1
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Tikhonov AN. The cytochrome b 6f complex: plastoquinol oxidation and regulation of electron transport in chloroplasts. PHOTOSYNTHESIS RESEARCH 2024; 159:203-227. [PMID: 37369875 DOI: 10.1007/s11120-023-01034-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
In oxygenic photosynthetic systems, the cytochrome b6f (Cytb6f) complex (plastoquinol:plastocyanin oxidoreductase) is a heart of the hub that provides connectivity between photosystems (PS) II and I. In this review, the structure and function of the Cytb6f complex are briefly outlined, being focused on the mechanisms of a bifurcated (two-electron) oxidation of plastoquinol (PQH2). In plant chloroplasts, under a wide range of experimental conditions (pH and temperature), a diffusion of PQH2 from PSII to the Cytb6f does not limit the intersystem electron transport. The overall rate of PQH2 turnover is determined mainly by the first step of the bifurcated oxidation of PQH2 at the catalytic site Qo, i.e., the reaction of electron transfer from PQH2 to the Fe2S2 cluster of the high-potential Rieske iron-sulfur protein (ISP). This point has been supported by the quantum chemical analysis of PQH2 oxidation within the framework of a model system including the Fe2S2 cluster of the ISP and surrounding amino acids, the low-potential heme b6L, Glu78 and 2,3,5-trimethylbenzoquinol (the tail-less analog of PQH2). Other structure-function relationships and mechanisms of electron transport regulation of oxygenic photosynthesis associated with the Cytb6f complex are briefly outlined: pH-dependent control of the intersystem electron transport and the regulatory balance between the operation of linear and cyclic electron transfer chains.
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Affiliation(s)
- Alexander N Tikhonov
- Department of Biophysics, Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow, Russian Federation, 119991.
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2
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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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3
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Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148951. [PMID: 36509126 DOI: 10.1016/j.bbabio.2022.148951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
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4
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Abou-Hamdan A, Mahler R, Grossenbacher P, Biner O, Sjöstrand D, Lochner M, Högbom M, von Ballmoos C. Functional design of bacterial superoxide:quinone oxidoreductase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148583. [PMID: 35671795 DOI: 10.1016/j.bbabio.2022.148583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/10/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
The superoxide anion - molecular oxygen reduced by a single electron - is produced in large amounts by enzymatic and adventitious reactions. It can perform a range of cellular functions, including bacterial warfare and iron uptake, signalling and host immune response in eukaryotes. However, it also serves as precursor for more deleterious species such as the hydroxyl anion or peroxynitrite and defense mechanisms to neutralize superoxide are important for cellular health. In addition to the soluble proteins superoxide dismutase and superoxide reductase, recently the membrane embedded diheme cytochrome b561 (CybB) from E. coli has been proposed to act as a superoxide:quinone oxidoreductase. Here, we confirm superoxide and cellular ubiquinones or menaquinones as natural substrates and show that quinone binding to the enzyme accelerates the reaction with superoxide. The reactivity of the substrates is in accordance with the here determined midpoint potentials of the two b hemes (+48 and -23 mV / NHE). Our data suggest that the enzyme can work near the diffusion limit in the forward direction and can also catalyse the reverse reaction efficiently under physiological conditions. The data is discussed in the context of described cytochrome b561 proteins and potential physiological roles of CybB.
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Affiliation(s)
- Abbas Abou-Hamdan
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Roman Mahler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Philipp Grossenbacher
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Olivier Biner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Dan Sjöstrand
- Stockholm center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Martin Lochner
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Martin Högbom
- Stockholm center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Christoph von Ballmoos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.
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5
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Salerno KM, Domenico J, Le NQ, Stiles CD, Solov’yov IA, Martino CF. Long-Time Oxygen Localization in Electron Transfer Flavoprotein. J Chem Inf Model 2022; 62:4191-4199. [PMID: 35998902 PMCID: PMC9472800 DOI: 10.1021/acs.jcim.2c00430] [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: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Reactive oxygen species (ROS) exert a wide range of biological effects from beneficial regulatory function to deleterious oxidative stress. The electron transfer flavoprotein (ETF) is ubiquitous to life and is associated with aerobic metabolism and ROS production due to its location in the mitochondria. Quantifying oxygen localization within the ETF complex is critical for understanding the potential for electron transfer and radical pair formation between flavin adenine dinucleotide (FAD) cofactor and superoxide during ROS formation. Our study employed all-atom molecular dynamics simulations and identified several novel, long-lived oxygen binding sites within the ETF complex that appear near the FAD cofactor. Site locations, the local electrostatic environment, and characteristic oxygen binding times for each site were evaluated to establish factors that may lead to possible charge transfer reactions and superoxide formation within the ETF complex. The study revealed that some oxygen binding sites are naturally linked to protein domain features, suggesting opportunities to engineer and control ROS production and subsequent dynamics.
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Affiliation(s)
- K. Michael Salerno
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q. Le
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D. Stiles
- The
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 Neurosensory Science, Carl von Ossietzky
University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F. Martino
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
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6
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Solov'yov IA, Sushko G, Friis I, Solov'yov AV. Multiscale modeling of stochastic dynamics processes with MBN Explorer. J Comput Chem 2022; 43:1442-1458. [PMID: 35708151 DOI: 10.1002/jcc.26948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/09/2022]
Abstract
Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN Explorer. Stochastic dynamics in MBN Explorer relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with MBN Explorer.
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Affiliation(s)
- Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Oldenburg, Germany.,Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.,Center for Nanoscale Dynamics (CENAD), Institut für Physik, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | | | - Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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7
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Knox PP, Lukashev EP, Korvatovskii BN, Seifullina NK, Goryachev SN, Allakhverdiev ES, Paschenko VZ. Effect of Dipyridamole on Membrane Energization and Energy Transfer in Chromatophores of Rba. sphaeroides. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1138-1148. [PMID: 36273882 PMCID: PMC9568914 DOI: 10.1134/s0006297922100078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Effect of dipyridamole (DIP) at concentrations up to 1 mM on fluorescent characteristics of light-harvesting complexes LH2 and LH1, as well as on conditions of photosynthetic electron transport chain in the bacterial chromatophores of Rba. sphaeroides was investigated. DIP was found to affect efficiency of energy transfer from the light-harvesting complex LH2 to the LH1-reaction center core complex and to produce the long-wavelength ("red") shift of the absorption band of light-harvesting bacteriochlorophyll molecules in the IR spectral region at 840-900 nm. This shift is associated with the membrane transition to the energized state. It was shown that DIP is able to reduce the photooxidized bacteriochlorophyll of the reaction center, which accelerated electron flow along the electron transport chain, thereby stimulating generation of the transmembrane potential on the chromatophore membrane. The results are important for clarifying possible mechanisms of DIP influence on the activity of membrane-bound functional proteins. In particular, they might be significant for interpreting numerous therapeutic effects of DIP.
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Affiliation(s)
- Peter P. Knox
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene P. Lukashev
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | | | - Sergey N. Goryachev
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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8
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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9
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Husen P, Solov'yov IA. Modeling the Energy Landscape of Side Reactions in the Cytochrome bc 1 Complex. Front Chem 2021; 9:643796. [PMID: 34095083 PMCID: PMC8170094 DOI: 10.3389/fchem.2021.643796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Much of the metabolic molecular machinery responsible for energy transduction processes in living organisms revolves around a series of electron and proton transfer processes. The highly redox active enzymes can, however, also pose a risk of unwanted side reactions leading to reactive oxygen species, which are harmful to cells and are a factor in aging and age-related diseases. Using extensive quantum and classical computational modeling, we here show evidence of a particular superoxide production mechanism through stray reactions between molecular oxygen and a semiquinone reaction intermediate bound in the mitochondrial complex III of the electron transport chain, also known as the cytochrome b c 1 complex. Free energy calculations indicate a favorable electron transfer from semiquinone occurring at low rates under normal circumstances. Furthermore, simulations of the product state reveal that superoxide formed at the Q o -site exclusively leaves the b c 1 complex at the positive side of the membrane and escapes into the intermembrane space of mitochondria, providing a critical clue in further studies of the harmful effects of mitochondrial superoxide production.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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10
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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11
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Jacobsen L, Husen P, Solov'yov IA. Inhibition Mechanism of Antimalarial Drugs Targeting the Cytochrome bc 1 Complex. J Chem Inf Model 2021; 61:1334-1345. [PMID: 33617262 DOI: 10.1021/acs.jcim.0c01148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasmodium falciparum (P. falciparum) is the main parasite known to cause malaria in humans. The antimalarial drug atovaquone is known to inhibit the Qo-site of the cytochrome bc1 complex of P. falciparum, which ultimately blocks ATP synthesis, leading to cell death. Through the years, mutations of the P. falciparum cytochrome bc1 complex, causing resistance to atovaquone, have emerged. The present investigation applies molecular dynamics (MD) simulations to study how the specific mutations Y279S and L282V, known to cause atovaquone resistance in malarial parasites, affect the inhibition mechanism of two known inhibitors. Binding free energy estimates were obtained through free energy perturbation calculations but were unable to confidently resolve the effects of mutations due to the great complexity of the binding environment. Meanwhile, basic mechanistic considerations from the MD simulations provide a detailed characterization of inhibitor binding modes and indicate that the Y279S mutation weakens the natural binding of the inhibitors, while no conclusive effect of the L282V mutation could be observed.
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Affiliation(s)
- Luise Jacobsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Strasse 9-11, 26129 Oldenburg, Germany
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12
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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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13
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Mourokh L, Vittadello M. Physical model of proton-pumping Q-cycle in respiratory and photosynthetic electron transport chains. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Korol V, Husen P, Sjulstok E, Nielsen C, Friis I, Frederiksen A, Salo AB, Solov’yov IA. Introducing VIKING: A Novel Online Platform for Multiscale Modeling. ACS OMEGA 2020; 5:1254-1260. [PMID: 31984283 PMCID: PMC6977254 DOI: 10.1021/acsomega.9b03802] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/29/2019] [Indexed: 05/17/2023]
Abstract
Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.
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Affiliation(s)
- Vasili Korol
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Peter Husen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Emil Sjulstok
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
- Neuroscience, University of Texas Southwestern Medical Center at
Dallas, Dallas 75390, Texas, United States
| | - Claus Nielsen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Ida Friis
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Anders Frederiksen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Adrian B. Salo
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Odense 5230, Denmark
- Department
of Physics, Carl von Ossietzky Universität
Oldenburg, Oldenburg 26111, Germany
- E-mail:
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15
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Husen P, Nielsen C, Martino CF, Solov'yov IA. Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein. J Chem Inf Model 2019; 59:4868-4879. [PMID: 31665600 DOI: 10.1021/acs.jcim.9b00702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacterized role in reactive oxygen species generation, apparently at the level of the electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) and/or its redox partner electron-transfer flavoprotein (ETF). These enzymes comprise a key pathway through which electrons are sequentially shuttled from several dehydrogenases to the respiratory chain. The exact mechanisms of superoxide production have not been fully established, but a crucial starting point would be the binding of molecular oxygen within one of the protein complexes. The present investigation offers a comprehensive computational approach for the determination of binding modes and characteristic binding times of small molecules inside proteins, which is then used to reveal several O2 binding sites near the flavin adenine dinucleotide cofactor of the ETF enzyme. The binding sites are further characterized to extract the necessary parameters for further studies of possible electron transfer between flavin and O2 leading to radical pair formation and possible superoxide production.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Odense , Denmark
| | - Claus Nielsen
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Odense , Denmark
| | - Carlos F Martino
- Biomedical and Chemical Engineering and Science Department , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Ilia A Solov'yov
- Department of Physics , Carl von Ossietzky Universität Oldenburg , Oldenburg , Germany
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16
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Vasavda C, Kothari R, Malla AP, Tokhunts R, Lin A, Ji M, Ricco C, Xu R, Saavedra HG, Sbodio JI, Snowman AM, Albacarys L, Hester L, Sedlak TW, Paul BD, Snyder SH. Bilirubin Links Heme Metabolism to Neuroprotection by Scavenging Superoxide. Cell Chem Biol 2019; 26:1450-1460.e7. [PMID: 31353321 DOI: 10.1016/j.chembiol.2019.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/04/2019] [Accepted: 07/07/2019] [Indexed: 12/26/2022]
Abstract
Bilirubin is one of the most frequently measured metabolites in medicine, yet its physiologic roles remain unclear. Bilirubin can act as an antioxidant in vitro, but whether its redox activity is physiologically relevant is unclear because many other antioxidants are far more abundant in vivo. Here, we report that depleting endogenous bilirubin renders mice hypersensitive to oxidative stress. We find that mice lacking bilirubin are particularly vulnerable to superoxide (O2⋅-) over other tested reactive oxidants and electrophiles. Whereas major antioxidants such as glutathione and cysteine exhibit little to no reactivity toward O2⋅-, bilirubin readily scavenges O2⋅-. We find that bilirubin's redox activity is particularly important in the brain, where it prevents excitotoxicity and neuronal death by scavenging O2⋅- during NMDA neurotransmission. Bilirubin's unique redox activity toward O2⋅- may underlie a prominent physiologic role despite being significantly less abundant than other endogenous and exogenous antioxidants.
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Affiliation(s)
- Chirag Vasavda
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruchita Kothari
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adarsha P Malla
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert Tokhunts
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Anthony Lin
- Duke University School of Medicine, Durham, NC 27701, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cristina Ricco
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Risheng Xu
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harry G Saavedra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juan I Sbodio
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adele M Snowman
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren Albacarys
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lynda Hester
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas W Sedlak
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bindu D Paul
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Solomon H Snyder
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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17
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Ghashghaeinia M, Köberle M, Mrowietz U, Bernhardt I. Proliferating tumor cells mimick glucose metabolism of mature human erythrocytes. Cell Cycle 2019; 18:1316-1334. [PMID: 31154896 PMCID: PMC6592250 DOI: 10.1080/15384101.2019.1618125] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mature human erythrocytes are dependent on anerobic glycolysis, i.e. catabolism (oxidation) of one glucose molecule to produce two ATP and two lactate molecules. Proliferating tumor cells mimick mature human erythrocytes to glycolytically generate two ATP molecules. They deliberately avoid or switch off their respiration, i.e. tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) machinery and consequently dispense with the production of additional 36 ATP molecules from one glucose molecule. This phenomenon is named aerobic glycolysis or Warburg effect. The present review deals with the fate of a glucose molecule after entering a mature human erythrocyte or a proliferating tumor cell and describes why it is useful for a proliferating tumor cell to imitate a mature erythrocyte. Blood consisting of plasma and cellular components (99% of the cells are erythrocytes) may be regarded as a mobile organ, constantly exercising a direct interaction with other organs. Therefore, the use of drugs, which influences the biological activity of erythrocytes, has an immediate effect on the entire organism. Abbreviations: TCA: tricarboxylic acid cycle; OXPHOS: oxidative phosphorylation; GSH: reduced state of glutathione; NFκB: Nuclear factor of kappa B; PKB (Akt): protein kinase B; NOS: nitric oxide synthase; IgG: immune globulin G; H2S: hydrogen sulfide; slanDCs: Human 6-sulfo LacNAc-expressing dendritic cells; IL-8: interleukin-8; LPS: lipopolysaccharide; ROS: reactive oxygen species; PPP: pentose phosphate pathway; NADPH: nicotinamide adenine dinucleotide phosphate hydrogen; R5P: ribose-5-phophate; NAD: nicotinamide adenine dinucleotide; FAD: flavin adenine dinucleotide; O2●−: superoxide anion; G6P: glucose 6-phosphate; HbO2: Oxyhemoglobin; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GAP: glyceraldehyde-3-phosphate; 1,3-BPG: 1,3-bis-phosphoglycerate; 2,3-BPG: 2,3-bisphosphoglycerte; PGAM1: phosphoglycerate mutase 1; 3-PG: 3-phosphoglycerate; 2-PG: 2-phosphoglycerate; MIPP1: Multiple inositol polyphosphate phosphatase; mTORC1: mammalian target of rapamycin complex 1; Ru5P: ribulose 5-phosphate; ox-PPP: oxidative branch of pentose phosphate pathway; PGK: phosphoglycerate kinase; IFN-γ: interferon-γ; LDH: lactate dehydrogenase; STAT3: signal transducer and activator of transcription 3; Rheb: Ras homolog enriched in Brain; H2O2: hydrogen peroxide; ROOH: lipid peroxide; SOD: superoxide dismutase; MRC: mitochondrial respiratory chain; MbFe2+-O2: methmyoglobin; RNR: ribonucleotide reductase; PRPP: phosphoribosylpyrophosphate; PPi: pyrophosphate; GSSG: oxidized state of glutathione; non-ox-PPP: non-oxidative branch of pentose phosphate pathway; RPI: ribose-5-phosphate isomerase; RPE: ribulose 5-phosphate 3-epimerase; X5P: xylulose 5-phosphate; TK: transketolase; TA: transaldolase; F6P: fructose-6-phosphate; AR2: aldose reductase 2; SD: sorbitol dehydrogenase; HK: hexokinase; MG: mehtylglyoxal; DHAP: dihydroxyacetone phosphate; TILs: tumor-infiltrating lymphocytes; MCTs: monocarboxylate transporters; pHi: intracellular pH; Hif-1α: hypoxia-induced factor 1; NHE1: sodium/H+ (Na+/H+) antiporter 1; V-ATPase: vacuolar-type proton ATPase; CAIX: carbonic anhydrase; CO2: carbon dioxide; HCO3−: bicarbonate; NBC: sodium/bicarbonate (Na+/HCO3−) symporter; pHe: extracellular pH; GLUT-1: glucose transporter 1; PGK-1: phosphoglycerate kinase 1
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Affiliation(s)
- Mehrdad Ghashghaeinia
- a Department of Dermatology , University Medical Center Schleswig-Holstein, Campus Kiel , Kiel , Germany
| | - Martin Köberle
- b Klinik und Poliklinik für Dermatologie und Allergologie, Fakultät für Medizin , Technische Universität München , Munich , Germany
| | - Ulrich Mrowietz
- a Department of Dermatology , University Medical Center Schleswig-Holstein, Campus Kiel , Kiel , Germany
| | - Ingolf Bernhardt
- c Laboratory of Biophysics, Faculty of Natural and Technical Sciences III , Saarland University , Saarbruecken , Germany
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18
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Nielsen C, Hui R, Lui WY, Solov’yov IA. Towards predicting intracellular radiofrequency radiation effects. PLoS One 2019; 14:e0213286. [PMID: 30870450 PMCID: PMC6417702 DOI: 10.1371/journal.pone.0213286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
Recent experiments have reported an effect of weak radiofrequency magnetic fields in the MHz-range on the concentrations of reactive oxygen species (ROS) in living cells. Since the energy that could possibly be deposited by the radiation is orders of magnitude smaller than the energy of molecular thermal motion, it was suggested that the effect was caused by the interaction of RF magnetic fields with transient radical pairs within the cells, affecting the ROS formation rates through the radical pair mechanism. It is, however, at present not entirely clear how to predict RF magnetic field effects at certain field frequency and intensity in nanoscale biomolecular systems. We suggest a possible recipe for interpreting the radiofrequency effects in cells by presenting a general workflow for calculation of the reactive perturbations inside a cell as a function of RF magnetic field strength and frequency. To justify the workflow, we discuss the effects of radiofrequency magnetic fields on generic spin systems to particularly illustrate how the reactive radicals could be affected by specific parameters of the experiment. We finally argue that the suggested workflow can be used to predict effects of radiofrequency magnetic fields on radical pairs in biological cells, which is specially important for wireless recharging technologies where one has to know of any harmful effects that exposure to such radiation might cause.
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Affiliation(s)
- Claus Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Ron Hui
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Wing-Yee Lui
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ilia A. Solov’yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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19
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Kimø SM, Friis I, Solov'yov IA. Atomistic Insights into Cryptochrome Interprotein Interactions. Biophys J 2018; 115:616-628. [PMID: 30078611 DOI: 10.1016/j.bpj.2018.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/11/2018] [Accepted: 06/29/2018] [Indexed: 11/30/2022] Open
Abstract
It is striking that the mechanism by which birds sense geomagnetic fields during the biannual migration seasons is not entirely understood. A protein believed to be responsible for avian magnetoreception is the flavoprotein cryptochrome (CRY), which fulfills many of the criteria for a magnetic field sensor. Some experiments, however, indicate that magnetoreception in birds may be disturbed by extremely weak radio frequency fields, an effect that likely cannot be described by an isolated CRY protein. An explanation can possibly be delivered if CRY binds to another protein inside a cell that would possess certain biochemical properties, and it is, therefore, important to identify possible intracellular CRY interaction partners. The goal of this study is to investigate a possible interaction between CRY4 and the iron-sulfur-containing assembly protein (ISCA1) from Erithacus rubecula (European robin), which has recently been proposed to be relevant for magnetic field sensing. The interaction between the proteins is established through classical molecular dynamics simulations for several possible protein-docking modes. The analysis of these simulations concludes that the ISCA1 complex and CRY4 are capable of binding; however, the peculiarities of this binding argue strongly against ISCA1 as relevant for magnetoreception.
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Affiliation(s)
- Sarafina M Kimø
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
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20
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Scavenging of superoxide by a membrane-bound superoxide oxidase. Nat Chem Biol 2018; 14:788-793. [PMID: 29915379 DOI: 10.1038/s41589-018-0072-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/05/2018] [Indexed: 01/12/2023]
Abstract
Superoxide is a reactive oxygen species produced during aerobic metabolism in mitochondria and prokaryotes. It causes damage to lipids, proteins and DNA and is implicated in cancer, cardiovascular disease, neurodegenerative disorders and aging. As protection, cells express soluble superoxide dismutases, disproportionating superoxide to oxygen and hydrogen peroxide. Here, we describe a membrane-bound enzyme that directly oxidizes superoxide and funnels the sequestered electrons to ubiquinone in a diffusion-limited reaction. Experiments in proteoliposomes and inverted membranes show that the protein is capable of efficiently quenching superoxide generated at the membrane in vitro. The 2.0 Å crystal structure shows an integral membrane di-heme cytochrome b poised for electron transfer from the P-side and proton uptake from the N-side. This suggests that the reaction is electrogenic and contributes to the membrane potential while also conserving energy by reducing the quinone pool. Based on this enzymatic activity, we propose that the enzyme family be denoted superoxide oxidase (SOO).
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21
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Maffeo C, Aksimentiev A. Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Res 2017; 45:12125-12139. [PMID: 29059392 PMCID: PMC5716091 DOI: 10.1093/nar/gkx917] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/28/2017] [Indexed: 01/10/2023] Open
Abstract
During DNA replication, the single-stranded DNA binding protein (SSB) wraps single-stranded DNA (ssDNA) with high affinity to protect it from degradation and prevent secondary structure formation. Although SSB binds ssDNA tightly, it can be repositioned along ssDNA to follow the advancement of the replication fork. Using all-atom molecular dynamics simulations, we characterized the molecular mechanism of ssDNA association with SSB. Placed in solution, ssDNA–SSB assemblies were observed to change their structure spontaneously; such structural changes were suppressed in the crystallographic environment. Repeat simulations of the SSB–ssDNA complex under mechanical tension revealed a multitude of possible pathways for ssDNA to come off SSB punctuated by prolonged arrests at reproducible sites at the SSB surface. Ensemble simulations of spontaneous association of short ssDNA fragments with SSB detailed a three-dimensional map of local affinity to DNA; the equilibrium amount of ssDNA bound to SSB was found to depend on the electrolyte concentration but not on the presence of the acidic tips of the SSB tails. Spontaneous formation of ssDNA bulges and their diffusive motion along SSB surface was directly observed in multiple 10-µs-long simulations. Such reptation-like motion was confined by DNA binding to high-affinity spots, suggesting a two-step mechanism for SSB diffusion.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Ave, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W Clark St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Ave, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W Clark St, Urbana, IL 61801, USA.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA
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22
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Knox PP, Lukashev EP, Seifullina NK, Gorokhov VV, Rubin AB. The influence of dipyridamole and its derivatives on the membrane energization state of Rhodobacter sphaeroides bacterial chromatophores. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917050153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Crofts AR, Rose SW, Burton RL, Desai AV, Kenis PJA, Dikanov SA. The Q-Cycle Mechanism of the bc1 Complex: A Biologist’s Perspective on Atomistic Studies. J Phys Chem B 2017; 121:3701-3717. [DOI: 10.1021/acs.jpcb.6b10524] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antony R. Crofts
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Stuart W. Rose
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Rodney L. Burton
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Amit V. Desai
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, 1008 West Hazelwood Drive, Urbana, Illinois 61801, United States
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24
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Javanainen M, Vattulainen I, Monticelli L. On Atomistic Models for Molecular Oxygen. J Phys Chem B 2017; 121:518-528. [PMID: 28004930 DOI: 10.1021/acs.jpcb.6b11183] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis and cellular respiration. Substantial scientific effort has been devoted to understanding every part of this cycle. Classical molecular dynamics (MD) simulations have been used to study some of the key processes involved in cellular respiration: O2 permeation through alveolar monolayers and cellular membranes, its binding to hemoglobin during transport in the bloodstream, as well as its transport along optimal pathways toward its reduction sites in proteins. Moreover, MD simulations can help interpret the results of several imaging techniques in which O2 is used because of its paramagnetic nature. However, despite the widespread use of computational models for the O2 molecule, their performances have never been systematically evaluated. In this paper, we assess the performances of 14 different models of O2 available in the literature by calculating four thermodynamic properties: density, heat of vaporization, free energy of hydration, and free energy of solvation in hexadecane. For each property, reliable experimental data are available. Most models perform reasonably well in predicting the correct trends, but they fail to reproduce the experimental data quantitatively. We then develop new models for O2, with and without a quadrupole moment, and compare their behavior with the behavior of previously published models. The new models show significant improvement in terms of density, heat of vaporization, and free energy of hydration. However, quantitative agreement with water-oil partitioning is not reached due to discrepancies between the calculated and measured free energies of solvation in hexadecane. We suggest that classical pairwise-additive models may be inadequate to properly describe the thermodynamics of solvation of apolar species, such as O2, in apolar solvents.
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Affiliation(s)
- Matti Javanainen
- Department of Physics, Tampere University of Technology , 33720 Tampere, Finland.,Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , 33720 Tampere, Finland.,Department of Physics, University of Helsinki , 00100 Helsinki, Finland.,MEMPHYS - Centre for Biomembrane Physics, University of Southern Denmark , 5230 Odense, Denmark
| | - Luca Monticelli
- University of Lyon, CNRS, UMR 5086 MMSB , 69367 Lyon, France
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25
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Salo AB, Husen P, Solov’yov IA. Charge Transfer at the Qo-Site of the Cytochrome bc1 Complex Leads to Superoxide Production. J Phys Chem B 2016; 121:1771-1782. [DOI: 10.1021/acs.jpcb.6b10403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adrian Bøgh Salo
- Department of Physics,
Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Peter Husen
- Department of Physics,
Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ilia A. Solov’yov
- Department of Physics,
Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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26
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Husen P, Solov'yov IA. Mutations at the Q o Site of the Cytochrome bc 1 Complex Strongly Affect Oxygen Binding. J Phys Chem B 2016; 121:3308-3317. [PMID: 27748117 DOI: 10.1021/acs.jpcb.6b08226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The homodimeric bc1 protein complex is embedded in membranes of mitochondria and photosynthetic bacteria, where it transports protons across the membrane to maintain an electrostatic potential used to drive ATP synthesis as part of the respiratory or photosynthetic pathways. The reaction cycle of the bc1 complex is driven by series of redox processes involving substrate molecules from the membrane, but occasional side reactions between an intermediate semiquinone substrate and molecular oxygen are suspected to be a source of toxic superoxide, which is believed to be a factor in aging. The present investigation employs molecular dynamics simulations to study the effect of mutations in the Qo binding sites of the bc1 complex on the ability of oxygen molecules to migrate to and bind at various locations within the complex. It is found that the mutations strongly affect the ability of oxygen to bind at the Qo sites, and moreover, different behavior of the two monomers of the bc1 complex is observed. The conformational differences at the Qo sites of the two monomers are studied in detail and discussed. The anionic form of semiquinone was identified as leading to the greatest opportunity for side reactions with oxygen.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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