1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ježek P, Jabůrek M, Holendová B, Engstová H, Dlasková A. Mitochondrial Cristae Morphology Reflecting Metabolism, Superoxide Formation, Redox Homeostasis, and Pathology. Antioxid Redox Signal 2023; 39:635-683. [PMID: 36793196 PMCID: PMC10615093 DOI: 10.1089/ars.2022.0173] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Significance: Mitochondrial (mt) reticulum network in the cell possesses amazing ultramorphology of parallel lamellar cristae, formed by the invaginated inner mitochondrial membrane. Its non-invaginated part, the inner boundary membrane (IBM) forms a cylindrical sandwich with the outer mitochondrial membrane (OMM). Crista membranes (CMs) meet IBM at crista junctions (CJs) of mt cristae organizing system (MICOS) complexes connected to OMM sorting and assembly machinery (SAM). Cristae dimensions, shape, and CJs have characteristic patterns for different metabolic regimes, physiological and pathological situations. Recent Advances: Cristae-shaping proteins were characterized, namely rows of ATP-synthase dimers forming the crista lamella edges, MICOS subunits, optic atrophy 1 (OPA1) isoforms and mitochondrial genome maintenance 1 (MGM1) filaments, prohibitins, and others. Detailed cristae ultramorphology changes were imaged by focused-ion beam/scanning electron microscopy. Dynamics of crista lamellae and mobile CJs were demonstrated by nanoscopy in living cells. With tBID-induced apoptosis a single entirely fused cristae reticulum was observed in a mitochondrial spheroid. Critical Issues: The mobility and composition of MICOS, OPA1, and ATP-synthase dimeric rows regulated by post-translational modifications might be exclusively responsible for cristae morphology changes, but ion fluxes across CM and resulting osmotic forces might be also involved. Inevitably, cristae ultramorphology should reflect also mitochondrial redox homeostasis, but details are unknown. Disordered cristae typically reflect higher superoxide formation. Future Directions: To link redox homeostasis to cristae ultramorphology and define markers, recent progress will help in uncovering mechanisms involved in proton-coupled electron transfer via the respiratory chain and in regulation of cristae architecture, leading to structural determination of superoxide formation sites and cristae ultramorphology changes in diseases. Antioxid. Redox Signal. 39, 635-683.
Collapse
Affiliation(s)
- Petr Ježek
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Jabůrek
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Blanka Holendová
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Engstová
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrea Dlasková
- Department No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| |
Collapse
|
3
|
Koone J, Simmang M, Saenger DL, Hunsicker-Wang LM, Shaw BF. Charge Regulation in a Rieske Proton Pump Pinpoints Zero, One, and Two Proton-Coupled Electron Transfer. J Am Chem Soc 2023; 145:16488-16497. [PMID: 37486967 PMCID: PMC10402712 DOI: 10.1021/jacs.3c03006] [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: 03/22/2023] [Indexed: 07/26/2023]
Abstract
The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZET) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZET can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from Thermus thermophilus (truncTtRp) and made 120 electrostatic measurements of ΔZET across pH. Across pH 5-10, truncTtRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncTtRp became more negative at pH 6.0 by one unit (ΔZET = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZET = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZET = +1.37 ± 0.60), consistent with 2PCET. These ΔZET values are attributed to protonation of H154 and H134. Across pH, redox potentials of TtRp (measured previously) correlated with protonation energies of H154 and H134 and ΔZET for truncTtRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.
Collapse
Affiliation(s)
- Jordan
C. Koone
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Mikaela Simmang
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Devin L. Saenger
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | | | - Bryan F. Shaw
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| |
Collapse
|
4
|
Abstract
We present a brief review of the mitochondrial respiratory chain with emphasis on complexes I, III and IV, which contribute to the generation of protonmotive force across the inner mitochondrial membrane, and drive the synthesis of ATP by the process called oxidative phosphorylation. The basic structural and functional details of these complexes are discussed. In addition, we briefly review the information on the so-called supercomplexes, aggregates of complexes I-IV, and summarize basic physiological aspects of cell respiration.
Collapse
Affiliation(s)
- Mårten Wikström
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland.
| | - Cristina Pecorilla
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
| | - Vivek Sharma
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland; Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
| |
Collapse
|
5
|
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: 5] [Impact Index Per Article: 2.5] [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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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: 20] [Impact Index Per Article: 5.0] [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.
Collapse
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:
| |
Collapse
|
8
|
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: 11] [Impact Index Per Article: 2.2] [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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
A modeling and simulation perspective on the mechanism and function of respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:510-523. [DOI: 10.1016/j.bbabio.2018.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
|
12
|
Pierce JD, Gupte R, Thimmesch A, Shen Q, Hiebert JB, Brooks WM, Clancy RL, Diaz FJ, Harris JL. Ubiquinol treatment for TBI in male rats: Effects on mitochondrial integrity, injury severity, and neurometabolism. J Neurosci Res 2018; 96:1080-1092. [DOI: 10.1002/jnr.24210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
Affiliation(s)
| | - Raeesa Gupte
- University of Kansas Medical Center, Hoglund Brain Institute
| | | | - Qiuhua Shen
- University of Kansas Medical Center, School of Nursing
| | | | - William M. Brooks
- University of Kansas Medical Center, Hoglund Brain Imaging Center, Department of Neurology
| | | | | | - Janna L. Harris
- University of Kansas Medical, Hoglund Brain Imaging Center, Department of Anatomy and Cell Biology
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|