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He W, Yang H, Li Y, Cui Y, Wei L, Xu T, Li Y, Zhang M. Identifying the toxic mechanisms of emerging electronic contaminations liquid crystal monomers and the construction of a priority control list for graded control. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175398. [PMID: 39128516 DOI: 10.1016/j.scitotenv.2024.175398] [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: 07/15/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Liquid crystal monomers (LCMs) are identified as emerging organic contaminations with largely unexplored health impacts. To elucidate their toxic mechanisms, support the establishment of environmental discharge and management standards, and promote effective LCMs control, this study constructs a database covering 20,545 potential targets of 1431 LCMs, highlighting 9 key toxic target proteins that disrupt the nervous system and metabolic functions. GO and KEGG pathway analysis suggests LCMs severely affect nervous system, linked to neurodegenerative diseases and mental health disorders, with toxicity variations driven by electronegativity and structural complexity of LCM terminal groups. To achieve tiered control of LCMs, construct toxicity risk control lists for 9 key toxic target proteins, suitable for the graded control of LCMs, management recommendations are provided based on toxicity levels. These lists were validated for reliability and offer reliable toxicity predictions for LCMs. SHAP analysis points to electronic properties, molecular shape, and structural characteristics of LCMs as primary health impact factors. As the first study integrating machine learning with computational toxicology to outline LCMs health impacts, it aims to enhance public understanding of LCM toxicity risks and support the development of environmental standards, effective management of LCM production and emissions, and reduction of public exposure risks.
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Affiliation(s)
- Wei He
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Hao Yang
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Yunxiang Li
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Yuhan Cui
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Luanxiao Wei
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Tingzhi Xu
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China.
| | - Yu Li
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing, China
| | - Meng Zhang
- College of Environmental Sciences and Engineering, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; The Key Laboratory of Water and Sediment Sciences, Ministry of Education, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100871, China.
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2
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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3
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He J, Dmochowski IJ. Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme. Biochemistry 2023; 62:1659-1669. [PMID: 37192381 PMCID: PMC10821772 DOI: 10.1021/acs.biochem.3c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe-protein interactions at the molecular level and inspire further biochemical investigations with noble gases.
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Affiliation(s)
- Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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4
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de Oliveira GAP, Arruda HRS, de Andrade GC, Silva JL. Evolutionary Role of Water-Accessible Cavities in Src Homology 2 (SH2) Domains. J Phys Chem B 2022; 126:8689-8698. [PMID: 36281877 DOI: 10.1021/acs.jpcb.2c05409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein excited states are fundamental in the understanding of biological function, despite the fact they are hardly observed using traditional biophysical methodologies. Pressure perturbation coupled with nuclear magnetic resonance (NMR) spectroscopy is a powerful physicochemical tool to glance at these low-populated high-energy states on a residue-by-residue basis and underpin mechanistic insights into protein functionalities. Here we performed pressure titrations using NMR spectroscopy and relaxation dispersion experiments to identify the low-lying energetic states of the c-Abl SH2 domain. By showing that the SH2 excited state contains a hydrated hydrophobic cavity, fast-exchange motions, and highly conserved residues facing the water-accessible hole, we discuss the implications of water-protein interactions in SH2 modules achieving high-affinity binding and promiscuous phospho-Tyr peptide recognition.
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Affiliation(s)
- Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Hiam R S Arruda
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Guilherme C de Andrade
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
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5
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Abiko LA, Dias Teixeira R, Engilberge S, Grahl A, Mühlethaler T, Sharpe T, Grzesiek S. Filling of a water-free void explains the allosteric regulation of the β 1-adrenergic receptor by cholesterol. Nat Chem 2022; 14:1133-1141. [PMID: 35953642 DOI: 10.1038/s41557-022-01009-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
Recent high-pressure NMR results indicate that the preactive conformation of the β1-adrenergic receptor (β1AR) harbours completely empty cavities of ~100 Å3 volume, which disappear in the active conformation of the receptor. Here we have localized these cavities using X-ray crystallography of xenon-derivatized β1AR crystals. One of the cavities is in direct contact with the cholesterol-binding pocket. Solution NMR shows that addition of the cholesterol analogue cholesteryl hemisuccinate impedes the formation of the active conformation of detergent-solubilized β1AR by blocking conserved G protein-coupled receptor microswitches, concomitant with an affinity reduction of both isoprenaline and G protein-mimicking nanobody Nb80 for β1AR detected by isothermal titration calorimetry. This wedge-like action explains the function of cholesterol as a negative allosteric modulator of β1AR. A detailed understanding of G protein-coupled receptor regulation by cholesterol by filling of a dry void and the easy scouting for such voids by xenon may provide new routes for the development of allosteric drugs.
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Affiliation(s)
| | | | - Sylvain Engilberge
- Paul Scherrer Institut, Villigen, Switzerland.,European Synchrotron Radiation Facility, Grenoble, France
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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6
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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7
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Wiebelhaus N, Singh N, Zhang P, Craig SL, Beratan DN, Fitzgerald MC. Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability. J Am Chem Soc 2022; 144:3925-3938. [PMID: 35213151 PMCID: PMC10166008 DOI: 10.1021/jacs.1c11900] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low-throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein target discovery. Here, we report the application of stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5000 methionine-containing peptides and over 5000 semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins, respectively, in the yeast proteome, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified are tied to previously established modes of action related to xenon's anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions. The sample preparation protocols and analytical methodologies developed here for xenon are also generally applicable to the discovery of a wide range of other protein-gas interactions in complex biological mixtures, such as cell lysates.
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Affiliation(s)
- Nancy Wiebelhaus
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Stephen L. Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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8
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Hammami I, Farjot G, Naveau M, Rousseaud A, Prangé T, Katz I, Colloc'h N. Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families. J Chem Inf Model 2022; 62:1318-1327. [PMID: 35179902 DOI: 10.1021/acs.jcim.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Argon belongs to the group of chemically inert noble gases, which display a remarkable spectrum of clinically useful biological properties. In an attempt to better understand noble gases, notably argon's mechanism of action, we mined a massive noble gas modeling database which lists all possible noble gas binding sites in the proteins from the Protein Data Bank. We developed a method of analysis to identify among all predicted noble gas binding sites the potentially relevant ones within protein families which are likely to be modulated by Ar. Our method consists in determining within structurally aligned proteins the conserved binding sites whose shape, localization, hydrophobicity, and binding energies are to be further examined. This method was applied to the analysis of two protein families where crystallographic noble gas binding sites have been experimentally determined. Our findings indicate that among the most conserved binding sites, either the most hydrophobic one and/or the site which has the best binding energy corresponds to the crystallographic noble gas binding sites with the best occupancies, therefore the best affinity for the gas. This method will allow us to predict relevant noble gas binding sites that have potential pharmacological interest and thus potential Ar targets that will be prioritized for further studies including in vitro validation.
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Affiliation(s)
- Islem Hammami
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France.,Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Géraldine Farjot
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Mikaël Naveau
- UAR 3408 US 50 CNRS INSERM Université de Caen-Normandie, GIP Cyceron, 14074 Caen, France
| | - Audrey Rousseaud
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Thierry Prangé
- CiTCoM UMR 8038 CNRS Université de Paris, Faculté de Pharmacie, 75006 Paris, France
| | - Ira Katz
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Nathalie Colloc'h
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France
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9
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Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
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10
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Schneider FI, Krieg SM, Lindauer U, Stoffel M, Ryang YM. Neuroprotective Effects of the Inert Gas Argon on Experimental Traumatic Brain Injury In Vivo with the Controlled Cortical Impact Model in Mice. BIOLOGY 2022; 11:biology11020158. [PMID: 35205025 PMCID: PMC8869506 DOI: 10.3390/biology11020158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Traumatic brain injuries remain one of the leading causes of death in the western world and developing countries. There is an urgent need for causal therapies for such injuries. The noble gas argon has already shown promising results in in-vitro models. The influence of argon on the extent of damage after a craniocerebral trauma will be investigated in this study, in vivo, in mice. After the trauma, the animals were examined for neurological impairments and their brains were removed to detect brain edema and microscopically detectable alterations. Abstract Argon has shown neuroprotective effects after traumatic brain injury (TBI) and cerebral ischemia in vitro and in focal cerebral ischemia in vivo. The purpose of this study is to show whether argon beneficially impacts brain contusion volume (BCV) as the primary outcome parameter, as well as secondary outcome parameters, such as brain edema, intracranial pressure (ICP), neurological outcome, and cerebral blood flow (CBF) in an in-vivo model. Subjects were randomly assigned to either argon treatment or room air. After applying controlled cortical impact (CCI) onto the dura with 8 m/s (displacement 1 mm, impact duration 150 ms), treatment was administered by a recovery chamber with 25%, 50%, or 75% argon and the rest being oxygen for 4 h after trauma. Two control groups received room air for 15 min and 24 h, respectively. Neurological testing and ICP measurements were performed 24 h after trauma, and brains were removed to measure secondary brain damage. The primary outcome parameter, BCV, and the secondary outcome parameter, brain edema, were not significantly reduced by argon treatment at any concentration. There was a highly significant decrease in ICP at 50% argon (p = 0.001), and significant neurological improvement (beamwalk missteps) at 25% and 50% argon (p = 0.01; p = 0.049 respectively) compared to control.
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Affiliation(s)
- Fritz I. Schneider
- Department of Neurosurgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany; (F.I.S.); (U.L.); (M.S.); (Y.-M.R.)
| | - Sandro M. Krieg
- Department of Neurosurgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany; (F.I.S.); (U.L.); (M.S.); (Y.-M.R.)
- Correspondence: ; Tel.: +49-89-4140-2151
| | - Ute Lindauer
- Department of Neurosurgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany; (F.I.S.); (U.L.); (M.S.); (Y.-M.R.)
- Department of Neurosurgery, Klinikum der RWTH Aachen, RWTH Aachen University, 52062 Aachen, Germany
| | - Michael Stoffel
- Department of Neurosurgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany; (F.I.S.); (U.L.); (M.S.); (Y.-M.R.)
- Department of Neurosurgery, Helios Kliniken, 47805 Krefeld, Germany
| | - Yu-Mi Ryang
- Department of Neurosurgery, Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany; (F.I.S.); (U.L.); (M.S.); (Y.-M.R.)
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Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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12
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Schuppe ER, Miles MC, Fuxjager MJ. Evolution of the androgen receptor: Perspectives from human health to dancing birds. Mol Cell Endocrinol 2020; 499:110577. [PMID: 31525432 DOI: 10.1016/j.mce.2019.110577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Androgenic hormones orchestrate the development and activation of diverse reproductive phenotypes across vertebrates. Although extensive work investigates how selection for these traits modifies individual elements of this signaling system (e.g., hormone or androgen receptor [AR] levels), we know less about natural variation in the AR sequence across vertebrates. Our knowledge of AR sequence mutations is largely limited to work in human patients or cell-lines, providing a framework to contextualize single mutations at the expense of evolutionary timescale. Here we unite both perspectives in a review that explores the functional significance of AR on a domain-by-domain basis, using existing knowledge to highlight how and why each region might evolve. We then examine AR sequence variation on different timescales by examining sequence variation in clades originating in the Cambrian (vertebrates; >500 mya) and Cretaceous (birds; >65 mya). In each case, we characterize how the receptor has changed over time and discuss which regions are most likely to evolve in response to selection. Overall, domains that are required for androgenic signaling to function (e.g., DNA- and ligand-binding) tend to be conserved. Meanwhile, areas that interface with co-regulatory molecules can exhibit notable variation even between closely related species. We propose that accumulating mutations in regulatory regions is one way that AR structure might act as a substrate for selection to guide the evolution of reproductive traits. By synthesizing literature across disciplines and highlighting the evolutionary potential of specific AR regions, we hope to inspire new avenues of integrative research into endocrine system evolution.
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Affiliation(s)
- Eric R Schuppe
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Meredith C Miles
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA
| | - Matthew J Fuxjager
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA.
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13
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Winkler DA, Warden AC, Prangé T, Colloc'h N, Thornton AW, Ramirez-Gil JF, Farjot G, Katz I. Massive in Silico Study of Noble Gas Binding to the Structural Proteome. J Chem Inf Model 2019; 59:4844-4854. [PMID: 31613613 DOI: 10.1021/acs.jcim.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas-protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas-protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop "atomic drugs" that can fully exploit their considerable and relatively unexplored potential in medicine.
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Affiliation(s)
- D A Winkler
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia.,Monash Institute of Pharmaceutical Sciences , Monash University , 392 Royal Parade , Parkville 3052 , Australia.,La Trobe Institute for Molecular Science , La Trobe University , Kingsbury Drive , Bundoora 3086 , Australia.,School of Pharmacy , University of Nottingham , Nottingham NG7 2QL , U.K
| | - A C Warden
- CSIRO Land and Water , Clunies Ross Street , Acton , New South Wales 2601 , Australia
| | - T Prangé
- CiTeCoM UMR 8038 CNRS University Paris Descartes , Paris 75006 , France
| | - N Colloc'h
- ISTCT UMR 6030 CNRS Université de Caen-Normandie CEA, CERVOxy Team, Centre Cyceron , Caen 14032 , France
| | - A W Thornton
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia
| | - J-F Ramirez-Gil
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - G Farjot
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - I Katz
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
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On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLoS Comput Biol 2019; 15:e1006665. [PMID: 30645590 PMCID: PMC6333327 DOI: 10.1371/journal.pcbi.1006665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023] Open
Abstract
Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450. Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry. In recent times, in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs. Even so, discovery of binding pathways of small molecules both at the primary binding site, as well as sites for allosteric control, is time consuming and often fortuitous. We provide here a framework within which critical conformational changes likely to occur during binding are quantified from statistical analysis of configurations of proteins in their apo, or inactive form, greatly simplifying identification of target residues. We illustrate this idea by analysing ligand binding pathways for three proteins T4- Lysozyme, P450 and Src kinase, which are active respectively in the immune system, metabolism and cancer.
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15
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Cavitation energies can outperform dispersion interactions. Nat Chem 2018; 10:1252-1257. [DOI: 10.1038/s41557-018-0146-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/24/2018] [Indexed: 01/07/2023]
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16
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Winkler DA, Katz I, Farjot G, Warden AC, Thornton AW. Decoding the Rich Biological Properties of Noble Gases: How Well Can We Predict Noble Gas Binding to Diverse Proteins? ChemMedChem 2018; 13:1931-1938. [PMID: 30003691 DOI: 10.1002/cmdc.201800434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/19/2022]
Abstract
The chemically inert noble gases display a surprisingly rich spectrum of useful biological properties. Relatively little is known about the molecular mechanisms behind these effects. It is clearly not feasible to conduct large numbers of pharmacological experiments on noble gases to identify activity. Computational studies of the binding of noble gases and proteins can address this paucity of information and provide insight into mechanisms of action. We used bespoke computational grid calculations to predict the positions of energy minima in the interactions of noble gases with diverse proteins. The method was validated by quantifying how well simulations could predict binding positions in 131 diverse protein X-ray structures containing 399 Xe and Kr atoms. We found excellent agreement between calculated and experimental binding positions of noble gases. 94 % of all crystallographic xenon atoms were within 1 Xe van der Waals (vdW) diameter of a predicted binding site, and 97 % lay within 2 vdW diameters. 100 % of crystallographic krypton atoms were within 1 Kr vdW diameter of a predicted binding site. We showed the feasibility of large-scale computational screening of all ≈60 000 unique structures in the Protein Data Bank. This will elucidate biochemical mechanisms by which these novel 'atomic drugs' elicit their valuable biochemical properties and identify new medical uses.
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Affiliation(s)
- David A Winkler
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
- Biochemistry and Genetics, La Trobe University, Kingsbury Drive, Bundoora, 3086, Australia
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052, Australia
| | - Ira Katz
- Early Drug Development, Air Liquide Santé International, Centre de Recherche Paris-Saclay, Jouy-en-Josas, France
- Department of Mechanical Engineering, Lafayette College, Easton, PA, USA
| | - Géraldine Farjot
- Early Drug Development, Air Liquide Santé International, Centre de Recherche Paris-Saclay, Jouy-en-Josas, France
| | - Andrew C Warden
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
| | - Aaron W Thornton
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
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Mondal J, Ahalawat N, Pandit S, Kay LE, Vallurupalli P. Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme. PLoS Comput Biol 2018; 14:e1006180. [PMID: 29775455 PMCID: PMC5979041 DOI: 10.1371/journal.pcbi.1006180] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/31/2018] [Accepted: 05/06/2018] [Indexed: 12/22/2022] Open
Abstract
Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition in a solvent-inaccessible cavity, contrary to the common perception of a single dominant pathway for ligand binding.
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Affiliation(s)
| | | | | | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children Program in Molecular Medicine, Toronto, Ontario, Canada
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18
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Kitahara R, Sakuraba S, Kameda T, Okuda S, Xue M, Mulder FAA. Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein Sci 2018; 27:769-779. [PMID: 29271012 DOI: 10.1002/pro.3371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/28/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022]
Abstract
The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O2 gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O2 in solvent to 8.9 mM, O2 -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O2 binding sites and their atomic coordinates from the 1/r6 distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O2 -accessible sites were identified in internal cavities: One site was consistent with the xenon-binding site in the protein in crystal, and the other site was established to be a novel ligand-binding site. MD simulations performed at 10 and 100 mM O2 revealed dioxygen ingress and egress as well as rotational and translational motions of O2 in the cavities. It is therefore suggested that conformational fluctuations within the ground-state ensemble transiently develop channels for O2 association with the internal protein cavities.
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Affiliation(s)
- Ryo Kitahara
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tomoshi Kameda
- Computational Omics Research Team, Artificial Intelligence Research Center, Advanced Industrial Science and Technology, Koto, Tokyo, 135-0064, Japan
| | - Sanshiro Okuda
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Mengjun Xue
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
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19
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Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prangé T. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure. Biophys J 2017; 113:2199-2206. [PMID: 29108649 DOI: 10.1016/j.bpj.2017.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 10/06/2017] [Indexed: 01/27/2023] Open
Abstract
Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie University, CERVOxy Team, Centre Cyceron, Caen, France.
| | - Philippe Carpentier
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, Grenoble, France; European Synchrotron Radiation Facility, Grenoble, France
| | - Laura C Montemiglio
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France
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Xenon for tunnelling analysis of the efflux pump component OprN. PLoS One 2017; 12:e0184045. [PMID: 28886086 PMCID: PMC5590881 DOI: 10.1371/journal.pone.0184045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.
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21
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Krimmer SG, Cramer J, Schiebel J, Heine A, Klebe G. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin. J Am Chem Soc 2017; 139:10419-10431. [DOI: 10.1021/jacs.7b05028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefan G. Krimmer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jonathan Cramer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Ulmer TF, Fragoulis A, Dohmeier H, Kroh A, Andert A, Stoppe C, Alizai H, Klink C, Coburn M, Neumann UP. Argon Delays Initiation of Liver Regeneration after Partial Hepatectomy in Rats. Eur Surg Res 2017; 58:204-215. [PMID: 28433997 DOI: 10.1159/000466690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/28/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND The liver can heal up to restitutio ad integrum following damage resulting from various causes. Different studies have demonstrated the protective effect of argon on various cells and organs. To the best of our knowledge, the organ-protective effects of the noble gas argon on the liver have not yet been investigated, although argon appears to influence signal paths that are well-known mediators of liver regeneration. We hypothesized that argon inhalation prior to partial hepatectomy (70%) has a positive effect on the initiation of liver regeneration in rats. METHODS Partial hepatectomy (70%) with or without inhaled argon (50 vol%) was performed for 1 h. Liver tissue was harvested after 3, 36, and 96 h to analyze the mRNA and protein expression of hepatocyte growth factor (HGF), interleukin-6 (IL-6), tumor necrosis factor-α, and extracellular signal-regulated kinase 1/2. Histological tissue samples were prepared for immunohistochemistry (bromodeoxyuridine [BrdU], Ki-67, and TUNEL) and blood was analyzed regarding the effects of argon on liver function. Statistical analyses were performed using 1-way ANOVA followed by the post hoc Tukey-Kramer test. RESULTS After 3 h, the primary outcome parameter of hepatocyte proliferation was significantly reduced with argon 50 vol% inhalation in comparison to nitrogen inhalation (BrdU: 15.7 ± 9.7 vs. 7.7 ± 3.1 positive cells/1,000 hepatocytes, p = 0.013; Ki-67: 17.6 ± 13.3 vs. 4.7 ± 5.4 positive cells/1,000 hepatocytes, p = 0.006). This was most likely mediated by significant downregulation of HGF (after 3 h: 5.2 ± 3.2 vs. 2.3 ± 1.0 fold, p = 0.032; after 96 h: 2.1 ± 0.5 vs. 1.3 ± 0.3 fold, p = 0.029) and IL-6 (after 3 h: 43.7 ± 39.6 vs. 8.5 ± 9.2 fold, p = 0.032). Nevertheless, we could detect no significant effect on the weight of the residual liver, liver-body weight ratio, or liver blood test results after argon inhalation. CONCLUSION Impairment of liver regeneration was apparent after argon 50 vol% inhalation that was most probably mediated by downregulation of HGF and IL-6 in the initial phase. However, the present study was not adequately powered to prove that argon has detrimental effects on the liver. Further studies are needed to evaluate the effects of argon on livers with preexisting conditions as well as on ischemia-reperfusion models.
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Affiliation(s)
- Tom Florian Ulmer
- Department of General, Visceral, and Transplantation Surgery, University Hospital of RWTH Aachen, Aachen, Germany
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The Molecular Pathway of Argon-Mediated Neuroprotection. Int J Mol Sci 2016; 17:ijms17111816. [PMID: 27809248 PMCID: PMC5133817 DOI: 10.3390/ijms17111816] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022] Open
Abstract
The noble gas argon has attracted increasing attention in recent years, especially because of its neuroprotective properties. In a variety of models, ranging from oxygen-glucose deprivation in cell culture to complex models of mid-cerebral artery occlusion, subarachnoid hemorrhage or retinal ischemia-reperfusion injury in animals, argon administration after individual injury demonstrated favorable effects, particularly increased cell survival and even improved neuronal function. As an inert molecule, argon did not show signs of adverse effects in the in vitro and in vivo model used, while being comparably cheap and easy to apply. However, the molecular mechanism by which argon is able to exert its protective and beneficial characteristics remains unclear. Although there are many pieces missing to complete the signaling pathway throughout the cell, it is the aim of this review to summarize the known parts of the molecular pathways and to combine them to provide a clear insight into the cellular pathway, starting with the receptors that may be involved in mediating argons effects and ending with the translational response.
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25
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Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. PLoS One 2016; 11:e0149795. [PMID: 26910105 PMCID: PMC4765991 DOI: 10.1371/journal.pone.0149795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022] Open
Abstract
GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.
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Affiliation(s)
- Ludovic Sauguet
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Zeineb Fourati
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Thierry Prangé
- Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
- * E-mail:
| | - Nathalie Colloc'h
- CNRS, UMR 6301, ISTCT CERVOxy group, GIP Cyceron, Caen, France
- UNICAEN, Normandie Univ., UMR 6301 ISTCT, Caen, France
- CEA, DSV/I2BM, UMR 6301 ISTCT, Caen, France
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Shar PA, Tao W, Gao S, Huang C, Li B, Zhang W, Shahen M, Zheng C, Bai Y, Wang Y. Pred-binding: large-scale protein-ligand binding affinity prediction. J Enzyme Inhib Med Chem 2016; 31:1443-50. [PMID: 26888050 DOI: 10.3109/14756366.2016.1144594] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Drug target interactions (DTIs) are crucial in pharmacology and drug discovery. Presently, experimental determination of compound-protein interactions remains challenging because of funding investment and difficulties of purifying proteins. In this study, we proposed two in silico models based on support vector machine (SVM) and random forest (RF), using 1589 molecular descriptors and 1080 protein descriptors in 9948 ligand-protein pairs to predict DTIs that were quantified by Ki values. The cross-validation coefficient of determination of 0.6079 for SVM and 0.6267 for RF were obtained, respectively. In addition, the two-dimensional (2D) autocorrelation, topological charge indices and three-dimensional (3D)-MoRSE descriptors of compounds, the autocorrelation descriptors and the amphiphilic pseudo-amino acid composition of protein are found most important for Ki predictions. These models provide a new opportunity for the prediction of ligand-receptor interactions that will facilitate the target discovery and toxicity evaluation in drug development.
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Affiliation(s)
- Piar Ali Shar
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Weiyang Tao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Shuo Gao
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chao Huang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Bohui Li
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Wenjuan Zhang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Mohamed Shahen
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Chunli Zheng
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yaofei Bai
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
| | - Yonghua Wang
- a Bioinformatics Center, College of Life Sciences, Northwest A & F University , Yangling , Shaanxi , China
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Abstract
Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in 1H, 15N, and 13C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.
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Sappidi P, Natarajan U. Polyelectrolyte conformational transition in aqueous solvent mixture influenced by hydrophobic interactions and hydrogen bonding effects: PAA-water-ethanol. J Mol Graph Model 2015; 64:60-74. [PMID: 26803232 DOI: 10.1016/j.jmgm.2015.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/18/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulations of poly(acrylic acid) PAA chain in water-ethanol mixture were performed for un-ionized and ionized cases at different degree-of-ionization 0%, 80% and 100% of PAA chain by Na(+) counter-ions and co-solvent (ethanol) concentration in the range 0-90vol% ethanol. Aspects of structure and dynamics were investigated via atom pair correlation functions, number and relaxation of hydrogen bonds, nearest-neighbor coordination numbers, and dihedral angle distribution function for back-bone and side-groups of the chain. With increase in ethanol concentration, chain swelling is observed for un-ionized chain (f=0) and on the contrary chain shrinkage is observed for partially and fully ionized cases (i.e., f=0.8 and 1). For un-ionized PAA, with increase in ethanol fraction ϕeth the number of PAA-ethanol hydrogen bonds increases while PAA-water decreases. Increase in ϕeth leads to PAA chain expansion for un-ionized case and chain shrinkage for ionized case, in agreement with experimental observations on this system. For ionized-PAA case, chain shrinkage is found to be influenced by intermolecular hydrogen bonding with water as well as ethanol. The localization of ethanol molecules near the un-ionized PAA backbone at higher levels of ethanol is facilitated by a displacement of water molecules indicating presence of specific ethanol hydration shell, as confirmed by results of the RDF curves and coordination number calculations. This behavior, controlled by hydrogen bonding provides a significant contribution to such a conformational transition behavior of the polyelectrolyte chain. The interactions between counter-ions and charges on the PAA chain also influence chain collapse. The underlying origins of polyelectrolyte chain collapse in water-alcohol mixtures are brought out for the first time via explicit MD simulations by this study.
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Affiliation(s)
- Praveenkumar Sappidi
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai 600036, India
| | - Upendra Natarajan
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai 600036, India.
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29
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Maeno A, Sindhikara D, Hirata F, Otten R, Dahlquist FW, Yokoyama S, Akasaka K, Mulder FAA, Kitahara R. Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme. Biophys J 2015; 108:133-45. [PMID: 25564860 DOI: 10.1016/j.bpj.2014.11.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/02/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022] Open
Abstract
Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the (1)H/(13)C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. (13)C and (1)H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.
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Affiliation(s)
- Akihiro Maeno
- High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Kinokawa, Wakayama, Japan; RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Daniel Sindhikara
- College of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Fumio Hirata
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Renee Otten
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry and Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara California
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan; Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kazuyuki Akasaka
- High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Kinokawa, Wakayama, Japan; RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center iNANO, University of Aarhus, Aarhus C, Denmark
| | - Ryo Kitahara
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan; College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan.
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30
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Gabdulkhakov AG, Kljashtorny VG, Dontsova MV. Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515010083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Sappidi P, Natarajan U. Influence of hydrogen bonding on the structural transition of poly(methacrylic acid) chain in water–ethanol solution by molecular dynamics simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.992018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Herold KF, Sanford RL, Lee W, Schultz MF, Ingólfsson HI, Andersen OS, Hemmings HC. Volatile anesthetics inhibit sodium channels without altering bulk lipid bilayer properties. J Gen Physiol 2014; 144:545-60. [PMID: 25385786 PMCID: PMC4242807 DOI: 10.1085/jgp.201411172] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 10/08/2014] [Indexed: 01/05/2023] Open
Abstract
Although general anesthetics are clinically important and widely used, their molecular mechanisms of action remain poorly understood. Volatile anesthetics such as isoflurane (ISO) are thought to alter neuronal function by depressing excitatory and facilitating inhibitory neurotransmission through direct interactions with specific protein targets, including voltage-gated sodium channels (Na(v)). Many anesthetics alter lipid bilayer properties, suggesting that ion channel function might also be altered indirectly through effects on the lipid bilayer. We compared the effects of ISO and of a series of fluorobenzene (FB) model volatile anesthetics on Na(v) function and lipid bilayer properties. We examined the effects of these agents on Na(v) in neuronal cells using whole-cell electrophysiology, and on lipid bilayer properties using a gramicidin-based fluorescence assay, which is a functional assay for detecting changes in lipid bilayer properties sensed by a bilayer-spanning ion channel. At clinically relevant concentrations (defined by the minimum alveolar concentration), both the FBs and ISO produced prepulse-dependent inhibition of Na(v) and shifted the voltage dependence of inactivation toward more hyperpolarized potentials without affecting lipid bilayer properties, as sensed by gramicidin channels. Only at supra-anesthetic (toxic) concentrations did ISO alter lipid bilayer properties. These results suggest that clinically relevant concentrations of volatile anesthetics alter Na(v) function through direct interactions with the channel protein with little, if any, contribution from changes in bulk lipid bilayer properties. Our findings further suggest that changes in lipid bilayer properties are not involved in clinical anesthesia.
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Affiliation(s)
- Karl F Herold
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - R Lea Sanford
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - William Lee
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Margaret F Schultz
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Helgi I Ingólfsson
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Olaf S Andersen
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
| | - Hugh C Hemmings
- Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065 Department of Anesthesiology, Department of Physiology and Biophysics, and Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065
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33
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Paragi Vedanthi PP, Doble M. Inhibition of microsomal prostaglandin E synthase-1 by phenanthrene imidazoles: a QSAR study. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1290-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia. Anesthesiology 2014; 121:1018-27. [DOI: 10.1097/aln.0000000000000435] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Background:
The mechanisms by which general anesthetics, including xenon and nitrous oxide, act are only beginning to be discovered. However, structural approaches revealed weak but specific protein–gas interactions.
Methods:
To improve knowledge, we performed x-ray crystallography studies under xenon and nitrous oxide pressure in a series of 10 binding sites within four proteins.
Results:
Whatever the pressure, we show (1) hydrophobicity of the gas binding sites has a screening effect on xenon and nitrous oxide binding, with a threshold value of 83% beyond which and below which xenon and nitrous oxide, respectively, binds to their sites preferentially compared to each other; (2) xenon and nitrous oxide occupancies are significantly correlated respectively to the product and the ratio of hydrophobicity by volume, indicating that hydrophobicity and volume are binding parameters that complement and oppose each other’s effects; and (3) the ratio of occupancy of xenon to nitrous oxide is significantly correlated to hydrophobicity of their binding sites.
Conclusions:
These data demonstrate that xenon and nitrous oxide obey different binding mechanisms, a finding that argues against all unitary hypotheses of narcosis and anesthesia, and indicate that the Meyer–Overton rule of a high correlation between anesthetic potency and solubility in lipids of general anesthetics is often overinterpreted. This study provides evidence that the mechanisms of gas binding to proteins and therefore of general anesthesia should be considered as the result of a fully reversible interaction between a drug ligand and a receptor as this occurs in classical pharmacology.
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Argon: systematic review on neuro- and organoprotective properties of an "inert" gas. Int J Mol Sci 2014; 15:18175-96. [PMID: 25310646 PMCID: PMC4227210 DOI: 10.3390/ijms151018175] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/12/2014] [Accepted: 09/23/2014] [Indexed: 01/21/2023] Open
Abstract
Argon belongs to the group of noble gases, which are regarded as chemically inert. Astonishingly some of these gases exert biological properties and during the last decades more and more reports demonstrated neuroprotective and organoprotective effects. Recent studies predominately use in vivo or in vitro models for ischemic pathologies to investigate the effect of argon treatment. Promising data has been published concerning pathologies like cerebral ischemia, traumatic brain injury and hypoxic ischemic encephalopathy. However, models applied and administration of the therapeutic gas vary. Here we provide a systematic review to summarize the available data on argon's neuro- and organoprotective effects and discuss its possible mechanism of action. We aim to provide a summary to allow further studies with a more homogeneous setting to investigate possible clinical applications of argon.
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36
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Hosey CM, Broccatelli F, Benet LZ. Predicting when biliary excretion of parent drug is a major route of elimination in humans. AAPS JOURNAL 2014; 16:1085-96. [PMID: 25004821 DOI: 10.1208/s12248-014-9636-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/27/2014] [Indexed: 01/29/2023]
Abstract
Biliary excretion is an important route of elimination for many drugs, yet measuring the extent of biliary elimination is difficult, invasive, and variable. Biliary elimination has been quantified for few drugs with a limited number of subjects, who are often diseased patients. An accurate prediction of which drugs or new molecular entities are significantly eliminated in the bile may predict potential drug-drug interactions, pharmacokinetics, and toxicities. The Biopharmaceutics Drug Disposition Classification System (BDDCS) characterizes significant routes of drug elimination, identifies potential transporter effects, and is useful in understanding drug-drug interactions. Class 1 and 2 drugs are primarily eliminated in humans via metabolism and will not exhibit significant biliary excretion of parent compound. In contrast, class 3 and 4 drugs are primarily excreted unchanged in the urine or bile. Here, we characterize the significant elimination route of 105 orally administered class 3 and 4 drugs. We introduce and validate a novel model, predicting significant biliary elimination using a simple classification scheme. The model is accurate for 83% of 30 drugs collected after model development. The model corroborates the observation that biliarily eliminated drugs have high molecular weights, while demonstrating the necessity of considering route of administration and extent of metabolism when predicting biliary excretion. Interestingly, a predictor of potential metabolism significantly improves predictions of major elimination routes of poorly metabolized drugs. This model successfully predicts the major elimination route for poorly permeable/poorly metabolized drugs and may be applied prior to human dosing.
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Affiliation(s)
- Chelsea M Hosey
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave., Room U-68, San Francisco, California, 94143-0912, USA
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37
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Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014; 588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.
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Affiliation(s)
- Nathalie Colloc'h
- CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France.
| | - Thierry Prangé
- LCRB UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France
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38
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Argon gas: a potential neuroprotectant and promising medical therapy. Med Gas Res 2014; 4:3. [PMID: 24533741 PMCID: PMC3996095 DOI: 10.1186/2045-9912-4-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/11/2014] [Indexed: 12/16/2022] Open
Abstract
Argon is a noble gas element that has demonstrated narcotic and protective abilities that may prove useful in the medical field. The earliest records of argon gas have exposed its ability to exhibit narcotic symptoms at hyperbaric pressures greater than 10 atmospheres with more recent evidence seeking to display argon as a potential neuroprotective agent. The high availability and low cost of argon provide a distinct advantage over using similarly acting treatments such as xenon gas. Argon gas treatments in models of brain injury such as in vitro Oxygen-Glucose-Deprivation (OGD) and Traumatic Brain Injury (TBI), as well as in vivo Middle Cerebral Artery Occlusion (MCAO) have largely demonstrated positive neuroprotective behavior. On the other hand, some warning has been made to potential negative effects of argon treatments in cases of ischemic brain injury, where increases of damage in the sub-cortical region of the brain have been uncovered. Further support for argon use in the medical field has been demonstrated in its use in combination with tPA, its ability as an organoprotectant, and its surgical applications. This review seeks to summarize the history and development of argon gas use in medical research as mainly a neuroprotective agent, to summarize the mechanisms associated with its biological effects, and to elucidate its future potential.
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Warshaviak DT, Khramtzov VV, Cascio D, Altenbach C, Hubbell WL. Structure and dynamics of an imidazoline nitroxide side chain with strongly hindered internal motion in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 232:53-61. [PMID: 23694751 PMCID: PMC3758229 DOI: 10.1016/j.jmr.2013.04.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/19/2013] [Accepted: 04/21/2013] [Indexed: 05/03/2023]
Abstract
A disulfide-linked imidazoline nitroxide side chain (V1) has a similar and highly constrained internal motion at diverse topological sites in a protein, unlike that for the disulfide-linked pyrroline nitroxide side chain (R1) widely used in site directed spin labeling EPR. Crystal structures of V1 at two positions in a helix of T4 Lysozyme and quantum mechanical calculations suggest the source of the constraints as intra-side chain interactions of the disulfide sulfur atoms with both the protein backbone and the 3-nitrogen in the imidazoline ring. These interactions apparently limit the conformation of the side chain to one of only three possible rotamers, two of which are observed in the crystal structure. An inter-spin distance measurement in frozen solution using double electron-electron resonance (DEER) gives a value essentially identical to that determined from the crystal structure of the protein containing two copies of V1, indicating that lattice forces do not dictate the rotamers observed. Collectively, the results suggest the possibility of predetermining a unique rotamer of V1 in helical structures. In general, the reduced rotameric space of V1 compared to R1 should simplify interpretation of inter-spin distance information in terms of protein structure, while the highly constrained internal motion is expected to extend the dynamic range for characterizing large amplitude nanosecond backbone fluctuations.
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Affiliation(s)
- Dora Toledo Warshaviak
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Valery V. Khramtzov
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, The Department of Internal Medicine, The Ohio State University, 473 West 12th Ave., room 201, Columbus, Ohio 43210
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Christian Altenbach
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Corresponding author , Jules Stein Eye Institute, UCLA, 100 Stein Plaza, Los Angeles, CA 90095, 310-206-8830
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40
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Tognotti D, Gabellieri E, Morelli E, Cioni P. Temperature and pressure dependence of azurin stability as monitored by tryptophan fluorescence and phosphorescence. The case of F29A mutant. Biophys Chem 2013; 182:44-50. [PMID: 23816248 DOI: 10.1016/j.bpc.2013.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
Abstract
The effects of a single-point, F29A, cavity-forming mutation on the unfolding thermodynamic parameters of azurin from Pseudomonas aeruginosa and on the internal dynamics of the protein fold under pressure were probed by the fluorescence and phosphorescence emission of Trp48, deeply buried in the compact hydrophobic core of the macromolecule. Pressure-induced unfolding, monitored by the shift in the fluorescence spectrum, led to a volume change of 70-90mlmol(-1). The difference in the unfolding volume between F29A and wild type azurin was smaller than the volume of the space theoretically created in the mutant, indicating that the cavity is, at least partially, filled with water molecules. The complex temperature dependence of the unfolding volume, for temperatures up to 20°C, suggests the formation of an expanded form of the protein and highlights how the packing efficiency of azurin appears to contribute to the magnitude of internal void volume at any given temperature. Changes in flexibility of the protein matrix around the chromophore were monitored by the intrinsic phosphorescence lifetime. At 40°C the application of pressure in the predenaturation range initially decreases the internal flexibility of azurin, the trend eventually reverting on approaching unfolding. The main difference between wild type and the cavity mutant is the inversion point which happens at 300MPa for wild type and at 150MPa for F29A. This suggests that, for the cavity mutant, pressure-induced internal hydration is more dominant than any compaction of the globular fold at relatively low pressures.
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Affiliation(s)
- Danika Tognotti
- Istituto di Biofisica, CNR, via G. Moruzzi 1, 56124 Pisa, Italy.
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41
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Sierra-Valdez FJ, Ruiz-Suárez JC. Noble Gases in Pure Lipid Membranes. J Phys Chem B 2013; 117:3167-72. [DOI: 10.1021/jp400367t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Zhou W, Huang C, Li Y, Duan J, Wang Y, Yang L. A systematic identification of multiple toxin–target interactions based on chemical, genomic and toxicological data. Toxicology 2013; 304:173-84. [DOI: 10.1016/j.tox.2012.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/26/2022]
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43
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Zaiss M, Schnurr M, Bachert P. Analytical solution for the depolarization of hyperpolarized nuclei by chemical exchange saturation transfer between free and encapsulated xenon (HyperCEST). J Chem Phys 2012; 136:144106. [DOI: 10.1063/1.3701178] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain. Proc Natl Acad Sci U S A 2011; 108:E881-9. [PMID: 21997213 DOI: 10.1073/pnas.1114038108] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Interior topological features, such as pockets and channels, have evolved in proteins to regulate biological functions by facilitating the diffusion of biomolecules. Decades of research using the globins as model heme proteins have clearly highlighted the importance of gas pockets around the heme in controlling the capture and release of O(2). However, much less is known about how ligand migration contributes to the diverse functions of other heme protein scaffolds. Heme nitric oxide/oxygen binding (H-NOX) domains are a conserved family of gas-sensing heme proteins with a divergent fold that are critical to numerous signaling pathways. Utilizing X-ray crystallography with xenon, a tunnel network has been shown to serve as a molecular pathway for ligand diffusion. Structure-guided mutagenesis results show that the tunnels have unexpected effects on gas-sensing properties in H-NOX domains. The findings provide insights on how the flux of biomolecules through protein scaffolds modulates protein chemistry.
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45
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Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy. Proc Natl Acad Sci U S A 2011; 108:16241-6. [PMID: 21911399 DOI: 10.1073/pnas.1111420108] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A disulfide-linked nitroxide side chain (R1) is the most widely used spin label for determining protein topology, mapping structural changes, and characterizing nanosecond backbone motions by site-directed spin labeling. Although the internal motion of R1 and the number of preferred rotamers are limited, translating interspin distance measurements and spatial orientation information into structural constraints is challenging. Here, we introduce a highly constrained nitroxide side chain designated RX as an alternative to R1 for these applications. RX is formed by a facile cross-linking reaction of a bifunctional methanethiosulfonate reagent with pairs of cysteine residues at i and i + 3 or i and i + 4 in an α-helix, at i and i + 2 in a β-strand, or with cysteine residues in adjacent strands in a β-sheet. Analysis of EPR spectra, a crystal structure of RX in T4 lysozyme, and pulsed electron-electron double resonance (ELDOR) spectroscopy on an immobilized protein containing RX all reveal a highly constrained internal motion of the side chain. Consistent with the constrained geometry, interspin distance distributions between pairs of RX side chains are narrower than those from analogous R1 pairs. As an important consequence of the constrained internal motion of RX, spectral diffusion detected with ELDOR reveals microsecond internal motions of the protein. Collectively, the data suggest that the RX side chain will be useful for distance mapping by EPR spectroscopy, determining spatial orientation of helical segments in oriented specimens, and measuring structural fluctuations on the microsecond time scale.
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46
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Measurement of radon and xenon binding to a cryptophane molecular host. Proc Natl Acad Sci U S A 2011; 108:10969-73. [PMID: 21690357 DOI: 10.1073/pnas.1105227108] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Xenon and radon have many similar properties, a difference being that all 35 isotopes of radon ((195)Rn-(229)Rn) are radioactive. Radon is a pervasive indoor air pollutant believed to cause significant incidence of lung cancer in many geographic regions, yet radon affinity for a discrete molecular species has never been determined. By comparison, the chemistry of xenon has been widely studied and applied in science and technology. Here, both noble gases were found to bind with exceptional affinity to tris-(triazole ethylamine) cryptophane, a previously unsynthesized water-soluble organic host molecule. The cryptophane-xenon association constant, K(a)=42,000 ± 2,000 M(-1) at 293 K, was determined by isothermal titration calorimetry. This value represents the highest measured xenon affinity for a host molecule. The partitioning of radon between air and aqueous cryptophane solutions of varying concentration was determined radiometrically to give the cryptophane-radon association constant K(a)=49,000 ± 12,000 M(-1) at 293 K.
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Cioni P, Gabellieri E. Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:934-41. [PMID: 20934540 DOI: 10.1016/j.bbapap.2010.09.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/22/2010] [Accepted: 09/30/2010] [Indexed: 11/25/2022]
Abstract
After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Via Moruzzi 1, 56100-Pisa, Italy.
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Perkins DI, Trudell JR, Crawford DK, Alkana RL, Davies DL. Molecular targets and mechanisms for ethanol action in glycine receptors. Pharmacol Ther 2010; 127:53-65. [PMID: 20399807 PMCID: PMC2891126 DOI: 10.1016/j.pharmthera.2010.03.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 03/23/2010] [Indexed: 11/23/2022]
Abstract
Glycine receptors (GlyRs) are recognized as the primary mediators of neuronal inhibition in the spinal cord, brain stem and higher brain regions known to be sensitive to ethanol. Building evidence supports the notion that ethanol acting on GlyRs causes at least a subset of its behavioral effects and may be involved in modulating ethanol intake. For over two decades, GlyRs have been studied at the molecular level as targets for ethanol action. Despite the advances in understanding the effects of ethanol in vivo and in vitro, the precise molecular sites and mechanisms of action for ethanol in ligand-gated ion channels in general, and in GlyRs specifically, are just now starting to become understood. The present review focuses on advances in our knowledge produced by using molecular biology, pressure antagonism, electrophysiology and molecular modeling strategies over the last two decades to probe, identify and model the initial molecular sites and mechanisms of ethanol action in GlyRs. The molecular targets on the GlyR are covered on a global perspective, which includes the intracellular, transmembrane and extracellular domains. The latter has received increasing attention in recent years. Recent molecular models of the sites of ethanol action in GlyRs and their implications to our understanding of possible mechanism of ethanol action and novel targets for drug development in GlyRs are discussed.
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Affiliation(s)
- Daya I. Perkins
- Alcohol and Brain Research Laboratories, Department of Pharmacology and Pharmaceutical Sciences (D.I.P. and R.L.A.), Department of Clinical Pharmacy & Pharmaceutical Economics and Policy (D.L.D.),School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - James R. Trudell
- Department of Anesthesia and Beckman Program for Molecular and Genetic Medicine, Stanford School of Medicine, Palo Alto, CA 94305, USA
| | | | - Ronald L. Alkana
- Alcohol and Brain Research Laboratories, Department of Pharmacology and Pharmaceutical Sciences (D.I.P. and R.L.A.), Department of Clinical Pharmacy & Pharmaceutical Economics and Policy (D.L.D.),School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daryl L. Davies
- Alcohol and Brain Research Laboratories, Department of Pharmacology and Pharmaceutical Sciences (D.I.P. and R.L.A.), Department of Clinical Pharmacy & Pharmaceutical Economics and Policy (D.L.D.),School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
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Metals in proteins: cluster analysis studies. J Mol Model 2010; 17:429-42. [DOI: 10.1007/s00894-010-0733-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 04/23/2010] [Indexed: 01/19/2023]
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Shi Y, Jiao D, Schnieders MJ, Ren P. Trypsin-ligand binding free energy calculation with AMOEBA. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:2328-31. [PMID: 19965178 DOI: 10.1109/iembs.2009.5335108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The binding free energies of several benzamidine -like inhibitors to trypsin were examined using a polarizable molecular mechanics potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was indicated to be the driving force for the binding. MD simulations show that the ligands form hydrogen bonds with trypsin and water molecules nearby in a competitive fashion. While the binding free energy is independent of the ligand dipole moment, it shows a strong correlation with the ligand molecular polarizability.
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Affiliation(s)
- Yue Shi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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