Canada T2N 1N4
- College
of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, P. R. China
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
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8
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Affiliation(s)
- Pascal Pernot
- Laboratoire de Chimie Physique, UMR8000 CNRS/Univ. Paris-Sud; 91405 Orsay France
| | - Fabien Cailliez
- Laboratoire de Chimie Physique, UMR8000 CNRS/Univ. Paris-Sud; 91405 Orsay France
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9
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Cailliez F, Müller P, Firmino T, Pernot P, de la Lande A. Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6–4) Photolyase. J Am Chem Soc 2016; 138:1904-15. [DOI: 10.1021/jacs.5b10938] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabien Cailliez
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, University
Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette
cedex, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pascal Pernot
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Narth C, Gillet N, Cailliez F, Lévy B, de la Lande A. Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations. Acc Chem Res 2015; 48:1090-7. [PMID: 25730126 DOI: 10.1021/ar5002796] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system to leave the crossing region. In the framework of open quantum systems, τFC is a short time approximation of the characteristic decoherence time of the electronic subsystem in interaction with its nuclear environment. The comparison of the respective values of τcoh and τFC allows us to probe the occurrence of non-Condon effects. We use ab initio MD simulations to analyze how decoherence appears in several biological cofactors. We conclude that we cannot account for its order of magnitude by considering only the atoms or bonds directly concerned with the transfer. Decoherence results from contributions from all atoms of the system appearing with a time delay that increases with the distance from the primarily concerned atoms or bonds. The delay and magnitude of the contributions depend on the chemical nature of the system. Finally, we present recent developments based on constrained DFT for efficient and accurate evaluations of the electronic coupling in ab initio MD simulations. These are promising methods to study the subtle fluctuations of the electronic coupling and the mechanisms of electronic decoherence in biological systems.
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Affiliation(s)
- Christophe Narth
- Laboratoire
de Chimie Théorique, CNRS UMR 7616, Université Pierre et Marie Curie, case courrier 137. 4, Place Jussieu, 75252 Cedex 05 Paris, France
| | - Natacha Gillet
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fabien Cailliez
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Bernard Lévy
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, CNRS UMR 8000, Université Paris Sud, Bâtiment
349 - Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
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Cailliez F, Müller P, Gallois M, de la Lande A. ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome. J Am Chem Soc 2014; 136:12974-86. [PMID: 25157750 DOI: 10.1021/ja506084f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°(-)). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud and CNRS , Orsay F-91405, France
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Cailliez F, Bourasseau A, Pernot P. Calibration of forcefields for molecular simulation: sequential design of computer experiments for building cost-efficient kriging metamodels. J Comput Chem 2013; 35:130-49. [PMID: 24318648 DOI: 10.1002/jcc.23475] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/23/2013] [Accepted: 10/06/2013] [Indexed: 11/09/2022]
Abstract
We present a global strategy for molecular simulation forcefield optimization, using recent advances in Efficient Global Optimization algorithms. During the course of the optimization process, probabilistic kriging metamodels are used, that predict molecular simulation results for a given set of forcefield parameter values. This enables a thorough investigation of parameter space, and a global search for the minimum of a score function by properly integrating relevant uncertainty sources. Additional information about the forcefield parameters are obtained that are inaccessible with standard optimization strategies. In particular, uncertainty on the optimal forcefield parameters can be estimated, and transferred to simulation predictions. This global optimization strategy is benchmarked on the TIP4P water model.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Chimie Physique, UMR8000, Univ. Paris-Sud and CNRS, Orsay, F-91405, France
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14
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Pernot P, Cailliez F. Comment on “Uncertainties in scaling factors for ab initio vibrational zero-point energies” [J. Chem. Phys. 130, 114102 (2009)] and “Calibration sets and the accuracy of vibrational scaling factors: A case study with the X3LYP hybrid functional” [J. Chem. Phys. 133, 114109 (2010)]. J Chem Phys 2011; 134:167101; author reply 167102-3. [DOI: 10.1063/1.3581022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Cailliez F, Pernot P. Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation. J Chem Phys 2011; 134:054124. [DOI: 10.1063/1.3545069] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Cailliez F, Boutin A, Demachy I, Fuchs AH. Thermodynamic study of water confinement in hydrophobic zeolites by Monte Carlo simulations. Molecular Simulation 2009. [DOI: 10.1080/08927020802398900] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Coudert FX, Cailliez F, Vuilleumier R, Fuchs AH, Boutin A. Water nanodroplets confined in zeolite pores. Faraday Discuss 2009; 141:377-98; discussion 443-65. [DOI: 10.1039/b804992k] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cailliez F, Trzpit M, Soulard M, Demachy I, Boutin A, Patarin J, Fuchs AH. Thermodynamics of water intrusion in nanoporous hydrophobic solids. Phys Chem Chem Phys 2008; 10:4817-26. [DOI: 10.1039/b807471b] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Trzpit M, Soulard M, Patarin J, Desbiens N, Cailliez F, Boutin A, Demachy I, Fuchs AH. The effect of local defects on water adsorption in silicalite-1 zeolite: a joint experimental and molecular simulation study. Langmuir 2007; 23:10131-9. [PMID: 17715950 DOI: 10.1021/la7011205] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report a joint experimental and molecular simulation study of water condensation in silicalite-1 zeolite. A sample was synthesized using the fluoride route and was found to contain essentially no defects. A second sample synthesized using the hydroxide route was found to contain a small amount of silanol groups. The thermodynamics of water condensation was studied in these two samples, as well as in a commercial sample, in order to understand the effect of local defects on water adsorption. The molecular simulation study enabled us to qualitatively reproduce the experimentally observed condensation thermodynamics features. A shift and a rounding of the condensation transition was observed with an increasing hydrophilicity of the local defect, but the condensation transition was still observed above the water saturation vapor pressure P0. Both experiments and simulations agree on the fact that a small water uptake can be observed at very low pressure, but that the bulk liquid does not form from the gas phase below P0. The picture that emerges from the observed water condensation mechanism is the existence of a heterogeneous internal surface that is overall hydrophobic, despite the existence of hydrophilic "patches". This heterogeneous surface configuration is thermodynamically stable in a wide range of reduced pressures (from P/P0 = 0.2 to a few thousands), until the condensation transition takes place.
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Affiliation(s)
- M Trzpit
- Laboratoire des Matériaux à Porosité Contrôlée, CNRS, Ecole Nationale Supérieure de Chimie de Mulhouse and Université de Haute-Alsace, 68093 Mulhouse, France
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Abstract
The extracellular domains of cadherins are known to play a major role in cell adhesion, although the structures involved in this process remain unclear. We have used molecular dynamics to characterize the conformational and thermodynamic properties of two of the dimer interfaces identified in E-cadherin crystals and involving the two outermost exodomains (EC1 and EC2): a dimer involving exchange of the N-terminal strand (referred to as the "swapped" dimer) and a "staggered" dimer involving an EC1-EC2 interface. The results show that the staggered dimer involves a much smaller interface area and is notably less stable than the swapped dimer. It is also found that, despite its stability, the swapped dimer undergoes a conformational transition leading to a structure closer to that experimentally observed for the homologous C-cadherin. Finally, comparing the simulated dimer structures with the sequences of E-, C-, and N-cadherins shows that the swapped dimer interface involves surprisingly few residues that vary from family to family and notably no changes between the E- and C-cadherin exodomains.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
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Abstract
BACKGROUND Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structure prediction. There are several methods available for assigning secondary structure if the three-dimensional structure of the protein is known. Unfortunately they differ in their definitions, particularly in the exact positions of the termini. Additionally, most existing methods rely on hydrogen bonding, which means that important secondary structural classes, such as isolated beta-strands and poly-proline helices cannot be identified as they do not have characteristic hydrogen-bonding patterns. For this reason we have developed a more accurate method for assigning secondary structure based on main chain geometry, which also allows a more comprehensive assignment of secondary structure. RESULTS We define secondary structure based on a number of geometric parameters. Helices are defined based on whether they fit inside an imaginary cylinder: residues must be within the correct radius of a central axis. Different types of helices (alpha, 3(10) or pi) are assigned on the basis of the angle between successive peptide bonds. beta-strands are assigned based on backbone dihedrals and with alternating peptide bonds. Thus hydrogen bonding is not required and beta-strands can be within a parallel sheet, antiparallel sheet, or can be isolated. Poly-proline helices are defined similarly, although with three-fold symmetry. CONCLUSION We find that our method better assigns secondary structure than existing methods. Specifically, we find that comparing our methods with those of others, amino-acid trends at helix caps are stronger, secondary structural elements less likely to be concatenated together and secondary structure guided sequence alignment is improved. We conclude, therefore, that secondary structure assignments using our method better reflects physical and evolutionary characteristics of proteins. The program is available from http://www.bioinf.man.ac.uk/~lovell/segno.shtml.
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Affiliation(s)
- Maria Vittoria Cubellis
- Biochemistry Dept, University of Cambridge, Cambridge CB2 1GA, UK
- Dipartimento di Biologia Strutturale e Funzionale, Napoli, Italy
| | - Fabien Cailliez
- Biochemistry Dept, University of Cambridge, Cambridge CB2 1GA, UK
- Institut de Biologie Physico-Chimique, Paris, France
| | - Simon C Lovell
- Biochemistry Dept, University of Cambridge, Cambridge CB2 1GA, UK
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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Abstract
E-cadherins belong to a family of membrane-bound, cellular adhesion proteins. Their adhesive properties mainly involve the two N-terminal extracellular domains (EC1 and EC2). The junctions between these domains are characterized by calcium ion binding sites, and calcium ions are essential for the correct functioning of E-cadherins. Calcium is believed to rigidify the extracellular portion of the protein, which, when complexed, adopts a rod-like conformation. Here, we use molecular dynamics simulations to investigate the dynamics of the EC1-2 portion of E-cadherin in the presence and in the absence of calcium ions. These simulations confirm that apo-cadherin shows much higher conformational flexibility on a nanosecond timescale than the calcium-bound form. It is also shown that although the apo-cadherin fragment can spontaneously complex potassium, these monovalent ions are incapable of rigidifying the interdomain junctions. In contrast, removal of the most solvent-exposed calcium ion at the EC1-2 junction does not significantly perturb the dynamical behavior of the fragment. We have also extended this study to the cis-dimer formed from two EC1-2 fragments, potentially involved in cellular adhesion. Here again, it is shown that the presence of calcium is an important factor in both rigidifying and stabilizing the complex.
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Affiliation(s)
- Fabien Cailliez
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Institut de Biologie Physico-Chimique, Paris 75005, France
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23
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Abstract
It is becoming clear that, in addition to structural properties, the mechanical properties of proteins can play an important role in their biological activity. It nevertheless remains difficult to probe these properties experimentally. Whereas single-molecule experiments give access to overall mechanical behavior, notably the impact of end-to-end stretching, it is currently impossible to directly obtain data on more local properties. We propose a theoretical method for probing the mechanical properties of protein structures at the single-amino acid level. This approach can be applied to both all-atom and simplified protein representations. The probing leads to force constants for local deformations and to deformation vectors indicating the paths of least mechanical resistance. It also reveals the mechanical coupling that exists between residues. Results obtained for a variety of proteins show that the calculated force constants vary over a wide range. An analysis of the induced deformations provides information that is distinct from that obtained with measures of atomic fluctuations and is more easily linked to residue-level properties than normal mode analyses or dynamic trajectories. It is also shown that the mechanical information obtained by residue-level probing opens a new route for defining so-called dynamical domains within protein structures.
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Affiliation(s)
- Isabelle Navizet
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris 75005, France
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