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Vukalović J, Maljković JB, Blanco F, García G, Predojević B, Marinković BP. Absolute Differential Cross-Sections for Elastic Electron Scattering from Sevoflurane Molecule in the Energy Range from 50-300 eV. Int J Mol Sci 2021; 23:21. [PMID: 35008454 PMCID: PMC8744708 DOI: 10.3390/ijms23010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/04/2022] Open
Abstract
We report the results of the measurements and calculations of the absolute differential elastic electron scattering cross-sections (DCSs) from sevoflurane molecule (C4H3F7O). The experimental absolute DCSs for elastic electron scattering were obtained for the incident electron energies from 50 eV to 300 eV, and for scattering angles from 25° to 125° using a crossed electron/target beams setup and the relative flow technique for calibration to the absolute scale. For the calculations, we have used the IAM-SCAR+I method (independent atom model (IAM) applying the screened additivity rule (SCAR) with interference terms included (I)). The molecular cross-sections were obtained from the atomic data by using the SCAR procedure, incorporating interference term corrections, by summing all the relevant atomic amplitudes, including the phase coefficients. In this approach, we obtain the molecular differential scattering cross-section (DCS), which, integrated over the scattered electron angular range, gives the integral scattering cross-section (ICS). Calculated cross-sections agree very well with experimental results, in the whole energy and angular range.
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Affiliation(s)
- Jelena Vukalović
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia; (J.V.); (J.B.M.)
- Faculty of Science, University of Banja Luka, Mladena Stojanovića 2, 78000 Banja Luka, Republic of Srpska, Bosnia and Herzegovina;
| | - Jelena B. Maljković
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia; (J.V.); (J.B.M.)
| | - Francisco Blanco
- Departamento de Estructura de la Materia Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain;
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 113-bis, 28006 Madrid, Spain;
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Branko Predojević
- Faculty of Science, University of Banja Luka, Mladena Stojanovića 2, 78000 Banja Luka, Republic of Srpska, Bosnia and Herzegovina;
| | - Bratislav P. Marinković
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia; (J.V.); (J.B.M.)
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2
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Burdick RK, Villabona-Monsalve JP, Mashour GA, Goodson T. Modern Anesthetic Ethers Demonstrate Quantum Interactions with Entangled Photons. Sci Rep 2019; 9:11351. [PMID: 31383882 PMCID: PMC6683176 DOI: 10.1038/s41598-019-47651-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/08/2019] [Indexed: 11/09/2022] Open
Abstract
Despite decades of research, the mechanism of anesthetic-induced unconsciousness remains incompletely understood, with some advocating for a quantum mechanical basis. Despite associations between general anesthesia and changes in physical properties such as electron spin, there has been no empirical demonstration that general anesthetics are capable of functional quantum interactions. In this work, we studied the linear and non-linear optical properties of the halogenated ethers sevoflurane (SEVO) and isoflurane (ISO), using UV-Vis spectroscopy, time dependent-density functional theory (TD-DFT) calculations, classical two-photon spectroscopy, and entangled two-photon spectroscopy. We show that both of these halogenated ethers interact with pairs of 800 nm entangled photons while neither interact with 800 nm classical photons. By contrast, nonhalogenated diethyl ether does not interact with entangled photons. This is the first experimental evidence that halogenated anesthetics can directly undergo quantum interaction mechanisms, offering a new approach to understanding their physicochemical properties.
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Affiliation(s)
- Ryan K Burdick
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - George A Mashour
- Center for Consciousness Science, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, 48109-5048, USA.
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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3
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The lowest-lying electronic states of isoflurane and sevoflurane in the 5.0–10.8 eV energy range investigated by experimental and theoretical methods. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Lozano A, da Silva FF, Blanco F, Limão-Vieira P, García G. Total electron scattering cross section from sevoflurane by 1–300 eV energy electron impact. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Ren H, Li X, Qu Y, Li F. Theoretical investigation on H abstraction reaction mechanisms and rate constants of sevoflurane with the OH radical. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Arcario MJ, Mayne CG, Tajkhorshid E. Atomistic models of general anesthetics for use in in silico biological studies. J Phys Chem B 2014; 118:12075-86. [PMID: 25303275 PMCID: PMC4207551 DOI: 10.1021/jp502716m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
While small molecules have been used
to induce anesthesia in a
clinical setting for well over a century, a detailed understanding
of the molecular mechanism remains elusive. In this study, we utilize
ab initio calculations to develop a novel set of CHARMM-compatible
parameters for the ubiquitous modern anesthetics desflurane, isoflurane,
sevoflurane, and propofol for use in molecular dynamics (MD) simulations.
The parameters generated were rigorously tested against known experimental
physicochemical properties including dipole moment, density, enthalpy
of vaporization, and free energy of solvation. In all cases, the anesthetic
parameters were able to reproduce experimental measurements, signifying
the robustness and accuracy of the atomistic models developed. The
models were then used to study the interaction of anesthetics with
the membrane. Calculation of the potential of mean force for inserting
the molecules into a POPC bilayer revealed a distinct energetic minimum
of 4–5 kcal/mol relative to aqueous solution at the level of
the glycerol backbone in the membrane. The location of this minimum
within the membrane suggests that anesthetics partition to the membrane
prior to binding their ion channel targets, giving context to the
Meyer–Overton correlation. Moreover, MD simulations of these
drugs in the membrane give rise to computed membrane structural parameters,
including atomic distribution, deuterium order parameters, dipole
potential, and lateral stress profile, that indicate partitioning
of anesthetics into the membrane at the concentration range studied
here, which does not appear to perturb the structural integrity of
the lipid bilayer. These results signify that an indirect, membrane-mediated
mechanism of channel modulation is unlikely.
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Affiliation(s)
- Mark J Arcario
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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7
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The hydrogen abstraction reaction mechanism and rate constants from 200K to 2000K between sevoflurane and chlorine atom: A theoretical investigation. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Brath U, Lau K, Van Petegem F, Erdélyi M. Mapping the sevoflurane-binding sites of calmodulin. Pharmacol Res Perspect 2014; 2:5. [PMID: 25505574 PMCID: PMC4186402 DOI: 10.1002/prp2.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/06/2014] [Indexed: 11/21/2022] Open
Abstract
General anesthetics, with sevoflurane (SF) being the first choice inhalational anesthetic agent, provide reversible, broad depressor effects on the nervous system yet have a narrow margin of safety. As characterization of low-affinity binding interactions of volatile substances is exceptionally challenging with the existing methods, none of the numerous cellular targets proposed as chief protagonists in anesthesia could yet be confirmed. The recognition that most critical functions modulated by volatile anesthetics are under the control of intracellular Ca2+ concentration, which in turn is primarily regulated by calmodulin (CaM), motivated us for characterization of the SF–CaM interaction. Solution NMR (Nuclear Magnetic Resonance) spectroscopy was used to identify SF-binding sites using chemical shift displacement, NOESY and heteronuclear Overhauser enhancement spectroscopy (HOESY) experiments. Binding affinities were measured using ITC (isothermal titration calorimetry). SF binds to both lobes of (Ca2+)4-CaM with low mmol/L affinity whereas no interaction was observed in the absence of Ca2+. SF does not affect the calcium binding of CaM. The structurally closely related SF and isoflurane are shown to bind to the same clefts. The SF-binding clefts overlap with the binding sites of physiologically relevant ion channels and bioactive small molecules, but the binding affinity suggests it could only interfere with very weak CaM targets.
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Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg SE-412 96, Gothenburg, Sweden
| | - Kelvin Lau
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver, British Columbia, V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver, British Columbia, V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg SE-412 96, Gothenburg, Sweden
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9
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Mishra BK, Lily M, Chakrabartty AK, Bhattacharjee D, Deka RC, Chandra AK. Theoretical investigation of atmospheric chemistry of volatile anaesthetic sevoflurane: reactions with the OH radicals and atmospheric fate of the alkoxy radical (CF3)2CHOCHFO: thermal decomposition vs. oxidation. NEW J CHEM 2014. [DOI: 10.1039/c3nj01408h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction profile (kcal mol−1) for (CF3)2CHOCHFO radical at the M06-2X/6-311++G(d,p) level.
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Affiliation(s)
| | - Makroni Lily
- Department of Chemistry
- North-Eastern Hill University
- Shillong, India
| | | | | | | | - Asit K. Chandra
- Department of Chemistry
- North-Eastern Hill University
- Shillong, India
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10
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Singh HJ, Gour NK, Rao PK, Tiwari L. Theoretical investigation on the kinetics and branching ratio of the gas phase reaction of sevoflurane with Cl atom. J Mol Model 2013; 19:4815-22. [DOI: 10.1007/s00894-013-1977-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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11
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Craddock TJA, St. George M, Freedman H, Barakat KH, Damaraju S, Hameroff S, Tuszynski JA. Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia. PLoS One 2012; 7:e37251. [PMID: 22761654 PMCID: PMC3382613 DOI: 10.1371/journal.pone.0037251] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 04/19/2012] [Indexed: 11/19/2022] Open
Abstract
The cytoskeleton is essential to cell morphology, cargo trafficking, and cell division. As the neuronal cytoskeleton is extremely complex, it is no wonder that a startling number of neurodegenerative disorders (including but not limited to Alzheimer's disease, Parkinson's disease and Huntington's disease) share the common feature of a dysfunctional neuronal cytoskeleton. Recently, concern has been raised about a possible link between anesthesia, post-operative cognitive dysfunction, and the exacerbation of neurodegenerative disorders. Experimental investigations suggest that anesthetics bind to and affect cytoskeletal microtubules, and that anesthesia-related cognitive dysfunction involves microtubule instability, hyper-phosphorylation of the microtubule-associated protein tau, and tau separation from microtubules. However, exact mechanisms are yet to be identified. In this paper the interaction of anesthetics with the microtubule subunit protein tubulin is investigated using computer-modeling methods. Homology modeling, molecular dynamics simulations and surface geometry techniques were used to determine putative binding sites for volatile anesthetics on tubulin. This was followed by free energy based docking calculations for halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) on the tubulin body, and C-terminal regions for specific tubulin isotypes. Locations of the putative binding sites, halothane binding energies and the relation to cytoskeleton function are reported in this paper.
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Affiliation(s)
| | - Marc St. George
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Holly Freedman
- Center of Marine Sciences, Foundation for Science and Technology, University of Algarve, Campus Gambelas, Faro, Portugal
| | - Khaled H. Barakat
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Stuart Hameroff
- Departments of Anesthesiology and Psychology, Center for Consciousness Studies, The University of Arizona Health Sciences Center, Tucson, Arizona, United States of America
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
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12
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Lesarri A, Vega-Toribio A, Suenram RD, Brugh DJ, Grabow JU. The conformational landscape of the volatile anesthetic sevoflurane. Phys Chem Chem Phys 2010; 12:9624-31. [PMID: 20505891 DOI: 10.1039/c002123g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most of the volatile haloorganic compounds used as anesthetics exhibit a heavy-atom frame large enough to allow for conformational changes. Even in the absence of directed intermolecular interactions, only some or just one of the possible conformations might have an appreciable abundance. In this realm, the structure of the anesthetic haloether sevoflurane (CH(2)F-O-CH(CF(3))(2)) has been resolved using Fourier-transform microwave (FT-MW) spectroscopy in a supersonic-jet expansion. In isolated conditions sevoflurane adopts a single conformation characterized by a gauche fluoromethoxy group and a near-symmetric orientation of the isopropyl group with respect to the ether plane (cis H-C(ipr)-O-C(F)). Substitution and effective structures have been calculated from the rotational spectra of all (13)C and (18)O monosubstituted isotopic species observed in natural abundance. The electric dipole moment components were determined from additional Stark effect measurements. The experimental structures and rotational data are compared with those obtained from supporting ab initio predictions using MP2 calculations and the B3LYP hybrid functional.
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Affiliation(s)
- Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Calle Doctor Mergelina, s/n, E-47011 Valladolid, Spain.
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13
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Subbotina JO, Johannes J, Lev B, Noskov SY. Halothane solvation in water and organic solvents from molecular simulations with new polarizable potential function. J Phys Chem B 2010; 114:6401-8. [PMID: 20411978 DOI: 10.1021/jp908339j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The partitioning of a substrate from one phase into another is a complex process with widespread applications: from chemical technology to the pharmaceutical industry. One particularly well-known and well-studied example is 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) trafficking through the lipid bilayer. Halothane is a model volatile anesthetic known to impact functions of model lipid bilayers, altering the structure and thickness upon its partitioning from the bulk phase. A number of theoretical and experimental investigations suggest the importance of electronic polarizability, determining a preference for halothane to partition in the interfacial systems as in lipid bilayers or binary solvents. The recently published protocol for the development of polarizable force fields based on the classical Drude model has provided fresh impetus to efforts directed at understanding the molecular principles governing complex thermodynamics of the hydrophobic hydration. Here, molecular simulations were combined with free energy simulations to study solvation of halothane in polarizable water and methanol. The absolute free energy of halothane solvation in different solvents (water, methanol, and n-hexane) has been evaluated for additive and polarizable models. It was found that both additive and polarizable models provide an adequate description of the halothane solvation in high-dielectric (polar) solvents such as water, but explicit accounting for electronic polarization is imperative for a correct description of the solvation thermodynamics in nonpolar systems. To study halothane dynamics in binary mixtures, all-atom molecular dynamics (MD) simulations for halothane-methanol mixtures in a wide range of concentrations were performed alongside an analysis of structural organization, dynamics, and thermodynamic properties to dissect the molecular determinants of the halothane solvation in polar and amphiphilic liquids such as methanol. Additionally, a theoretical test of the hypothesis on the weak hydrogen bonding of halothane and methanol in the condensed phase is provided, which was presented on the basis of spectroscopic analysis of the C-H vibrations in different gas-phase complexes. The simulations performed in the condensed phase suggest that hydrophobic interactions between halothane and methanol play a dominant role in preferential solvation.
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Affiliation(s)
- Julia O Subbotina
- Institute for BioComplexity and Informatics and Department for Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada T2N 1N4
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14
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Liu LT, Willenbring D, Xu Y, Tang P. General anesthetic binding to neuronal alpha4beta2 nicotinic acetylcholine receptor and its effects on global dynamics. J Phys Chem B 2009; 113:12581-9. [PMID: 19697903 DOI: 10.1021/jp9039513] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The neuronal alpha4beta2 nicotinic acetylcholine receptor (nAChR) is a target for general anesthetics. Currently available experimental structural information is inadequate to understand where anesthetics bind and how they modulate the receptor motions essential to function. Using our published open-channel structure model of alpha4beta2 nAChR, we identified and evaluated six amphiphilic interaction sites for the volatile anesthetic halothane via flexible ligand docking and subsequent 20-ns molecular dynamics simulations. Halothane binding energies ranged from -6.8 to -2.4 kcal/mol. The primary binding sites were located at the interface of extracellular and transmembrane domains, where halothane perturbed conformations of, and widened the gap among, the Cys loop, the beta1-beta2 loop, and the TM2-TM3 linker. The halothane with the highest binding affinity at the interface between the alpha4 and beta2 subunits altered interactions between the protein and nearby lipids by competing for hydrogen bonds. Gaussian network model analyses of the alpha4beta2 nAChR structures at the end of 20-ns simulations in the absence or presence of halothane revealed profound changes in protein residue mobility. The concerted motions critical to protein function were also perturbed considerably. Halothane's effect on protein dynamics was not confined to the residues adjacent to the binding sites, indicating an action on a more global scale.
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Affiliation(s)
- Lu Tian Liu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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15
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Olejniczak A, Katrusiak A, Metrangolo P, Resnati G. Molecular association in 2-bromo-2-chloro-1,1,1-trifluoroethane (Halothane). J Fluor Chem 2009. [DOI: 10.1016/j.jfluchem.2008.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Streiff JH, Jones KA. Volatile anesthetic binding to proteins is influenced by solvent and aliphatic residues. J Chem Inf Model 2008; 48:2066-73. [PMID: 18808106 DOI: 10.1021/ci800206a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The main objective of this work was to characterize VA binding sites in multiple anesthetic target proteins. A computational algorithm was used to quantify the solvent exclusion and aliphatic character of amphiphilic pockets in the structures of VA binding proteins. VA binding sites in the protein structures were defined as the pockets with solvent exclusion and aliphatic character that exceeded minimum values observed in the VA binding sites of serum albumin, firefly luciferase, and apoferritin. We found that the structures of VA binding proteins are enriched in these pockets and that the predicted binding sites were consistent with experimental determined binding locations in several proteins. Autodock3 was used to dock the simulated molecules of 1,1,1,2,2-pentafluoroethane, difluoromethyl 1,1,1,2-tetrafluoroethyl ether, and sevoflurane and the isomers of halothane and isoflurane into these potential binding sites. We found that the binding of the various VA molecules to the amphiphilic pockets is driven primarily by VDW interactions and to a lesser extent by weak hydrogen bonding and electrostatic interactions. In addition, the trend in Delta G binding values follows the Meyer-Overton rule. These results suggest that VA potencies are related to the VDW interactions between the VA ligand and protein target. It is likely that VA bind to sites with a high degree of solvent exclusion and aliphatic character because aliphatic residues provide favorable VDW contacts and weak hydrogen bond donors. Water molecules occupying these sites maintain pocket integrity, associate with the VA ligand, and diminish the unfavorable solvation enthalpy of the VA. Water molecules displaced into the bulk by the VA ligand may provide an additional favorable enthalpic contribution to VA binding. Anesthesia is a component of many health related procedures, the outcomes of which could be improved with a better understanding of the molecular targets and mechanisms of anesthetic action.
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Affiliation(s)
- John H Streiff
- Department of Anesthesiology, University of Alabama at Birmingham, 901 19th Street South, Birmingham, AL 35294-1150, USA.
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17
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Four-alpha-helix bundle with designed anesthetic binding pockets. Part II: halothane effects on structure and dynamics. Biophys J 2008; 94:4464-72. [PMID: 18310239 DOI: 10.1529/biophysj.107.117853] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As a model of the protein targets for volatile anesthetics, the dimeric four-alpha-helix bundle, (Aalpha(2)-L1M/L38M)(2), was designed to contain a long hydrophobic core, enclosed by four amphipathic alpha-helices, for specific anesthetic binding. The structural and dynamical analyses of (Aalpha(2)-L1M/L38M)(2) in the absence of anesthetics (another study) showed a highly dynamic antiparallel dimer with an asymmetric arrangement of the four helices and a lateral accessing pathway from the aqueous phase to the hydrophobic core. In this study, we determined the high-resolution NMR structure of (Aalpha(2)-L1M/L38M)(2) in the presence of halothane, a clinically used volatile anesthetic. The high-solution NMR structure, with a backbone root mean-square deviation of 1.72 A (2JST), and the NMR binding measurements revealed that the primary halothane binding site is located between two side-chains of W15 from each monomer, different from the initially designed anesthetic binding sites. Hydrophobic interactions with residues A44 and L18 also contribute to stabilizing the bound halothane. Whereas halothane produces minor changes in the monomer structure, the quaternary arrangement of the dimer is shifted by about half a helical turn and twists relative to each other, which leads to the closure of the lateral access pathway to the hydrophobic core. Quantitative dynamics analyses, including Modelfree analysis of the relaxation data and the Carr-Purcell-Meiboom-Gill transverse relaxation dispersion measurements, suggest that the most profound anesthetic effect is the suppression of the conformational exchange both near and remote from the binding site. Our results revealed a novel mechanism of an induced fit between anesthetic molecule and its protein target, with the direct consequence of protein dynamics changing on a global rather than a local scale. This mechanism may be universal to anesthetic action on neuronal proteins.
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18
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Szarecka A, Xu Y, Tang P. Dynamics of firefly luciferase inhibition by general anesthetics: Gaussian and anisotropic network analyses. Biophys J 2007; 93:1895-905. [PMID: 17513367 PMCID: PMC1959537 DOI: 10.1529/biophysj.106.102780] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The new crystal structures of the product-bound firefly luciferase combined with the previously determined substrate-free structures allow for a detailed analysis of the dynamics basis for the luciferase enzymatic activities. Using the Gaussian network model and the anisotropic network model, we show here that the superposition of the three slowest anisotropic network model modes, consisting of the bending, rotating, and rocking motions of the C-domain, accounts for large rearrangement of domains from the substrate-free (open) to product-bound (closed) conformation and thus constitutes a critical component of the enzyme's functions. The analysis also offers a unique platform to reexamine the molecular mechanism of the anesthetic inhibition of the firefly luciferase. Through perturbing the protein backbone network by introducing additional nodes to represent anesthetics, we found that the presence of two representative anesthetics, halothane and n-decanol, in different regions of luciferase had distinctively different effects on the protein's global motion. Only at the interface of the C- and N-domains did the anesthetics cause the most profound reduction in the overall flexibility of the C-domain and the concomitant increase in the flexibility of the loop, where the substitution of a conserved lysine residue was found experimentally to lead to >2-3 orders of magnitude reduction in activity. These anesthetic-induced dynamics changes can alter the normal function of the protein, appearing as an epiphenomenon of an "inhibition". The implication of the study is that a leading element for general anesthetic action on proteins is to disrupt the modes of motion essential to protein functions.
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Affiliation(s)
- Agnieszka Szarecka
- Departments of Anesthesiology, Pharmacology, and Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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19
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Trogdon G, Murray JS, Concha MC, Politzer P. Molecular surface electrostatic potentials and anesthetic activity. J Mol Model 2006; 13:313-8. [PMID: 17024409 DOI: 10.1007/s00894-006-0145-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2005] [Revised: 07/31/2006] [Indexed: 10/24/2022]
Abstract
General anesthetics apparently act through weak, noncovalent and reversible interactions with certain sites in appropriate brain proteins. As a means of gaining insight into the factors underlying anesthetic potency, we have analyzed the computed electrostatic potentials V (S)(r) on the surfaces of 20 molecules with activities that vary between zero and high. Our results are fully consistent with, and help to interpret, what has been observed experimentally. We find that an intermediate level of internal charge separation is required; this is measured by Pi, the average absolute deviation of V (S)(r), and the approximate window is 7 < Pi < 13 kcal mol(-1). This fits in well with the fact that anesthetics need to be lipid soluble, but also to have some degree of hydrophilicity. We further show that polyhalogenated alkanes and ethers, which include the most powerful known anesthetics, have strong positive potentials, V (S,max), associated with their hydrogens, chlorines and bromines (but not fluorines). These positive sites may impede the functioning of key brain proteins, for example by disrupting their normal hydrogen-bond patterns. It has indeed been recognized for some time that the most active polyhalogenated alkanes and ethers contain hydrogens usually in combination with chlorines and/or bromines.
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Affiliation(s)
- Gavin Trogdon
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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Macięga E, Makulski W, Jackowski K, Blicharska B. Multinuclear NMR studies of gaseous and liquid sevoflurane. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.09.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yonkunas MJ, Xu Y, Tang P. Anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations. Biophys J 2005; 89:2350-6. [PMID: 16040747 PMCID: PMC1366735 DOI: 10.1529/biophysj.105.063396] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nature and the sites of interactions between anesthetic halothane and homodimeric Delta5-3-ketosteroid isomerase (KSI) are characterized by flexible ligand docking and confirmed by 1H-15N NMR. The dynamics consequence of halothane interaction and the implication of the dynamic changes to KSI function are studied by multiple 5-ns molecular dynamics simulations in the presence and absence of halothane. Both docking and MD simulations show that halothane prefer the amphiphilic dimeric interface to the hydrophobic active site of KSI. Halothane occupancy at the dimer interface disrupted the intersubunit hydrogen bonding formed either directly through side chains of polar residues or indirectly through the mediation of the interfacial water molecules. Moreover, in the presence of halothane, the exchange rate of the bound waters with bulk water was increased. Halothane perturbation to the dimer interface affected the overall flexibility of the active site. This action is likely to contribute to the halothane-induced reduction of the KSI activity. The allosteric halothane modulation of the dynamics-function relationship of KSI without direct competition at the enzymatic active sites may be generalized to offer a unifying explanation of anesthetic action on a diverse range of multidomain neuronal proteins that are potentially relevant to clinical general anesthesia.
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Affiliation(s)
- Michael J Yonkunas
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Liu R, Loll PJ, Eckenhoff RG. Structural basis for high‐affinity volatile anesthetic binding in a natural 4‐helix bundle protein. FASEB J 2005; 19:567-76. [PMID: 15791007 DOI: 10.1096/fj.04-3171com] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Physiologic sites for inhaled anesthetics are presumed to be cavities within transmembrane 4-alpha-helix bundles of neurotransmitter receptors, but confirmation of binding and structural detail of such sites remains elusive. To provide such detail, we screened soluble proteins containing this structural motif, and found only one that exhibited evidence of strong anesthetic binding. Ferritin is a 24-mer of 4-alpha-helix bundles; both halothane and isoflurane bind with K(A) values of approximately 10(5) M(-1), higher than any previously reported inhaled anesthetic-protein interaction. The crystal structures of the halothane/apoferritin and isoflurane/apoferritin complexes were determined at 1.75 A resolution, revealing a common anesthetic binding pocket within an interhelical dimerization interface. The high affinity is explained by several weak polar contacts and an optimal host/guest packing relationship. Neither the acidic protons nor ether oxygen of the anesthetics contribute to the binding interaction. Compared with unliganded apoferritin, the anesthetic produced no detectable alteration of structure or B factors. The remarkably high affinity of the anesthetic/apoferritin complex implies greater selectivity of protein sites than previously thought, and suggests that direct protein actions may underlie effects at lower than surgical levels of anesthetic, including loss of awareness.
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Affiliation(s)
- Renyu Liu
- Department of Anesthesia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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23
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Saladino AC, Tang P. Optimization of Structures and LJ Parameters of 1-Chloro-1,2,2-trifluorocyclobutane and 1,2-Dichlorohexafluorocyclobutane. J Phys Chem A 2004. [DOI: 10.1021/jp046662i] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander C. Saladino
- Department of Anesthesiology and Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Pei Tang
- Department of Anesthesiology and Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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Liu Z, Xu Y, Saladino AC, Wymore T, Tang P. Parametrization of 2-Bromo-2-Chloro-1,1,1-Trifluoroethane (Halothane) and Hexafluoroethane for Nonbonded Interactions. J Phys Chem A 2004. [DOI: 10.1021/jp0368482] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhanwu Liu
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Yan Xu
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Alexander C. Saladino
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Troy Wymore
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Pei Tang
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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Tang P, Xu Y. Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: the implication of molecular mechanisms of general anesthesia. Proc Natl Acad Sci U S A 2002; 99:16035-40. [PMID: 12438684 PMCID: PMC138560 DOI: 10.1073/pnas.252522299] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interactions of volatile anesthetics with the central nervous system are characterized by low yet specific binding affinities. Although neurotransmitter-gated ion channels are considered the primary anesthetic targets, the mechanism of action at the molecular level remains elusive. We consider here the theoretical implications of channel dynamics on anesthetic action in a simplified membrane-channel system. Large-scale 2.2-ns all-atom molecular dynamics simulations were performed to study the effects of halothane, a clinical anesthetic, on a gramicidin A (gA) channel in a fully hydrated dimyristoyl phosphatidylcholine membrane. In agreement with experimental results, anesthetics preferentially target the anchoring residues at the channel-lipid-water interface. Although the anesthetic effect on channel structure is minimal, the presence of halothane profoundly affects channel dynamics. For 2.2-ns simulation, the rms fluctuation of gA backbone in the lipid core increases from approximately equal 1 A in the absence of anesthetics to approximately equal 1.5 A in the presence of halothane. Autocorrelation analysis reveals that halothane (i) has no effect on the subpicosecond librational motion, (ii) prolongs the backbone autocorrelation time in the 10- to 100-ps time scale, and (iii) significantly decreases the asymptotic values of generalized order parameter and correlation time of nanosecond motions for the inner but not the outer residues. The simulation results discount the viewpoint of a structure-function paradigm that overrates the importance of structural fitting between general anesthetics and yet-unidentified hydrophobic protein pockets. Instead, the results underscore the global, as opposed to local, effects of anesthetics on protein dynamics as the underlying mechanisms for the action of general anesthetics and possibly of other low-affinity drugs.
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Affiliation(s)
- Pei Tang
- Departments of Anesthesiology and Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Liu R, Pidikiti R, Ha CE, Petersen CE, Bhagavan NV, Eckenhoff RG. The role of electrostatic interactions in human serum albumin binding and stabilization by halothane. J Biol Chem 2002; 277:36373-9. [PMID: 12118010 DOI: 10.1074/jbc.m205479200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Electrostatic interactions have been proposed as a potentially important force for anesthetics and protein binding but have not yet been tested directly. In the present study, we used wild-type human serum albumin (HSA) and specific site-directed mutants as a native protein model to investigate the role of electrostatic interactions in halothane binding. Structural geometry analysis of the HSA-halothane complex predicted an absence of significant electrostatic interactions, and direct binding (tryptophan fluorescence and zonal elution chromatography) and stability experiments (hydrogen exchange) confirmed that loss of charge in the binding sites, by charged to uncharged mutations and by changing ionic strength of the buffer, generally increased both regional (tryptophan region) and global halothane/HSA affinity. The results indicate that electrostatic interactions (full charges) either do not contribute or diminish halothane binding to HSA, leaving only the more general hydrophobic and van der Waals forces as the major contributors to the binding interaction.
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Affiliation(s)
- Renyu Liu
- Department of Anesthesia, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, USA
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Eckenhoff RG, Knoll FJ, Greenblatt EP, Dailey WP. Halogenated diazirines as photolabel mimics of the inhaled haloalkane anesthetics. J Med Chem 2002; 45:1879-86. [PMID: 11960499 DOI: 10.1021/jm0104926] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The inhaled anesthetics are low affinity volatile compounds whose mechanism of action remains unclear, in part due to the difficulty of determining their binding targets. Photolabeling may help resolve this difficulty, and thus we have synthesized six compounds (four previously unreported) with structural and physical similarity to halothane (1-bromo-1-chloro-2,2,2-trifluoroethane), a commonly used clinical anesthetic. These compounds incorporate either a diazo, diazirine, or azido group to provide photolability in the long-UV range and to provide a highly reactive photolysis product. While several of the compounds have immobilizing activity in tadpoles, it is complicated by either toxicity or very low potency. One compound however, a halogenated three-carbon diazirine 4, is a potent anesthetic, is apparently nontoxic, potentiates GABA(A) Cl(-) currents, and stabilizes serum albumin, all of which are features of halothane. When tagged with radioactivity, this compound should serve as a reasonable probe of haloalkane anesthetic binding targets and sites.
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Affiliation(s)
- Roderic G Eckenhoff
- Department of Anesthesia, University of Pennsylvania Health System, 3400 Spruce Street, Philadelphia, Pennsylvania 19104-4283, USA.
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