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Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N. How Do Short Chain Nonionic Detergents Destabilize G-Protein-Coupled Receptors? J Am Chem Soc 2016; 138:15425-15433. [PMID: 27792324 PMCID: PMC5148649 DOI: 10.1021/jacs.6b08742] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stability of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial for their purification in a biologically relevant state, and it is well-known that short chain detergents such as octylglucoside are more denaturing than long chain detergents such as dodecylmaltoside. However, the molecular basis for this phenomenon is poorly understood. To gain insights into the mechanism of detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabilized adenosine receptor (A2AR) mutants embedded in either a lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides. A2AR mutants in dodecylmaltoside or phospholipid showed low flexibility and good interhelical packing. In contrast, A2AR mutants in either octylglucoside or nonylglucoside showed decreased α-helicity in transmembrane regions, decreased α-helical packing, and the interpenetration of detergent molecules between transmembrane α-helices. This was not observed in octylglucoside containing phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased the energetic stability of the receptor by wedging into crevices on the hydrophobic surface of A2AR, increasing packing interactions within the receptor and stiffening the detergent micelle. The data suggest a three-stage process for the initial events in the destabilization of GPCRs by octylglucoside: (i) highly mobile detergent molecules form small micelles around the receptor; (ii) loss of α-helicity and decreased interhelical packing interactions in transmembrane regions are promoted by increased receptor thermal motion; (iii) transient separation of transmembrane helices allowed penetration of detergent molecules into the core of the receptor. The relative hydration of the headgroup and alkyl chain correlates with detergent harshness and suggests new avenues to develop milder versions of octylglucoside for receptor crystallization.
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Affiliation(s)
- Sangbae Lee
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Allen Mao
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Nathan Robertson
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, AL7 3AX, UK
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, USA
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
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Witt I, Witt HT, Di Fiore D, Rögner M, Hinrichs W, Saenger W, Granzin J, Betzel C, Dauter Z. X-Ray Characterization of Single Crystals of the Reaction Center I of Water Splitting Photosynthesis. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/bbpc.198800358] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Zabara A, Negrini R, Onaca-Fischer O, Mezzenga R. Perforated bicontinuous cubic phases with pH-responsive topological channel interconnectivity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3602-9. [PMID: 23677679 DOI: 10.1002/smll.201300348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 05/25/2023]
Abstract
Lipidic lyotropic liquid crystals are at the frontline of current research for release of target therapeutic molecules due to their unique structural complexity and the possibility of engineering stimuli-triggered release of both hydrophilic and hydrophobic molecules. One of the most suitable lipidic mesophases for the encapsulation and delivery of drugs is the reversed double diamond bicontinuous cubic phase, in which two distinct and parallel networks of ∼4 nm water channels percolate independently through the lipid bilayers, following a Pn3m space group symmetry. In the unperturbed Pn3m structure, the two sets of channels act as autonomous and non-communicating 3D transport pathways. Here, a novel type of bicontinuous cubic phase is introduced, where the presence of OmpF membrane proteins at the bilayers provides unique topological interconnectivities among the two distinct sets of water channels, enabling molecular active gating among them. By a combination of small-angle X-ray scattering, release and ion conductivity experiments, it is shown that, without altering the Pn3m space group symmetry or the water channel diameter, the newly designed perforated bicontinuous cubic phase attains transport properties well beyond those of the standard mesophase, allowing faster, sustained release of bioactive target molecules. By further exploiting the pH-mediated pore-closing response mechanism of the double amino acid half-ring architecture in the membrane protein, the pores of the perforated mesophase can be opened and closed with a pH trigger, enabling a fine modulation of the transport properties by only moderate changes in pH, which could open unexplored opportunities in the targeted delivery of bioactive compounds.
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Affiliation(s)
- Alexandru Zabara
- ETH Zürich, Food & Soft Materials Science, Department of Health Science & Technology, Schmelzbergstrasse 9, LFO E23, 8092 Zürich, Switzerland
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Efremov RG, Sazanov LA. Structure of Escherichia coli OmpF porin from lipidic mesophase. J Struct Biol 2012; 178:311-8. [PMID: 22484237 DOI: 10.1016/j.jsb.2012.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/13/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022]
Abstract
Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a "membrane lyzozyme". The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins.
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Affiliation(s)
- Rouslan G Efremov
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
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5
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Schulz GE. A new classification of membrane protein crystals. J Mol Biol 2011; 407:640-6. [PMID: 21315729 DOI: 10.1016/j.jmb.2011.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
Although being much smaller than the number of soluble proteins in the Protein Data Bank, the number of membrane proteins therein now approaches 700, and a statistical analysis becomes meaningful. Such an analysis showed that the conventional subdivision into monotopic, β-barrel and α-helical membrane proteins is appropriate but should be amended by a classification according to the detergent micelle structure in the crystal, which can be derived from the packing of the membrane-immersed parts of the proteins. The crystal packing density is specific for the three conventional types of membrane proteins and soluble proteins. It is also specific for three observed detergent arrangements that are micelle pockets, micelle filaments and micelle sheets, demonstrating that the detergent structure affects crystallization. The packing density distribution of crystals from integral membrane proteins has approximately the same shape as that of soluble proteins but is by a factor of two broader and shifted to lower density. It seems unlikely that the differences can be explained by a mere solvent expansion due to the required detergent. The crystallized membrane proteins were further analyzed with respect to protein mass, oligomerization and crystallographic asymmetric unit, space group, crystal ordering and symmetry. The results provide a new view on membrane proteins.
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Affiliation(s)
- Georg E Schulz
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21,D-79104 Freiburg im Breisgau, Germany.
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Dorset DL, Engel A, Massalski A, Rosenbusch JP. Three Dimensional Structure of a Membrane Pore: Electron Microscopical Analysis of Escherichia coli Outer Membrane Matrix Porin. Biophys J 2010; 45:128-9. [PMID: 19431536 DOI: 10.1016/s0006-3495(84)84135-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Zulauf M, Timmins PA, Garavito RM. Neutron Crystallography of a Membrane Protein: Localization of Detergent and Protein at 20-å Resolution. Biophys J 2010; 49:96-8. [PMID: 19431665 DOI: 10.1016/s0006-3495(86)83607-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Debenhofer J, Huber R, Michel H. Die strukturelle Grundlage der Lichtreaktionen in Bakterien. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/nadc.19860340504] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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VDAC, a multi-functional mitochondrial protein regulating cell life and death. Mol Aspects Med 2010; 31:227-85. [PMID: 20346371 DOI: 10.1016/j.mam.2010.03.002] [Citation(s) in RCA: 530] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 03/17/2010] [Indexed: 01/22/2023]
Abstract
Research over the past decade has extended the prevailing view of the mitochondrion to include functions well beyond the generation of cellular energy. It is now recognized that mitochondria play a crucial role in cell signaling events, inter-organellar communication, aging, cell proliferation, diseases and cell death. Thus, mitochondria play a central role in the regulation of apoptosis (programmed cell death) and serve as the venue for cellular decisions leading to cell life or death. One of the mitochondrial proteins controlling cell life and death is the voltage-dependent anion channel (VDAC), also known as mitochondrial porin. VDAC, located in the mitochondrial outer membrane, functions as gatekeeper for the entry and exit of mitochondrial metabolites, thereby controlling cross-talk between mitochondria and the rest of the cell. VDAC is also a key player in mitochondria-mediated apoptosis. Thus, in addition to regulating the metabolic and energetic functions of mitochondria, VDAC appears to be a convergence point for a variety of cell survival and cell death signals mediated by its association with various ligands and proteins. In this article, we review what is known about the VDAC channel in terms of its structure, relevance to ATP rationing, Ca(2+) homeostasis, protection against oxidative stress, regulation of apoptosis, involvement in several diseases and its role in the action of different drugs. In light of our recent findings and the recently solved NMR- and crystallography-based 3D structures of VDAC1, the focus of this review will be on the central role of VDAC in cell life and death, addressing VDAC function in the regulation of mitochondria-mediated apoptosis with an emphasis on structure-function relations. Understanding structure-function relationships of VDAC is critical for deciphering how this channel can perform such a variety of functions, all important for cell life and death. This review also provides insight into the potential of VDAC1 as a rational target for new therapeutics.
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Welte W, Wacker T, Leis M, Kreutz W, Shiozawa J, Gad'on N, Drews G. Crystallization of the photosynthetic light-harvesting pigment-protein complex B800-850 of Rhodopseudomonas capsulata. FEBS Lett 2001. [DOI: 10.1016/0014-5793(85)80311-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Rosenbusch JP, Lustig A, Grabo M, Zulauf M, Regenass M. Approaches to determining membrane protein structures to high resolution: do selections of subpopulations occur? Micron 2001; 32:75-90. [PMID: 10900383 DOI: 10.1016/s0968-4328(00)00021-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three different methods are currently used for the study of high-resolution structures of membrane proteins: X-ray crystallography, electron crystallography, and nuclear magnetic resonance (NMR) spectroscopy. Thus far, all methods combined have yielded a rather modest number of crystal structures that have been solved at the atomic level. It is hypothesized here that different methods may select different populations of proteins on the basis of various properties. Thus, protein stability may be a significant factor in the formation of three-dimensional (3D) crystals from detergent solutions, since exposure of hydrophobic protein zones to water may cause structural perturbation or denaturation in conformationally labile proteins. This is different in the formation of two-dimensional (2D) crystals where a protein remains protected in its native membrane environment. A biological selection mechanism may therefore be operative in that highly ordered lattices may form only if strong protein-protein interactions are relevant in vivo, thereby limiting the number of proteins that are amenable to electron crystallography. Keeping a protein in a bilayer environment throughout 3D crystallization maintains the lateral pressure existing in native membranes. This can be accomplished by using lipidic cubic phases. Alternatively, the hydrophobic interface of a membrane protein may be spared from contact with water by crystallization from organic solvents where the polar caps are protected in reverse micelles by using appropriate detergents. Some of the criteria that are useful in optimizing the various approaches are given. While the usefulness of complementary methods seems obvious, the results presented may be particularly critical in recognizing key problems in other structural approaches.
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Affiliation(s)
- J P Rosenbusch
- Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056, Basel, Switzerland.
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13
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Shen JR, Kamiya N. Crystallization and the crystal properties of the oxygen-evolving photosystem II from Synechococcus vulcanus. Biochemistry 2000; 39:14739-44. [PMID: 11101288 DOI: 10.1021/bi001402m] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photosystem II (PSII) complex highly active in oxygen evolution was purified and crystallized from a thermophilic cyanobacterium, Synechococcus vulcanus. The PSII complex in the crystals contained the D1/D2 reaction center subunits, CP47 and CP43 (two chlorophyll-binding core antenna proteins of photosystem II), cytochrome b-559 alpha- and beta-subunits, several low molecular weight subunits, and three extrinsic proteins, that is, 33 and 12 kDa proteins and cytochrome c-550. The PSII complex also retained a high rate of oxygen evolution. The apparent molecular mass of the PSII in the crystals was determined to be 580 kDa by gel filtration chromatography, indicating that the PSII crystallized is a dimer. The crystals diffracted to a maximum resolution of 3.5 A at a cryogenic temperature using X-rays from a synchrotron radiation source, SPring-8. The crystals belonged to an orthorhombic system, and the space group was P2(1)2(1)2(1) with unit cell dimensions of a = 129.7 A, b = 226.5 A, and c = 307.8 A. Each asymmetric unit contained one PSII dimer, which gave rise to a specific volume (V(M)) of 3.6 A(3)/Da based on the calculated molecular mass of 310 kDa for a PSII monomer and an estimated solvent content of 66%. Multiple data sets of native crystals have been collected and processed to 4.0 A, indicating that our crystals are suitable for structure analysis at this resolution.
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Affiliation(s)
- J R Shen
- Photosynthesis Research Laboratory and Division of Bio-Crystallography Technology, RIKEN Harima Institute, Koto 1-1-1, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.
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Affiliation(s)
- Hirofumi TANI
- Laboratory of Bioanalytical Chemistry, Graduate School of Engineering, Hokkaido University
| | - Tamio KAMIDATE
- Laboratory of Bioanalytical Chemistry, Graduate School of Engineering, Hokkaido University
| | - Hiroto WATANABE
- Laboratory of Bioanalytical Chemistry, Graduate School of Engineering, Hokkaido University
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Locher KP, Rosenbusch JP. Oligomeric states and siderophore binding of the ligand-gated FhuA protein that forms channels across Escherichia coli outer membranes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:770-5. [PMID: 9288896 DOI: 10.1111/j.1432-1033.1997.t01-1-00770.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The channel-forming FhuA protein, which translocates ferrichrome across Escherichia coli outer membranes, binds 1 mol ligand/mol monomer in detergent solution. The protein is homogenous and migrates as a single band with a mobility corresponding to 77 kDa in SDS/PAGE electrophoresis. Analytical ultracentrifugation revealed a monodisperse species (s(20,w) = 3.8 S) with a mass of 77,800 +/- 3200 Da. The properties of ligand binding, determined by two independent methods, revealed one binding site/monomer, but are complicated by a pronounced convexity of the Scatchard plot and a Hill coefficient calculated to be 2.5. This strongly suggests that oligomeric species are present. Cross-linking agents revealed the existence of possibly transient, mostly dimeric and trimeric species. The difference between the FhuA protein in detergent solution and in its native membrane environment may be related to the removal of lateral pressure that exists in situ.
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Affiliation(s)
- K P Locher
- Biozentrum, University of Basel, Switzerland
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16
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Shiloff BA, Behrens PQ, Kwan SW, Lee JH, Abell CW. Monoamine oxidase B isolated from bovine liver exists as large oligomeric complexes in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:41-50. [PMID: 8954151 DOI: 10.1111/j.1432-1033.1996.0041r.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The quaternary structure and subunit composition of bovine liver monoamine oxidase B (MAO B) was investigated using size-exclusion chromatography, sucrose gradient centrifugation and electron microscopy. Purified enzyme was subjected to Superdex gel filtration column chromatography in the presence of the non-ionic detergents, n-octyl beta-D-glucopyranoside (octyl glucoside) and Triton X-100R-PC (Triton). The specific activity and elution profiles indicate that the enzyme exists as a dimer and preferentially functions as larger oligomeric complexes. Distribution of the oligomeric forms of MAO B was found to be dependent upon protein concentration. Dilution of the enzyme, however, had little or no effect upon the specific activity profiles. In Triton and octyl glucoside, plots of specific activity versus molecular mass displayed a sigmoidal shape. The chromatographic data suggest that detergent-solubilized bovine liver MAO B exists as cooperative oligomeric enzyme complexes. Similarly, sucrose density gradient centrifugation of purified MAO B exhibited a direct correlation between enzyme activity and molecular mass of the MAO complexes. MAO B activity was found to be widely distributed throughout the sucrose gradient and the highest enzyme activity was contained in the high-density sucrose layers. MAO B specific activity is dependent upon the size of the protein complexes and, therefore, oligomerization of the enzyme may play a role in the regulation of MAO B. Transmission electron microscopy of purified MAO B was performed using protein prepared by octyl glucoside extraction. Purified enzyme was applied to Formvar-coated copper grids and negatively stained with methylamine tungstate. MAO-B-specific monoclonal antibody (MAO B-1C2) conjugated to colloidal gold was used as a probe. Contrast enhancement of the electron microscopy data showed that detergent-depleted enzyme tends to aggregate in a linear arrangement of oligomeric complexes. Our data suggest that the MAO B oligomeric complexes are hexamers which contain threefold rotational symmetry. The individual complexes have globular morphology and the hexamers appear to be composed of a trimer of MAO B homodimers.
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Affiliation(s)
- B A Shiloff
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin 78712-1074, USA
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17
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Hebert TE, Moffett S, Morello JP, Loisel TP, Bichet DG, Barret C, Bouvier M. A peptide derived from a beta2-adrenergic receptor transmembrane domain inhibits both receptor dimerization and activation. J Biol Chem 1996; 271:16384-92. [PMID: 8663163 DOI: 10.1074/jbc.271.27.16384] [Citation(s) in RCA: 593] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
One of the assumptions of the mobile receptor hypothesis as it relates to G protein-coupled receptors is that the stoichiometry of receptor, G protein, and effector is 1:1:1 (Bourne, H. R., Sanders, D. A., and McCormick, F.(1990) Nature 348, 125-132). Many studies on the cooperativity of agonist binding are incompatible with this notion and have suggested that both G proteins and their associated receptors can be oligomeric. However, a clear physical demonstration that G protein-coupled receptors can indeed interact as dimers and that such interactions may have functional consequences was lacking. Here, using differential epitope tagging we demonstrate that beta2-adrenergic receptors do form SDS-resistant homodimers and that transmembrane domain VI of the receptor may represent part of an interface for receptor dimerization. The functional importance of dimerization is supported by the observation that a peptide derived from this domain that inhibits dimerization also inhibits beta-adrenergic agonist-promoted stimulation of adenylyl cyclase activity. Moreover, agonist stimulation was found to stabilize the dimeric state of the receptor, while inverse agonists favored the monomeric species, which suggests that interconversion between monomeric and dimeric forms may be important for biological activity.
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MESH Headings
- Adenylyl Cyclases/metabolism
- Amino Acid Sequence
- Animals
- Baculoviridae
- Cell Line
- Chlorocebus aethiops
- Chromatography, Affinity
- Cricetinae
- Cricetulus
- Humans
- Isoproterenol/pharmacology
- Macromolecular Substances
- Molecular Sequence Data
- Peptide Fragments/pharmacology
- Proto-Oncogene Proteins c-myc/biosynthesis
- Receptor, Muscarinic M2
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/isolation & purification
- Receptors, Adrenergic, beta-2/physiology
- Receptors, Dopamine D2/chemistry
- Receptors, Dopamine D2/physiology
- Receptors, Muscarinic/biosynthesis
- Receptors, Vasopressin/biosynthesis
- Receptors, Vasopressin/chemistry
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Recombinant Proteins/isolation & purification
- Sequence Tagged Sites
- Spodoptera
- Transfection
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Affiliation(s)
- T E Hebert
- Département de biochimie, Université de Montréal, Montréal, Quebec, Canada H3C 3J7
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Pebay-Peyroula E, Garavito RM, Rosenbusch JP, Zulauf M, Timmins PA. Detergent structure in tetragonal crystals of OmpF porin. Structure 1995; 3:1051-9. [PMID: 8590000 DOI: 10.1016/s0969-2126(01)00241-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND The high-resolution structures of five porins have been solved by X-ray crystallography including the trigonal crystal form of the trimeric OmpF porin from Escherichia coli. In an accompanying article, the structure of the tetragonal form of OmpF porin is presented. In contrast to the trigonal crystal form, the protein surfaces normally in contact with lipids in the membrane are exposed and interact with amphiphiles in the tetragonal crystal. Thus, the tetragonal form can be used to investigate protein-detergent interactions. RESULTS Using single-crystal neutron diffraction studies and two different detergents (one of them deuterated in its hydrophobic moiety), details of the amphiphile-protein interactions are revealed. Detergent molecules bind to the so-called hydrophobic zone that surrounds the OmpF porin trimer and which is exposed to lipid in the native environment. The aromatic rings on both sides of the hydrophobic zone coincide with the boundary between non-polar and polar moieties of the detergents. CONCLUSIONS In the tetragonal crystal form of OmpF porin, the membrane-exposed area is accessible from the aqueous solution. It is coated by a film of detergent molecules, which presumably mimics the interactions of the protein with lipids in the biological membrane. In the trigonal form, protein-protein interactions predominate in the hydrophobic zone. These may reflect the tight interactions between trimers that are observed in the biological membrane.
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Cowan SW, Garavito RM, Jansonius JN, Jenkins JA, Karlsson R, König N, Pai EF, Pauptit RA, Rizkallah PJ, Rosenbusch JP, Rummel G, Schirmer T. The structure of OmpF porin in a tetragonal crystal form. Structure 1995; 3:1041-50. [PMID: 8589999 DOI: 10.1016/s0969-2126(01)00240-4] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND OmpF porin is a trimeric integral membrane protein responsible for the passive transport of small hydrophilic molecules, such as nutrients and waste products, across the outer membrane of Escherichia coli. Very few membrane proteins have been crystallized in three dimensions, yet this stable protein can be obtained in several crystal forms. Comparison of the structures of the same membrane protein in two different packing environments is of major interest, because it allows us to explore the integrity of the structure outside the natural membrane environment. RESULTS The structure of OmpF porin in a tetragonal crystal form with two trimers per asymmetric unit has been determined at 3.2 A resolution and compared with that obtained previously in a trigonal crystal form. The lattice contacts involve only polar atoms, whereas extensive hydrophobic protein-protein interactions were found in the trigonal lattice. The trimer structure is virtually identical in both. CONCLUSIONS Our comparison reveals that the overall structure of OmpF is not influenced by crystal lattice constraints and, thus, presumably bears close resemblance to the in vivo structure. The tetragonal crystal structure has provided the starting model for the phasing of neutron diffraction data obtained from this crystal form, as described in an accompanying article.
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Affiliation(s)
- S W Cowan
- Department of Structural Biology, University of Basel, Switzerland
| | - R M Garavito
- Department of Microbiology, University of Basel, Switzerland
| | - J N Jansonius
- Department of Structural Biology, University of Basel, Switzerland
| | - J A Jenkins
- Department of Structural Biology, University of Basel, Switzerland
| | - R Karlsson
- Department of Structural Biology, University of Basel, Switzerland
| | - N König
- Department of Microbiology, University of Basel, Switzerland
| | - E F Pai
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - R A Pauptit
- Department of Structural Biology, University of Basel, Switzerland
| | | | - J P Rosenbusch
- Department of Microbiology, University of Basel, Switzerland
| | - G Rummel
- Department of Microbiology, University of Basel, Switzerland
| | - T Schirmer
- Department of Structural Biology, University of Basel, Switzerland
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Blaauw M, Dekker N, Verheij HM, Kalk KH, Dijkstra BW. Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli. FEBS Lett 1995; 373:10-2. [PMID: 7589423 DOI: 10.1016/0014-5793(95)01002-v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The outer membrane phospholipase A (OMPLA) of Escherichia coli is one of the few integral outer membrane proteins displaying enzymatic activity. It is encoded as a mature protein of 269 amino acids preceded by a signal sequence of 20 amino acids. There is no sequence homology with water-soluble lipases and phospholipases. Crystals of the mature enzyme were obtained at 22 degrees C from 24-28% (v/v) 2-methyl-2,4-pentanediol in Bis-Tris buffer, pH 5.9-6.0, with 1 mM calcium chloride and 1.5% (w/v) beta-octylglucoside. They have the symmetry of the trigonal spacegroup P3(1)21 (or P3(2)21) with cell dimensions of a = b = 79.6 A and c = 102.8 A (alpha = beta = 90 degrees, gamma = 120 degrees). Native crystals diffract to a resolution of 2.6 A.
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Affiliation(s)
- M Blaauw
- Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands
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22
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Ostermeier C, Iwata S, Ludwig B, Michel H. Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase. NATURE STRUCTURAL BIOLOGY 1995; 2:842-6. [PMID: 7552705 DOI: 10.1038/nsb1095-842] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Crystallization of membrane proteins, a prerequisite for their X-ray crystallographic analysis, remains difficult. Here, we demonstrate that the crystallization of the cytochrome c oxidase from Paracoccus denitrificans can be mediated by co-crystallization with an antibody Fv fragment. The crystals obtained contain all four subunits of this membrane protein complex and the Fv fragment. The approach of co-crystallizing membrane proteins with antibody fragments should be useful in obtaining well-ordered crystals of membrane proteins in general.
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Affiliation(s)
- C Ostermeier
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann, Frankfurt/Main, Germany
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23
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Three-dimensional crystallization of the light-harvesting complex from Mantoniella squamata (Prasinophyceae) requires an adequate purification procedure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1995. [DOI: 10.1016/0005-2728(95)00085-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Affiliation(s)
- W Welte
- Fakultät für Biologie, Universität Konstanz, Germany
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25
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Soulimane T, Gohlke U, Huber R, Buse G. Three-dimensional crystals of cytochrome-c oxidase from Thermus thermophilus diffracting to 3.8 A resolution. FEBS Lett 1995; 368:132-4. [PMID: 7615066 DOI: 10.1016/0014-5793(95)00623-h] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ba3-type cytochrome-c oxidase from Thermus thermophilus has been crystallized in its native form. Crystallization was achieved by the batch and the vapour diffusion sitting drop methods using polyethylene glycol monomethyl ether 2000 as precipitating agent in the presence of octyl-beta-D-thioglucoside as detergent. The crystals diffract to 3.8 A, belong to the space group P2 or P2(1) and have unit cell dimensions of a = 80.7 A; b = 116.0 A; c = 156.9 A and beta = 104.4 degrees. The asymmetric unit contains two ba3-type oxidase molecules.
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Affiliation(s)
- T Soulimane
- Rheinisch-Westfälische Technische Hochschule, Institut für Biochemie, Klinikum Aachen, Germany
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26
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Fourel D, Bernadac A, Pagès JM. Involvement of exposed polypeptide loops in trimeric stability and membrane insertion of Escherichia coli OmpF porin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 222:625-30. [PMID: 8020499 DOI: 10.1111/j.1432-1033.1994.tb18905.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Different ompF-ompC gene fusions were used to analyse the regions involved in the stable trimerization and membrane insertion of the Escherichia coli OmpF porin. The stability of the trimers formed from the various hybrids was analysed. Three classes of trimer instability are observed related to the presence of different exposed polypeptide loops of OmpF. In all cases, amino acids located between residue 115 and residue 144 of OmpF are necessary to promote a correct and stable trimeric conformation. However, immunogold labelling studies indicate the correct insertion of the protein in the outer membrane despite a marked instability of some hybrid porins. The location of the residues involved in trimer stability is discussed with regards to both the three-dimensional structure and the folding of OmpF.
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Affiliation(s)
- D Fourel
- Centre de Biochimie et de Biologie, Marseille, France
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27
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Electron Crystallography of Organic Molecules. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/s0065-2539(08)60548-x] [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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28
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29
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Chapter 14 Lipid-protein interactions in controlled membrane protein array and crystal formation. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60243-4] [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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30
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Partenskii MB, Jordan PC. Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches. Q Rev Biophys 1992; 25:477-510. [PMID: 1284092 DOI: 10.1017/s0033583500004388] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peter Läuger introduced me (P.C.J.) to the field of ion-channel electrostatics while I was a sabbatical visitor at Konstanz in 1978–79. Läuger pointed out that the relative conductance of hydrophobic ions through phosphatidyl choline (PC) and glyceryl monooleate (GMO) membranes differed by a factor of about 100 (Hladky & Haydon, 1973), quite consistent with the difference in the water-membrane potential differences in the two systems (Pickar & Benz, 1978). However, cation conductance through gramicidin channels spanning these membranes only differs by a factor of 2–3 (Bamberg et al. 1976). Why? It is the pursuit of an answer to this question which led me into my researches in this field.
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Affiliation(s)
- M B Partenskii
- Department of Chemistry, Brandeis University, Waltham, MA 02254-9110
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31
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Abstract
The crystal structure of porin from Rhodobacter capsulatus has been refined using the simulated annealing method. The final model consists of all 301 amino acid residues well obeying standard geometry, three calcium ions, 274 solvent molecules, three detergent molecules and one unknown ligand modeled as a detergent molecule. The final crystallographic R-factor is 18.6% based on 42,851 independent reflections in the resolution range 10 to 1.8 A. The model is described in detail.
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Affiliation(s)
- M S Weiss
- Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany
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32
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Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, Rosenbusch JP. Crystal structures explain functional properties of two E. coli porins. Nature 1992; 358:727-33. [PMID: 1380671 DOI: 10.1038/358727a0] [Citation(s) in RCA: 1142] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel beta-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge distribution affects ion selectivity. The structures explain at the molecular level functional characteristics and their alterations by known mutations.
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Affiliation(s)
- S W Cowan
- Department of Structural Biology, University of Basel, Switzerland
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33
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Tucker AD, Jackman S, Parker MW, Tsernoglou D. Crystallization and preliminary X-ray analysis of phosphoporin from the outer membrane of Escherichia coli. J Mol Biol 1991; 222:881-4. [PMID: 1722257 DOI: 10.1016/0022-2836(91)90582-q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phosphoporin is a pore-forming transmembrane protein that spans the outer membrane of Escherichia coli and facilitates the diffusion of phosphates and phosphorylated compounds. Phosphoporin has been crystallized in several different crystal forms, although only one appears to be suitable for X-ray analysis. These crystals, which are hexagonal plates, diffract X-rays to 3 A resolution and belong to the space-group P6(3)22, with unit cell dimensions a = b = 121 A and c = 111 A.
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Affiliation(s)
- A D Tucker
- European Molecular Biology Laboratory, Heidelberg, Germany
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34
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Weiss MS, Abele U, Weckesser J, Welte W, Schiltz E, Schulz GE. Molecular architecture and electrostatic properties of a bacterial porin. Science 1991; 254:1627-30. [PMID: 1721242 DOI: 10.1126/science.1721242] [Citation(s) in RCA: 399] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.
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Affiliation(s)
- M S Weiss
- Institut für Organische Chemie und Biochemie, Freiburg, Federal Republic of Germany
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35
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Banks JL. Structure and ligand binding in membrane-bound proteins and immunoglobulins. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1071:393-406. [PMID: 1661158 DOI: 10.1016/0304-4157(91)90004-g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- J L Banks
- Department of Biomedical Engineering, Boston University, MA 02215
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36
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Buehler L, Kusumoto S, Zhang H, Rosenbusch J. Plasticity of Escherichia coli porin channels. Dependence of their conductance on strain and lipid environment. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54249-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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37
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Pauptit RA, Schirmer T, Jansonius JN, Rosenbusch JP, Parker MW, Tucker AD, Tsernoglou D, Weiss MS, Schultz GE. A common channel-forming motif in evolutionarily distant porins. J Struct Biol 1991; 107:136-45. [PMID: 1725488 DOI: 10.1016/1047-8477(91)90017-q] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Four new crystal packings of Escherichia coli porins are presented (phosphoporin, maltoporin, and two crystal forms of matrix porin). These were determined by molecular replacement methods using a polyalanine trial model acquired from the refined coordinates of porin from Rhodobacter capsulatus. The successful molecular replacement shows that the dominant motif found in R. capsulatus porin (a 16-stranded antiparallel beta-barrel) also applies to the E. coli porins, despite the lack of significant amino acid sequence homology. A 30 degrees-40 degrees tilt of the beta-strands with respect to the membrane normal was derived from the intensity distributions in the X-ray diffraction patterns for each porin studied, stressing their similarity. In view of the evolutionary distance between enteric and photosynthetic bacteria, the antiparallel beta-barrel may have significance as a basic structural motif for the formation of bacterial membrane channel structures.
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38
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Köster W, Gudmundsdottir A, Lundrigan MD, Seiffert A, Kadner RJ. Deletions or duplications in the BtuB protein affect its level in the outer membrane of Escherichia coli. J Bacteriol 1991; 173:5639-47. [PMID: 1885541 PMCID: PMC208292 DOI: 10.1128/jb.173.18.5639-5647.1991] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Escherichia coli btuB product is an outer membrane protein that mediates the TonB-coupled active transport of cobalamins and the uptake of the E colicins and bacteriophage BF23. The roles of various segments of the BtuB protein in its function or cellular localization were investigated by analysis of several genetic constructs. Hybrid proteins in which various lengths from the amino terminus of BtuB were linked to alkaline phosphatase (btuB::phoA genes) were all secreted across the cytoplasmic membrane. The BtuB-PhoA proteins that carried up to 327 amino acids of BtuB appeared to reside in the periplasmic space, whereas hybrid proteins containing at least 399 amino acids of BtuB were associated with the outer membrane. Eleven in-frame internal deletion mutations that spanned more than half of the mature sequence were prepared by combining appropriate restriction fragments from btuB variants with 6-bp linker insertions. None of the deleted proteins was able to complement any BtuB functions, and only three of them were detectable in the outer membrane, suggesting that most of the deletions affected sequences needed for stable association with the outer membrane. Duplications covering the same portions of BtuB were prepared in the same manner. All of these partial duplication variants complemented all BtuB functions, although some gave substantially reduced levels of activity. These proteins were found in the outer membrane, although some were subject to proteolytic cleavage within or near the duplicated segment. These results indicate that the insertion of BtuB into the outer membrane requires the presence of several regions of teh BtuB protein and that the presence of extra or redundant segments of the protein can be tolerated during its insertion and function.
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Affiliation(s)
- W Köster
- Department of Microbiology, School of Medicine, University of Virginia, Charlottesville 22908
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39
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Almog O, Shoham G, Michaeli D, Nechushtai R. Monomeric and trimeric forms of photosystem I reaction center of Mastigocladus laminosus: crystallization and preliminary characterization. Proc Natl Acad Sci U S A 1991; 88:5312-6. [PMID: 1905020 PMCID: PMC51862 DOI: 10.1073/pnas.88.12.5312] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Photosystem I (PSI) reaction centers (RCs) of the thermophilic cyanobacterium Mastigocladus laminosus were purified and characterized. The PSI RC was obtained in two forms, monomeric and trimeric. The two forms contained the same number of pigments per P700 and displayed similar photochemical activities. The two forms had nearly identical polypeptide subunit compositions; the only observed difference was an additional subunit of about 12 kDa observed in the trimeric form. The purified preparations of both the monomeric and the trimeric forms were used for crystallization and preliminary crystallographic analysis. The trimeric PSI RC preparations produced several three-dimensional crystal forms, one of which, the "hexagonal needle" form (THN), had a hexagonal unit cell with dimensions of 300 x 300 x 160 A, containing four PSI RC trimers. The monomeric preparations also produced single crystals of several forms under various crystallization conditions. One of these crystal forms, the "hexagonal plate" (MHP), diffracted to a resolution of about 5.5 A. It had a hexagonal unit cell with dimensions of 192 x 192 x 163 A, containing six PSI RC monomers. Comparison of the PSI RCs in the crystals with those in the precrystallization preparations demonstrated that neither the monomeric nor the trimeric form of PSI RC was altered by the crystallization process. Both forms retained their original polypeptide subunit composition and their pigment content.
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Affiliation(s)
- O Almog
- Department of Inorganic Chemistry, Hebrew University of Jerusalem, Israel
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40
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Pauptit RA, Zhang H, Rummel G, Schirmer T, Jansonius JN, Rosenbusch JP. Trigonal crystals of porin from Escherichia coli. J Mol Biol 1991; 218:505-7. [PMID: 1850001 DOI: 10.1016/0022-2836(91)90696-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trigonal crystals of the integral membrane protein porin from Escherichia coli have been grown and characterized. They belong to space group P321 with unit cell constants a = b = LL8.4, c = 52.7 A, alpha = beta = 90 degrees, gamma = 120 degrees. The crystals grow as well-defined hexagonal prisms to a size of 0.25 mm in all dimensions, and diffract to 2.7 A. The molecular symmetry coincides with 3-fold crystallographic symmetry, giving two trimers per unit cell (1 monomer/asymmetric unit). This corresponds to VM = 2.9 A3/Da. Native X-ray data to 3.0 A resolution have been collected on a FAST area detector and a search for heavy atom derivatives is underway.
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Affiliation(s)
- R A Pauptit
- Department of Microbiology, University of Basel, Switzerland
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41
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Weiss MS, Kreusch A, Schiltz E, Nestel U, Welte W, Weckesser J, Schulz GE. The structure of porin from Rhodobacter capsulatus at 1.8 A resolution. FEBS Lett 1991; 280:379-82. [PMID: 1707373 DOI: 10.1016/0014-5793(91)80336-2] [Citation(s) in RCA: 258] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structure of the porin from Rhodobacter capsulatus was determined at a resolution of 1.8 A. The analysis started from a closely related crystal structure that had been solved at a medium resolution of 3 A using multiple isomorphous replacement and solvent flattening. The new structure contains the complete sequence of 301 amino acid residues. Refinement of the model is under way; the present R-factor is 22% with good geometry. Except for the lengths of several loops, the resulting chain fold corresponds to the medium resolution model. The membrane channel is lined by a large number of ionogenic side chains with characteristic segregation of differently charged groups.
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Affiliation(s)
- M S Weiss
- Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany
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42
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Rath P, Bousché O, Merrill AR, Cramer WA, Rothschild KJ. Fourier transform infrared evidence for a predominantly alpha-helical structure of the membrane bound channel forming COOH-terminal peptide of colicin E1. Biophys J 1991; 59:516-22. [PMID: 1710937 PMCID: PMC1281217 DOI: 10.1016/s0006-3495(91)82268-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The structure of the membrane bound state of the 178-residue thermolytic COOH-terminal channel forming peptide of colicin E1 was studied by polarized Fourier transform infrared (FTIR) spectroscopy. This fragment was reconstituted into DMPC liposomes at varying peptide/lipid ratios ranging from 1/25-1/500. The amide I band frequency of the protein indicated a dominant alpha-helical secondary structure with limited beta- and random structures. The amide I and II frequencies are at 1,656 and 1,546 cm-1, close to the frequency of the amide I and II bands of rhodopsin, bacteriorhodopsin and other alpha-helical proteins. Polarized FTIR of oriented membranes revealed that the alpha-helices have an average orientation less than the magic angle, 54.6 degrees, relative to the membrane normal. Almost all of the peptide groups in the membrane-bound channel protein undergo rapid hydrogen/deuterium (H/D) exchange. These results are contrasted to the alpha-helical membrane proteins, bacteriorhodopsin, and rhodopsin.
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Affiliation(s)
- P Rath
- Physics Department, Boston University, Massachusetts 02215
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43
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Sansom MS. The biophysics of peptide models of ion channels. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1991; 55:139-235. [PMID: 1715999 DOI: 10.1016/0079-6107(91)90004-c] [Citation(s) in RCA: 347] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- M S Sansom
- Department of Zoology, University of Nottingham, U.K
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44
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Role of a disulfide bond in the thermal stability of the LamB protein trimer in Escherichia coli outer membrane. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52373-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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45
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Terstappen GC, Kula MR. Selective Extraction and Quantitation of Polyoxyethylene Detergents and its Application in Protein Determination. ANAL LETT 1990. [DOI: 10.1080/00032719008052558] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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46
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Abstract
Gram-negative bacteria such asEscherichia coli(E. coli) andSalmonella typhimurium(S. typhimurium) have two layers of membranes in the cellular envelope – the cytoplasmic membrane and the outer membrane (Fig. I). Between these membranes is a periplasmic space in which there is a peptidoglycan layer that provides the cells with mechanical rigidity. In this periplasmic space, there are also a variety of hydrolases and binding proteins. The composition of the outer membrane is somewhat unusual. This membrane bilayer is asymmetric, having an inner (periplasmic) leaflet composed of phospholipids and an outer (extracellular) leaflet formed by lipopolysaccharide (LPS). Unlike phospholipids having two acyl chains, LPS has six or seven saturated fatty acid chains (see reviews, Lugtenberg & Van Alphen, 1983; Nikaido & Vaara, 1985; Nakae, 1986). The head groups of LPS have a strong affinity for divalent cations such as Ca2+, and given a sufficient concentration of these ions the outer membrane can form quite a formidable permeability barrier through this head group/salt bridge network (Nikaido & Vaara, 1985). The function of the outer membrane is to serve as a protective envelope against hostile environments such as those in the intestinal tract of animals where harmful and toxic substances - for example, bile salts and various enzymes - are often found. The outer membrane itself would be impermeable to most hydrophilic solutes were it not for the presence of membrane channels. The presence of a large number of pore-forming proteins provides both specific and nonspecific diffusion pathways across the outer membrane for solutes such as nutrients and waste products to diffuse into or out of the cell.
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Affiliation(s)
- B K Jap
- Division of Cell and Molecular Biology, Lawrence Berkeley Laboratory, University of California, Berkeley 94720
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47
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Dorset DL. Anomeric exchange and the structure of n-alkyl D-glucopyranosides. A study of binary phase behavior. Carbohydr Res 1990; 206:193-205. [PMID: 2073632 DOI: 10.1016/0008-6215(90)80060-g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
X-Ray diffraction and calorimetric data from the alpha and beta anomers of n-alkyl D-glucopyranosides are analyzed to describe the molecular packing and co-solubility in the crystalline and liquid-crystalline phases. In the smectogenic chain-length series, the beta-glucosides are co-soluble, with almost ideal mixing in the crystalline and meso-phases for chain-length differences of two carbon atoms. The smectic phases of octyl alpha- and beta-glucosides are also co-soluble and a time sequence of phase diagrams (as well as lamellar X-ray data), as the solid obtained from the cooled melt is equilibrated, indicate that a metastable co-crystalline phase may exist until the respective hydrogen-bonding schemes are established. Lamellar spacings from a homologous series of the beta anomers indicate that both the crystal structure and smectic-layer packings involve bilayer stacking of the molecules, a result that is difficult to reconcile with the respective surface-area requirements of the molecular acyl chain and sugar moieties.
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Affiliation(s)
- D L Dorset
- Electron Diffraction Department, Medical Foundation of Buffalo, Inc., NY 14203
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48
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49
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Weiss MS, Wacker T, Weckesser J, Welte W, Schulz GE. The three-dimensional structure of porin from Rhodobacter capsulatus at 3 A resolution. FEBS Lett 1990; 267:268-72. [PMID: 2165921 DOI: 10.1016/0014-5793(90)80942-c] [Citation(s) in RCA: 183] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The crystal structure of porin from Rhodobacter capsulatus strain 37b4 has been solved at 3.0 A (1 A = 0.1 nm) resolution by multiple isomorphous replacement and solvent-flattening. The three pores of the trimer are well defined in the electron density map. Each pore consists of a 16-stranded beta-barrel which traverses the membrane as a tube. Near its center the tube is narrowed by chain segments protruding from the inner wall of the barrel that form an eye-let with an irregular cross-section of about 6 A by 10 A. The eye-let has an axial length of about 10 A; it defines the exclusion limit for diffusing particles.
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Affiliation(s)
- M S Weiss
- Institut für Organische Chemie und Biochemie, Freiburg, FRG
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50
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Abstract
Significant progress in the elucidation of folding patterns of membrane proteins has been made over the past 10 years; yet, the scope of our knowledge remains extremely limited. Several difficulties beset the rational selection of crystallization conditions, of which the problem of the colloidal properties of detergent solutions is only one. In this report, specific critical parameters of colloidal solutions are considered: the shape of surfactant micelles and their clustering near phase transitions. If recognized, these properties may be exploited for crystallization. Yet, a systematic search of parameters remains necessary if the chances of obtaining a better view of the scope of membrane protein folding patterns are to be increased.
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