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Hayakawa ESH, Ueki M, Alhatmi E, Oiki S, Tokumasu F, Mitchell DC, Iwamoto M. Different lateral packing stress in acyl chains alters KcsA orientation and structure in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184338. [PMID: 38763269 DOI: 10.1016/j.bbamem.2024.184338] [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: 09/25/2023] [Revised: 04/26/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
The molecular structures of the various intrinsic lipids in membranes regulate lipid-protein interactions. These different lipid structures with unique volumes produce different lipid molecular packing stresses/lateral stresses in lipid membranes. Most studies examining lipid packing effects have used phosphatidylcholine and phosphatidylethanolamine (PE), which are the main phospholipids of eukaryotic cell membranes. In contrast, Gram-negative or Gram-positive bacterial membranes are composed primarily of phosphatidylglycerol (PG) and PE, and the physical and thermodynamic properties of each acyl chain in PG at the molecular level remain unresolved. In this study, we used 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG, 16:0-18:1 PG) and 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (PAPG, 16:0-20:4 PG) to prepare lipid bilayers (liposome) with the rod-type fluorescence probe DPH. We measured the lipid packing conditions by determining the rotational freedom of DPH in POPG or PAPG bilayers. Furthermore, we investigated the effect of different monoacyl chains on a K+ channel (KcsA) structure when embedded in POPG or PAPG membranes. The results revealed that differences in the number of double bonds and carbon chain length in the monoacyl chain at sn-2 affected the physicochemical properties of the membrane and the structure and orientation of KcsA.
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Affiliation(s)
- Eri Saki H Hayakawa
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan.
| | - Misuzu Ueki
- Division of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui 910-1193, Japan
| | - Elmukhtar Alhatmi
- Department of Physics, Portland State University, Portland, OR 97201-0751, USA
| | - Shigetoshi Oiki
- Biomedical Imaging Research Center, University of Fukui, 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui 910-1193, Japan
| | - Fuyuki Tokumasu
- Department of Cellular Architecture Studies, Division of Shionogi Global Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of Laboratory Sciences, Graduate School of Health Sciences, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Drake C Mitchell
- Department of Physics, Portland State University, Portland, OR 97201-0751, USA
| | - Masayuki Iwamoto
- Division of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui 910-1193, Japan
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Struts AV, Barmasov AV, Fried SDE, Hewage KSK, Perera SMDC, Brown MF. Osmotic stress studies of G-protein-coupled receptor rhodopsin activation. Biophys Chem 2024; 304:107112. [PMID: 37952496 DOI: 10.1016/j.bpc.2023.107112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/14/2023]
Abstract
We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
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Affiliation(s)
- Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Laboratory of Biomolecular NMR, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Alexander V Barmasov
- Department of Biophysics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia; Department of Physics, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Steven D E Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kushani S K Hewage
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | | | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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3
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Abstract
Although G-protein–coupled receptors (GPCRs) control vast physiological pathways, their activation remains chemically and physically enigmatic. Our osmotic stress studies of the visual receptor rhodopsin have redefined the standard model of GPCR signaling by revealing the essential role of bulk water. We show results consistent with a large number of water molecules flooding the rhodopsin interior during activation to stabilize the effector binding conformation. These results suggest a model of GPCR activation in which the receptor becomes solvent-swollen upon formation of the active state. We thus demonstrate the mechanism whereby water acts as a powerful allosteric modulator of a pharmacologically important membrane protein family. The Rhodopsin family of G-protein–coupled receptors (GPCRs) comprises the targets of nearly a third of all pharmaceuticals. Despite structural water present in GPCR X-ray structures, the physiological relevance of these solvent molecules to rhodopsin signaling remains unknown. Here, we show experimental results consistent with the idea that rhodopsin activation in lipid membranes is coupled to bulk water movements into the protein. To quantify hydration changes, we measured reversible shifting of the metarhodopsin equilibrium due to osmotic stress using an extensive series of polyethylene glycol (PEG) osmolytes. We discovered clear evidence that light activation entails a large influx of bulk water (∼80–100 molecules) into the protein, giving insight into GPCR activation mechanisms. Various size polymer osmolytes directly control rhodopsin activation, in which large solutes are excluded from rhodopsin and dehydrate the protein, favoring the inactive state. In contrast, small osmolytes initially forward shift the activation equilibrium until a quantifiable saturation point is reached, similar to gain-of-function protein mutations. For the limit of increasing osmolyte size, a universal response of rhodopsin to osmotic stress is observed, suggesting it adopts a dynamic, hydrated sponge-like state upon photoactivation. Our results demand a rethinking of the role of water dynamics in modulating various intermediates in the GPCR energy landscape. We propose that besides bound water, an influx of bulk water plays a necessary role in establishing the active GPCR conformation that mediates signaling.
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4
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G‐Protein‐Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202003342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | | | - Steven D. E. Fried
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Michael C. Pitman
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Andrey V. Struts
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russia
| | - Michael F. Brown
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Department of Physics University of Arizona Tucson AZ 85721 USA
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5
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G-Protein-Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2020; 60:2288-2295. [PMID: 32596956 DOI: 10.1002/anie.202003342] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/28/2020] [Indexed: 12/31/2022]
Abstract
Visual rhodopsin is an important archetype for G-protein-coupled receptors, which are membrane proteins implicated in cellular signal transduction. Herein, we show experimentally that approximately 80 water molecules flood rhodopsin upon light absorption to form a solvent-swollen active state. An influx of mobile water is necessary for activating the photoreceptor, and this finding is supported by molecular dynamics (MD) simulations. Combined force-based measurements involving osmotic and hydrostatic pressure indicate the expansion occurs by changes in cavity volumes, together with greater hydration in the active metarhodopsin-II state. Moreover, we discovered that binding and release of the C-terminal helix of transducin is coupled to hydration changes as may occur in visual signal amplification. Hydration-dehydration explains signaling by a dynamic allosteric mechanism, in which the soft membrane matter (lipids and water) has a pivotal role in the catalytic G-protein cycle.
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Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Steven D E Fried
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Anna R Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael C Pitman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA
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6
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Teng D, Chen J, Li D, Wu Z, Li W, Tang Y, Liu G. Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators. J Chem Inf Model 2020; 60:3214-3230. [DOI: 10.1021/acs.jcim.0c00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Dan Teng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jianhui Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dongping Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Mallikarjunaiah KJ, Kinnun JJ, Petrache HI, Brown MF. Flexible lipid nanomaterials studied by NMR spectroscopy. Phys Chem Chem Phys 2019; 21:18422-18457. [DOI: 10.1039/c8cp06179c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in solid-state nuclear magnetic resonance spectroscopy inform the emergence of material properties from atomistic-level interactions in membrane lipid nanostructures.
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Affiliation(s)
- K. J. Mallikarjunaiah
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
| | - Jacob J. Kinnun
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Horia I. Petrache
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
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8
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Blankenship E, Vahedi-Faridi A, Lodowski DT. The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation. Structure 2015; 23:2358-2364. [PMID: 26526852 DOI: 10.1016/j.str.2015.09.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/27/2015] [Accepted: 09/06/2015] [Indexed: 11/15/2022]
Abstract
Rhodopsin, a light-activated G protein coupled receptor (GPCR), has been the subject of numerous biochemical and structural investigations, serving as a model receptor for GPCRs and their activation. We present the 2.3-Å resolution structure of native source rhodopsin stabilized in a conformation competent for G protein binding. An extensive water-mediated hydrogen bond network linking the chromophore binding site to the site of G protein binding is observed, providing connections to conserved motifs essential for GPCR activation. Comparison of this extensive solvent-mediated hydrogen-bonding network with the positions of ordered solvent in earlier crystallographic structures of rhodopsin photointermediates reveals both static structural and dynamic functional water-protein interactions present during the activation process. When considered along with observations that solvent occupies similar positions in the structures of other GPCRs, these analyses strongly support an integral role for this dynamic ordered water network in both rhodopsin and GPCR activation.
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Affiliation(s)
- Elise Blankenship
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ardeschir Vahedi-Faridi
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T Lodowski
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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9
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Zhang XC, Cao C, Zhou Y, Zhao Y. Proton transfer-mediated GPCR activation. Protein Cell 2014; 6:12-7. [PMID: 25319942 PMCID: PMC4286134 DOI: 10.1007/s13238-014-0106-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 09/28/2014] [Indexed: 12/29/2022] Open
Abstract
G-protein coupled receptors (GPCRs) play essential roles in signal transduction from the environment into the cell. While many structural features have been elucidated in great detail, a common functional mechanism on how the ligand-binding signal is converted into a conformational change on the cytoplasmic face resulting in subsequent activation of downstream effectors remain to be established. Based on available structural and functional data of the activation process in class-A GPCRs, we propose here that a change in protonation status, together with proton transfer via conserved structural elements located in the transmembrane region, are the key elements essential for signal transduction across the membrane.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China,
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10
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Sun X, Ågren H, Tu Y. Functional Water Molecules in Rhodopsin Activation. J Phys Chem B 2014; 118:10863-73. [DOI: 10.1021/jp505180t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xianqiang Sun
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
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11
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Tehan BG, Bortolato A, Blaney FE, Weir MP, Mason JS. Unifying family A GPCR theories of activation. Pharmacol Ther 2014; 143:51-60. [PMID: 24561131 DOI: 10.1016/j.pharmthera.2014.02.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 10/25/2022]
Abstract
Several new pairs of active and inactive GPCR structures have recently been solved enabling detailed structural insight into the activation process, not only of rhodopsin but now also of the β2 adrenergic, M2 muscarinic and adenosine A2A receptors. Combined with structural analyses they have enabled us to examine the different recent theories proposed for GPCR activation and show that they are all indeed parts of the same process, and are intrinsically related through their effect on the central hydrophobic core of GPCRs. This new unifying general process of activation is consistent with the identification of known constitutively active mutants and an in-depth conservational analysis of significant residues implicated in the process.
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Affiliation(s)
- Benjamin G Tehan
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom.
| | - Andrea Bortolato
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Frank E Blaney
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Malcolm P Weir
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Jonathan S Mason
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
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12
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Chaudhuri A, Basu P, Haldar S, Kombrabail M, Krishnamoorthy G, Rajarathnam K, Chattopadhyay A. Organization and dynamics of the N-terminal domain of chemokine receptor CXCR1 in reverse micelles: effect of graded hydration. J Phys Chem B 2013; 117:1225-33. [PMID: 23311880 DOI: 10.1021/jp3095352] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water plays a fundamental role in the folding, structure, dynamics, and function of proteins and peptides. The extracellular N-terminal domain of chemokine receptors is crucial in mediating binding affinity, receptor selectivity, and regulating function. The flexible N-terminal domain becomes ordered in membranes and membrane-mimetic assemblies, thereby indicating that the membrane could play an important role in regulating CXC chemokine receptor 1 (CXCR1) function. In view of the role of hydration in lipid-protein interactions in membranes, we explored the organization and dynamics of a 34-mer peptide of the CXCR1 N-terminal domain in reverse micelles by utilizing a combination of fluorescence-based approaches and circular dichroism spectroscopy. Our results show that the secondary structure adopted by the CXCR1 N-domain is critically dependent on hydration. The tryptophan residues of the CXCR1 N-domain experience motional restriction and exhibit red edge excitation shift (REES) upon incorporation in reverse micelles. REES and fluorescence lifetime exhibit reduction with increasing reverse micellar hydration. Time-resolved fluorescence anisotropy measurements reveal the effect of hydration on peptide rotational dynamics. Taken together, these results constitute the first report demonstrating modulation in the organization and dynamics of the N-terminal domain of a chemokine receptor in a membrane-like environment of varying hydration. We envisage that these results are relevant in the context of hydration in the function of G protein-coupled receptors.
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Affiliation(s)
- Arunima Chaudhuri
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
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13
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Hussain S, Franck JM, Han S. Transmembrane Protein Activation Refined by Site-Specific Hydration Dynamics. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201206147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Hussain S, Franck JM, Han S. Transmembrane protein activation refined by site-specific hydration dynamics. Angew Chem Int Ed Engl 2013; 52:1953-8. [PMID: 23307344 DOI: 10.1002/anie.201206147] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/18/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93016, USA
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15
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Rivera JL, Lima E. Efecto desorbedor del metanol en la membrana celular. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2013. [DOI: 10.1016/s1405-888x(13)72080-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Abstract
Membrane biochemists are becoming increasingly aware of the role of lipid-protein interactions in diverse cellular functions. This review describes how conformational changes in membrane proteins, involving folding, stability, and membrane shape transitions, potentially involve elastic remodeling of the lipid bilayer. Evidence suggests that membrane lipids affect proteins through interactions of a relatively long-range nature, extending beyond a single annulus of next-neighbor boundary lipids. It is assumed the distance scale of the forces is large compared to the molecular range of action. Application of the theory of elasticity to flexible soft surfaces derives from classical physics and explains the polymorphism of both detergents and membrane phospholipids. A flexible surface model (FSM) describes the balance of curvature and hydrophobic forces in lipid-protein interactions. Chemically nonspecific properties of the lipid bilayer modulate the conformational energetics of membrane proteins. The new biomembrane model challenges the standard model (the fluid mosaic model) found in biochemistry texts. The idea of a curvature force field based on data first introduced for rhodopsin gives a bridge between theory and experiment. Influences of bilayer thickness, nonlamellar-forming lipids, detergents, and osmotic stress are all explained by the FSM. An increased awareness of curvature forces suggests that research will accelerate as structural biology becomes more closely entwined with the physical chemistry of lipids in explaining membrane structure and function.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry and Biochemistry and Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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17
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Effect of channel mutations on the uptake and release of the retinal ligand in opsin. Proc Natl Acad Sci U S A 2012; 109:5247-52. [PMID: 22431612 DOI: 10.1073/pnas.1117268109] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the retinal binding pocket of rhodopsin, a Schiff base links the retinal ligand covalently to the Lys296 side chain. Light transforms the inverse agonist 11-cis-retinal into the agonist all-trans-retinal, leading to the active Meta II state. Crystal structures of Meta II and the active conformation of the opsin apoprotein revealed two openings of the 7-transmembrane (TM) bundle towards the hydrophobic core of the membrane, one between TM1/TM7 and one between TM5/TM6, respectively. Computational analysis revealed a putative ligand channel connecting the openings and traversing the binding pocket. Identified constrictions within the channel motivated this study of 35 rhodopsin mutants in which single amino acids lining the channel were replaced. 11-cis-retinal uptake and all-trans-retinal release were measured using UV/visible and fluorescence spectroscopy. Most mutations slow or accelerate both uptake and release, often with opposite effects. Mutations closer to the Lys296 active site show larger effects. The nucleophile hydroxylamine accelerates retinal release 80 times but the action profile of the mutants remains very similar. The data show that the mutations do not probe local channel permeability but rather affect global protein dynamics, with the focal point in the ligand pocket. We propose a model for retinal/receptor interaction in which the active receptor conformation sets the open state of the channel for 11-cis-retinal and all-trans-retinal, with positioning of the ligand at the active site as the kinetic bottleneck. Although other G protein-coupled receptors lack the covalent link to the protein, the access of ligands to their binding pocket may follow similar schemes.
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Clemons TD, Evans CW, Zdyrko B, Luzinov I, Fitzgerald M, Dunlop SA, Harvey AR, Iyer KS, Stubbs KA. Multifunctional nanoadditives for the thermodynamic and kinetic stabilization of enzymes. NANOSCALE 2011; 3:4085-4087. [PMID: 21897968 DOI: 10.1039/c1nr10786k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stabilization of enzymes has become a major focus in the quest to improve the activity, sustainability and recyclability of enzymes for their successful integration into both industry and medicine. Here, we describe the kinetic and thermodynamic stabilization of a variety of enzymes in the presence of cationic multifunctional polymeric nanoparticles.
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Affiliation(s)
- Tristan D Clemons
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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19
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Grossfield A. Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1868-78. [DOI: 10.1016/j.bbamem.2011.03.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/23/2011] [Accepted: 03/21/2011] [Indexed: 01/28/2023]
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Mallikarjunaiah K, Leftin A, Kinnun JJ, Justice MJ, Rogozea AL, Petrache HI, Brown MF. Solid-state ²H NMR shows equivalence of dehydration and osmotic pressures in lipid membrane deformation. Biophys J 2011; 100:98-107. [PMID: 21190661 PMCID: PMC3010004 DOI: 10.1016/j.bpj.2010.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 11/02/2010] [Accepted: 11/08/2010] [Indexed: 11/28/2022] Open
Abstract
Lipid bilayers represent a fascinating class of biomaterials whose properties are altered by changes in pressure or temperature. Functions of cellular membranes can be affected by nonspecific lipid-protein interactions that depend on bilayer material properties. Here we address the changes in lipid bilayer structure induced by external pressure. Solid-state ²H NMR spectroscopy of phospholipid bilayers under osmotic stress allows structural fluctuations and deformation of membranes to be investigated. We highlight the results from NMR experiments utilizing pressure-based force techniques that control membrane structure and tension. Our ²H NMR results using both dehydration pressure (low water activity) and osmotic pressure (poly(ethylene glycol) as osmolyte) show that the segmental order parameters (S(CD)) of DMPC approach very large values of ≈ 0.35 in the liquid-crystalline state. The two stresses are thermodynamically equivalent, because the change in chemical potential when transferring water from the interlamellar space to the bulk water phase corresponds to the induced pressure. This theoretical equivalence is experimentally revealed by considering the solid-state ²H NMR spectrometer as a virtual osmometer. Moreover, we extend this approach to include the correspondence between osmotic pressure and hydrostatic pressure. Our results establish the magnitude of the pressures that lead to significant bilayer deformation including changes in area per lipid and volumetric bilayer thickness. We find that appreciable bilayer structural changes occur with osmotic pressures in the range of 10-100 atm or lower. This research demonstrates the applicability of solid-state ²H NMR spectroscopy together with bilayer stress techniques for investigating the mechanism of pressure sensitivity of membrane proteins.
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Affiliation(s)
| | - Avigdor Leftin
- Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Jacob J. Kinnun
- Department of Physics, University of Arizona, Tucson, Arizona
| | - Matthew J. Justice
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana
| | - Adriana L. Rogozea
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana
| | - Horia I. Petrache
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana
| | - Michael F. Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona
- Department of Physics, University of Arizona, Tucson, Arizona
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21
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Soubias O, Teague WE, Hines KG, Mitchell DC, Gawrisch K. Contribution of membrane elastic energy to rhodopsin function. Biophys J 2010; 99:817-24. [PMID: 20682259 DOI: 10.1016/j.bpj.2010.04.068] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 04/16/2010] [Accepted: 04/23/2010] [Indexed: 11/16/2022] Open
Abstract
We considered the issue of whether shifts in the metarhodopsin I (MI)-metarhodopsin II (MII) equilibrium from lipid composition are fully explicable by differences in bilayer curvature elastic stress. A series of six lipids with known spontaneous radii of monolayer curvature and bending elastic moduli were added at increasing concentrations to the matrix lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the MI-MII equilibrium measured by flash photolysis followed by recording UV-vis spectra. The average area-per-lipid molecule and the membrane hydrophobic thickness were derived from measurements of the (2)H NMR order parameter profile of the palmitic acid chain in POPC. For the series of ethanolamines with different levels of headgroup methylation, shifts in the MI-MII equilibrium correlated with changes in membrane elastic properties as expressed by the product of spontaneous radius of monolayer curvature, bending elastic modulus, and lateral area per molecule. However, for the entire series of lipids, elastic energy explained the shifts only partially. Additional contributions correlated with the capability of the ethanolamine headgroups to engage in hydrogen bonding with the protein, independent of the state of ethanolamine methylation, with introduction of polyunsaturated sn-2 hydrocarbon chains, and with replacement of the palmitic acid sn-1 chains by oleic acid. The experiments point to the importance of interactions of rhodopsin with particular lipid species in the first layer of lipids surrounding the protein as well as to membrane elastic stress in the lipid-protein domain.
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Affiliation(s)
- Olivier Soubias
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
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22
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Structural waters define a functional channel mediating activation of the GPCR, rhodopsin. Proc Natl Acad Sci U S A 2009; 106:14367-72. [PMID: 19706523 DOI: 10.1073/pnas.0901074106] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Structural water molecules may act as prosthetic groups indispensable for proper protein function. In the case of allosteric activation of G protein-coupled receptors (GPCRs), water likely imparts structural plasticity required for agonist-induced signal transmission. Inspection of structures of GPCR superfamily members reveals the presence of conserved embedded water molecules likely important to GPCR function. Coupling radiolytic hydroxyl radical labeling with rapid H(2)O(18) solvent mixing, we observed no exchange of these structural waters with bulk solvent in either ground state or for the Meta II or opsin states. However, the radiolysis approach permitted labeling of selected side chain residues within the transmembrane helices and revealed activation-induced changes in local structural constraints likely mediated by dynamics of both water and protein. These results suggest both a possible general mechanism for water-dependent communication in family A GPCRs based on structural conservation, and a strategy for probing membrane protein structure.
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23
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Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors. Proc Natl Acad Sci U S A 2009; 106:8555-60. [PMID: 19433801 DOI: 10.1073/pnas.0903545106] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
G protein-coupled receptors with seven transmembrane alpha-helices (GPCRs) comprise the largest receptor superfamily and are involved in detecting a wide variety of extracellular stimuli. The availability of high-resolution crystal structures of five prototypical GPCRs, bovine and squid rhodopsin, engineered A(2A)-adenosine, beta(1)- and beta(2)-adrenergic receptors, permits comparative analysis of features common to these and likely all GPCRs. We provide an analysis of the distribution of water molecules in the transmembrane region of these GPCR structures and find conserved contacts with microdomains demonstrated to be involved in receptor activation. Colocalization of water molecules associating with highly conserved and functionally important residues in several of these GPCR crystal structures supports the notion that these waters are likely to be as important to proper receptor function as the conserved residues. Moreover, in the absence of large conformational changes in rhodopsin after photoactivation, we propose that ordered waters contribute to the functional plasticity needed to transmit activation signals from the retinal-binding pocket to the cytoplasmic face of rhodopsin and that fundamental features of the mechanism of activation, involving these conserved waters, are shared by many if not all family A receptors.
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24
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Möller M, Alexiev U. Surface Charge Changes upon Formation of the Signaling State in Visual Rhodopsin. Photochem Photobiol 2009; 85:501-8. [DOI: 10.1111/j.1751-1097.2008.00528.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K. Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin. J Mol Biol 2008; 381:478-86. [PMID: 18585736 DOI: 10.1016/j.jmb.2008.05.036] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 05/14/2008] [Accepted: 05/16/2008] [Indexed: 11/27/2022]
Abstract
Rhodopsin, the membrane protein responsible for dim-light vision, until recently was the only G-protein-coupled receptor (GPCR) with a known crystal structure. As a result, there is enormous interest in studying its structure, dynamics, and function. Here we report the results of three all-atom molecular dynamics simulations, each at least 1.5 micros, which predict that substantial changes in internal hydration play a functional role in rhodopsin activation. We confirm with (1)H magic angle spinning NMR that the increased hydration is specific to the metarhodopsin-I intermediate. The internal water molecules interact with several conserved residues, suggesting that changes in internal hydration may be important during the activation of other GPCRs. The results serve to illustrate the synergism of long-time-scale molecular dynamics simulations and NMR in enhancing our understanding of GPCR function.
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Affiliation(s)
- Alan Grossfield
- IBM TJ Watson Research Center, 1101 Kitchawan Road, PO Box 218, Yorktown Heights, NY 10598, USA
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26
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Rhodopsin's active state is frozen like a DEER in the headlights. Proc Natl Acad Sci U S A 2008; 105:7343-4. [PMID: 18492801 DOI: 10.1073/pnas.0804122105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Wittenberg NJ, Zheng L, Winograd N, Ewing AG. Short-chain alcohols promote accelerated membrane distention in a dynamic liposome model of exocytosis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:2637-2642. [PMID: 18278956 PMCID: PMC2553711 DOI: 10.1021/la703171u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have used amperometric measurements in a model system consisting of two liposomes connected with a membrane nanotube to monitor catechol release during artificial exocytosis and thereby to elucidate the effect of small-chain alcohols on this dynamic membrane process. To determine the rate of membrane shape change, catechol release during membrane distention was monitored amperometrically, and the presence of alcohols in the buffer was shown to accelerate the membrane distention process in a concentration-dependent manner. Compression isotherms for the same lipid composition in the absence and presence of ethanol and 1-propanol were measured to determine how these short-chain alcohols affect the lipid packing in monolayers. The isotherms show a marked decrease in lipid packing density that is dependent on the particular alcohol and its concentration. Comparison of the electrochemical and isotherm results suggests a correlation between decreasing lipid packing density and increasing rates of membrane shape change.
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Affiliation(s)
- Nathan J Wittenberg
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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28
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Ly HV, Longo ML. The influence of short-chain alcohols on interfacial tension, mechanical properties, area/molecule, and permeability of fluid lipid bilayers. Biophys J 2005; 87:1013-33. [PMID: 15298907 PMCID: PMC1304443 DOI: 10.1529/biophysj.103.034280] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used micropipette aspiration to directly measure the area compressibility modulus, bending modulus, lysis tension, lysis strain, and area expansion of fluid phase 1-stearoyl, 2-oleoyl phosphatidylcholine (SOPC) lipid bilayers exposed to aqueous solutions of short-chain alcohols at alcohol concentrations ranging from 0.1 to 9.8 M. The order of effectiveness in decreasing mechanical properties and increasing area per molecule was butanol>propanol>ethanol>methanol, although the lysis strain was invariant to alcohol chain-length. Quantitatively, the trend in area compressibility modulus follows Traube's rule of interfacial tension reduction, i.e., for each additional alcohol CH(2) group, the concentration required to reach the same area compressibility modulus was reduced roughly by a factor of 3. We convert our area compressibility data into interfacial tension values to: confirm that Traube's rule is followed for bilayers; show that alcohols decrease the interfacial tension of bilayer-water interfaces less effectively than oil-water interfaces; determine the partition coefficients and standard Gibbs adsorption energy per CH(2) group for adsorption of alcohol into the lipid headgroup region; and predict the increase in area per headgroup as well as the critical radius and line tension of a membrane pore for each concentration and chain-length of alcohol. The area expansion predictions were confirmed by direct measurements of the area expansion of vesicles exposed to flowing alcohol solutions. These measurements were fitted to a membrane kinetic model to find membrane permeability coefficients of short-chain alcohols. Taken together, the evidence presented here supports a view that alcohol partitioning into the bilayer headgroup region, with enhanced partitioning as the chain-length of the alcohol increases, results in chain-length-dependent interfacial tension reduction with concomitant chain-length-dependent reduction in mechanical moduli and membrane thickness.
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Affiliation(s)
- Hung V Ly
- Department of Chemical Engineering and Material Science, University of California, Davis, California, USA
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29
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Karnaukhova E, Vasileiou C, Wang A, Berova N, Nakanishi K, Borhan B. Circular dichroism of heterochromophoric and partially regenerated purple membrane: Search for exciton coupling. Chirality 2005; 18:72-83. [PMID: 16385624 DOI: 10.1002/chir.20222] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In order to determine the origin of the bisignate CD spectra of native purple membrane, heterochromophoric analogues containing bacteriorhodopsin regenerated with native all-trans-retinal and retinal analogues were investigated. The data collected for the purple membrane samples containing two different chromophores suggest the additive character of the CD spectra. This conclusion was supported by a series of spectra using 5,6-dihydroretinal and 3-dehydroretinal and by using 33% regenerated PM in buffer and in presence of osmolytes. Our results support the idea of conformational heterogeneity of the chromophores in the bR in the trimer, suggesting that the three bR subunits in the trimer are not conformationally equal, and therefore, the bisignate CD spectrum of bR in the purple membrane occurs rather due to a superposition of the CD spectra from variously distorted bR subunits in the trimer than interchromophoric exciton-coupling interactions.
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Affiliation(s)
- Elena Karnaukhova
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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30
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Alves ID, Salgado GFJ, Salamon Z, Brown MF, Tollin G, Hruby VJ. Phosphatidylethanolamine enhances rhodopsin photoactivation and transducin binding in a solid supported lipid bilayer as determined using plasmon-waveguide resonance spectroscopy. Biophys J 2004; 88:198-210. [PMID: 15501933 PMCID: PMC1304998 DOI: 10.1529/biophysj.104.046722] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flash photolysis studies have shown that the membrane lipid environment strongly influences the ability of rhodopsin to form the key metarhodopsin II intermediate. Here we have used plasmon-waveguide resonance (PWR) spectroscopy, an optical method sensitive to both mass and conformation, to probe the effects of lipid composition on conformational changes of rhodopsin induced by light and due to binding and activation of transducin (G(t)). Octylglucoside-solubilized rhodopsin was incorporated by detergent dilution into solid-supported bilayers composed either of egg phosphatidylcholine or various mixtures of a nonlamellar-forming lipid (dioleoylphosphatidylethanolamine; DOPE) together with a lamellar-forming lipid (dioleoylphosphatidylcholine; DOPC). Light-induced proteolipid conformational changes as a function of pH correlated well with previous flash photolysis studies, indicating that the PWR spectral shifts monitored metarhodopsin II formation. The magnitude of these effects, and hence the extent of the conformational transition, was found to be proportional to the DOPE content. Our data are consistent with previous suggestions that lipids having a negative spontaneous curvature favor elongation of rhodopsin during the activation process. In addition, measurements of the G(t)/rhodopsin interaction in a DOPC/DOPE (25:75) bilayer at pH 5 demonstrated that light activation increased the affinity for G(t) from 64 nM to 0.7 nM, whereas G(t) affinity for dark-adapted rhodopsin was unchanged. By contrast, in DOPC bilayers the affinity of G(t) for light-activated rhodopsin was only 18 nM at pH 5. Moreover exchange of GDP for GTP gamma S was also monitored by PWR spectroscopy. Only the light-activated receptor was able to induce this exchange which was unaffected by DOPE incorporation. These findings demonstrate that nonbilayer-forming lipids can alter functionally linked conformational changes of G-protein-coupled receptors in membranes, as well as their interactions with downstream effector proteins.
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Affiliation(s)
- Isabel D. Alves
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Gilmar F. J. Salgado
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Zdzislaw Salamon
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Michael F. Brown
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Gordon Tollin
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
| | - Victor J. Hruby
- Department of Biochemistry and Molecular Biophysics, and Department of Chemistry, University of Arizona, Tucson, Arizona
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31
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Rand RP. Probing the role of water in protein conformation and function. Philos Trans R Soc Lond B Biol Sci 2004; 359:1277-84; discussion 1284-5. [PMID: 15306382 PMCID: PMC1693414 DOI: 10.1098/rstb.2004.1504] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Life began in a bath of water and has never escaped it. Cellular function has forced the evolution of many mechanisms ensuring that cellular water concentration has never changed significantly. To free oneself of any conceptual distinction among all small molecules, solutes and solvents, means that experiments to probe water's specific role in molecular function can be designed like any classical chemical reaction. Such an 'osmotic stress' strategy will be described in general and for an enzyme, hexokinase. Water behaves like a reactant that competes with glucose in binding to hexokinase, and modulates its conformational change and activity. This 'osmotic stress' strategy, now applied to many very different systems, shows that water plays a significant role, energetically, in most macromolecular reactions. It can be required to fill obligatory space, it dominates nearest non-specific interactions between large surfaces, it can be a reactant modulating conformational change; all this in addition to its more commonly perceived static role as an integral part of stereospecific intramolecular structure.
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Affiliation(s)
- R P Rand
- Department of Biological Sciences, Brock University, St Catharines, Ontario L2S 3A1, Canada.
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32
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Alexiev U, Rimke I, Pöhlmann T. Elucidation of the nature of the conformational changes of the EF-interhelical loop in bacteriorhodopsin and of the helix VIII on the cytoplasmic surface of bovine rhodopsin: a time-resolved fluorescence depolarization study. J Mol Biol 2003; 328:705-19. [PMID: 12706727 DOI: 10.1016/s0022-2836(03)00326-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformation of the AB-loop and EF-loop of bacteriorhodopsin and of the fourth cytoplasmic loop (helix VIII) of bovine rhodopsin were assessed by a combination of time-resolved fluorescence depolarization and site-directed fluorescence labeling. The fluorescence anisotropy decays were measured employing a tunable Ti:sapphire laser/microchannel plate based single-photon counting apparatus with picosecond time resolution. This method allows measurement of the diffusional dynamics of the loops directly on a nanosecond time-scale. We implemented the method to study model peptides and two-helix systems representing sequences of bacteriorhodopsin. Thus, we systematically analyzed the anisotropic behavior of four different fluorescent dyes covalently bound to a single cysteine residue on the protein surface and assigned the anisotropy decay components to the modes of motion of the protein and its segments. We have identified two mechanisms of loop conformational changes in the functionally intact proteins bacteriorhodopsin and bovine rhodopsin. First, we found a surface potential-dependent transition between two conformational states of the EF-loop of bacteriorhodopsin, detected with the fluorescent dye bound to position 160. A transition between the two conformational states at 150mM KCl and 20 degrees C requires a surface potential change that corresponds to Deltasigma approximately -1.0e(-)/bacteriorhodopsin molecule. We suggest, that the surface potential-based switch of the EF-loop is the missing link between the movement of helix F and the transient surface potential change detected during the photocycle of bacteriorhodopsin. Second, in the visual pigment rhodopsin, with the fluorescent dye bound to position 316, a particularly striking pH-dependent conformational change of the fourth loop on the cytoplasmic surface was analyzed. The loop mobility increased from pH 5 to 8. The midpoint of this transition is at pH 6.2 and correlates with the midpoint of the pH-dependent equilibrium between the active metarhodopsin II and the inactive metarhodopsin I state.
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Affiliation(s)
- U Alexiev
- Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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33
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Lee AG. Lipid-protein interactions in biological membranes: a structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1612:1-40. [PMID: 12729927 DOI: 10.1016/s0005-2736(03)00056-7] [Citation(s) in RCA: 639] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipid molecules bound to membrane proteins are resolved in some high-resolution structures of membrane proteins. An analysis of these structures provides a framework within which to analyse the nature of lipid-protein interactions within membranes. Membrane proteins are surrounded by a shell or annulus of lipid molecules, equivalent to the solvent layer surrounding a water-soluble protein. The lipid bilayer extends right up to the membrane protein, with a uniform thickness around the protein. The surface of a membrane protein contains many shallow grooves and protrusions to which the fatty acyl chains of the surrounding lipids conform to provide tight packing into the membrane. An individual lipid molecule will remain in the annular shell around a protein for only a short period of time. Binding to the annular shell shows relatively little structural specificity. As well as the annular lipid, there is evidence for other lipid molecules bound between the transmembrane alpha-helices of the protein; these lipids are referred to as non-annular lipids. The average thickness of the hydrophobic domain of a membrane protein is about 29 A, with a few proteins having significantly smaller or greater thicknesses than the average. Hydrophobic mismatch between a membrane protein and the surrounding lipid bilayer generally leads to only small changes in membrane thickness. Possible adaptations in the protein to minimise mismatch include tilting of the helices and rotation of side chains at the ends of the helices. Packing of transmembrane alpha-helices is dependent on the chain length of the surrounding phospholipids. The function of membrane proteins is dependent on the thickness of the surrounding lipid bilayer, sometimes on the presence of specific, usually anionic, phospholipids, and sometimes on the phase of the phospholipid.
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Affiliation(s)
- A G Lee
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, SO16 7PX, Southampton, UK.
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34
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Higo J, Nakasako M. Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole. J Comput Chem 2002; 23:1323-36. [PMID: 12214315 DOI: 10.1002/jcc.10100] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.
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Affiliation(s)
- Junichi Higo
- Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science and BIRD, JST (Japan Science and Technology Corporation), 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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35
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Abstract
Protein-water interactions are key to biological function. They have an underlying dynamic component that pervades the functional roles associated both with particular systems and with the properties of proteins in general. This article focuses on the specific ways in which the dynamics of water are important to protein structure, motion and adaptability to changes in the protein environment.
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Affiliation(s)
- Carla Mattos
- Dept Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695-7622, USA.
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36
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Nakasako M, Tsuchiya F, Arata Y. Roles of hydration water molecules in molecular packing of the killer toxin from Pichia farinosa in its crystalline state investigated by cryogenic X-ray crystallography. Biophys Chem 2002; 95:211-25. [PMID: 12062381 DOI: 10.1016/s0301-4622(01)00258-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The hydration structures around the killer toxin from Pichia farinosa were investigated by cryogenic X-ray crystallography. In particular, those contributing to the molecular association and the crystal contacts were analyzed with respect to the geometry and the networks of hydrogen bonds. The hydration water molecules attached on the surface so as to make up the surface shape in the contact complementary and mediated the intermolecular interactions through the networks of hydrogen bonds. Careful inspection of the contact area led to a proposal as to the molecular association mode of the toxin to determine the biological function in cells. In addition, the water-associated protein-protein interactions were approximated well by a simple theoretical equation on the solvation force expected in confined geometry. The present analysis may provide a way to analyze the crystal contact and molecular recognition in macromolecules in aqueous solution.
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Affiliation(s)
- Masayoshi Nakasako
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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37
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Goldbeck RA, Paquette SJ, Kliger DS. The effect of water on the rate of conformational change in protein allostery. Biophys J 2001; 81:2919-34. [PMID: 11606302 PMCID: PMC1301756 DOI: 10.1016/s0006-3495(01)75932-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The influence of solvation on the rate of quaternary structural change is investigated in human hemoglobin, an allosteric protein in which reduced water activity destabilizes the R state relative to T. Nanosecond absorption spectroscopy of the heme Soret band was used to monitor protein relaxation after photodissociation of aqueous HbCO complex under osmotic stress induced by the nonbinding cosolute poly(ethylene glycol) (PEG). Photolysis data were analyzed globally for six exponential time constants and amplitudes as a function of osmotic stress and viscosity. Increases in time constants associated with geminate rebinding, tertiary relaxation, and quaternary relaxation were observed in the presence of PEG, along with a decrease in the fraction of hemes rebinding CO with the slow rate constant characteristic of the T state. An analysis of these results along with those obtained by others for small cosolutes showed that both osmotic stress and solvent viscosity are important determinants of the microscopic R --> T rate constant. The size and direction of the osmotic stress effect suggests that at least nine additional water molecules are required to solvate the allosteric transition state relative to the R-state hydration, implying that the transition state has a greater solvent-exposed area than either end state.
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Affiliation(s)
- R A Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.
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Isele J, Sakmar TP, Siebert F. Rhodopsin activation affects the environment of specific neighboring phospholipids: an FTIR spectroscopic study. Biophys J 2000; 79:3063-71. [PMID: 11106612 PMCID: PMC1301183 DOI: 10.1016/s0006-3495(00)76541-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Rhodopsin is a member of a superfamily of G-protein-coupled receptors that transduce signals across membranes. We used Fourier-transform infrared (FTIR) difference spectroscopy to study the interaction between rhodopsin and lipid bilayer upon receptor activation. A difference band at 1744 cm(-1) (+)/1727 cm(-1) (-) was identified in the FTIR-difference spectrum of rhodopsin mutant D83N/E122Q in which spectral difference bands arising from the carbonyl stretching frequencies of protonated carboxylic acid groups were removed by mutation. As the band was abolished by detergent delipidation, we suggested that it arose from carbonyl groups of phospholipid fatty acid esters. Rhodopsin and the D83N/E122Q mutant were reconstituted into various (13)C-labeled 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine vesicles and probed. The 1744-cm(-1) (+)/1727 cm(-1) (-) band could be unequivocally assigned to a change in the lipid ester carbonyl stretch upon receptor activation, with roughly equal contribution from both lipid esters. The band intensity scaled with the amount of rhodopsin but not with the amount of lipid, excluding the possibility that it was due to the bulk lipid phase. We also excluded the possibility that the lipid band represents a change in the number of boundary lipids or a general alteration in the boundary lipid environment upon formation of metarhodopsin II. Instead, the data suggest that the lipid band represents the change of a specific lipid-receptor interaction that is coupled to protein conformational changes.
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Affiliation(s)
- J Isele
- Sektion Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität, D-79104 Freiburg, Germany
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Abstract
This study investigated the enhancement effect of gramicidin, a cationic ionophore, on percutaneous absorption of a model drug, benzoic acid (BA), through rat abdominal skin. The mechanisms by which gramicidin increased skin permeability to BA were also investigated. Degree of hydration measured by the Karl Fisher method, the concentration gradient measured by cryostat analysis, and lipid concentration measured by the Fiske-Subbarow method were evaluated and compared. The results showed that BA permeation profiles through rat abdominal skin followed dose- and volume-dependent patterns. The pretreatment of gramicidin increased the permeation rate of BA through rat abdominal skin compared with the untreated control (18.89 vs. 10.86 microg/cm2/hour). Change in skin permeation rate of BA after gramicidin pretreatment was closely correlated with the remaining skin water content. There were no significant differences in the amounts of phospholipid phosphorous between gramicidin pretreated and untreated skin. The enhancing effect of gramicidin on percutaneous absorption of a model drug is mainly attributed to increasing the diffusivity in the hydration domain of the skin and rearranging the lipid bilayer in the stratum corneum.
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Affiliation(s)
- C H Lee
- University of Missouri-Kansas City, MO 64110, USA.
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Mitchell DC, Litman BJ. Effect of ethanol and osmotic stress on receptor conformation. Reduced water activity amplifies the effect of ethanol on metarhodopsin II formation. J Biol Chem 2000; 275:5355-60. [PMID: 10681509 DOI: 10.1074/jbc.275.8.5355] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The combined effects of ethanol and osmolytes on both the extent of formation of metarhodopsin II (MII), which binds and activates transducin, and on acyl chain packing were examined in rod outer segment disc membranes. The ethanol-induced increase in MII formation was amplified by the addition of neutral osmolytes. This enhancement was linear with osmolality. At 360 milliosmolal, the osmolality of human plasma, 50 mM ethanol was 2.7 times more potent than at 0 osmolality, demonstrating the importance of water activity in in vitro experiments dealing with ethanol potency. Ethanol disordered acyl chain packing, and increasing osmolality enhanced this acyl chain disordering. Prior osmotic stress data showed a release of 35 +/- 2 water molecules upon MII formation. Ethanol increases this number to 49 water molecules, suggesting that ethanol replaces 15 additional water molecules upon MII formation. Amplification of ethanol effects on MII formation and acyl chain packing by osmolytes suggests that ethanol increases the equilibrium concentration of MII both by disordering acyl chain packing and by disrupting rhodopsin-water hydrogen bonds, demonstrating a direct effect of ethanol on rhodopsin. At physiologically relevant levels of osmolality and ethanol, about 90% of ethanol's effect is due to disordered acyl chain packing.
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Affiliation(s)
- D C Mitchell
- Section of Fluorescence Studies, Laboratory of Membrane Biophysics and Biochemistry, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland 20853, USA
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Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Chapter 3 Late photoproducts and signaling states of bovine rhodopsin. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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