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Soler DC, Kowatz T, Sloan AE, McCormick TS, Cooper KD, Stepanyan R, Engel A, Vahedi-Faridi A. A region within the third extracellular loop of rat Aquaporin 6 precludes trafficking to plasma membrane in a heterologous cell line. Sci Rep 2021; 11:13673. [PMID: 34211055 PMCID: PMC8249660 DOI: 10.1038/s41598-021-93117-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022] Open
Abstract
The inability to over-express Aquaporin 6 (AQP6) in the plasma membrane of heterologous cells has hampered efforts to further characterize the function of this aquaglyceroporin membrane protein at atomic detail using crystallographic approaches. Using an Aquaporin 3-tGFP Reporter (AGR) system we have identified a region within loop C of AQP6 that is responsible for severely hampering plasma membrane expression. Serine substitution corroborated that amino acids present within AQP6194–213 of AQP6 loop C contribute to intracellular endoplasmic reticulum (ER) retention. This intracellular retention signal may preclude proper plasma membrane trafficking and severely curtail expression of AQP6 in heterologous expression systems.
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Affiliation(s)
- D C Soler
- The Department of Neurosurgery, Case Western Reserve University, Cleveland, USA.
| | - T Kowatz
- Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106-4965, USA
| | - A E Sloan
- The Department of Neurosurgery, Case Western Reserve University, Cleveland, USA.,Brain Tumor and Neuro-Oncology Center, University Hospitals Cleveland Medical Center, Cleveland, USA
| | - T S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, USA.,Murdough Family Center for Psoriasis, Case Western Reserve University, Cleveland, USA
| | - K D Cooper
- Department of Dermatology, Case Western Reserve University, Cleveland, USA.,Murdough Family Center for Psoriasis, Case Western Reserve University, Cleveland, USA
| | - R Stepanyan
- Department of Otolaryngology-HNS, Case Western Reserve University, Cleveland, USA.,Department of Neurosciences, Case Western Reserve University, Cleveland, USA
| | - A Engel
- Biozentrum, University of Basel, Basel, Switzerland
| | - A Vahedi-Faridi
- Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106-4965, USA
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Michenkova M, Taki S, Blosser MC, Hwang HJ, Kowatz T, Moss FJ, Occhipinti R, Qin X, Sen S, Shinn E, Wang D, Zeise BS, Zhao P, Malmstadt N, Vahedi-Faridi A, Tajkhorshid E, Boron WF. Carbon dioxide transport across membranes. Interface Focus 2021; 11:20200090. [PMID: 33633837 PMCID: PMC7898146 DOI: 10.1098/rsfs.2020.0090] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/30/2022] Open
Abstract
Carbon dioxide (CO2) movement across cellular membranes is passive and governed by Fick's law of diffusion. Until recently, we believed that gases cross biological membranes exclusively by dissolving in and then diffusing through membrane lipid. However, the observation that some membranes are CO2 impermeable led to the discovery of a gas molecule moving through a channel; namely, CO2 diffusion through aquaporin-1 (AQP1). Later work demonstrated CO2 diffusion through rhesus (Rh) proteins and NH3 diffusion through both AQPs and Rh proteins. The tetrameric AQPs exhibit differential selectivity for CO2 versus NH3 versus H2O, reflecting physico-chemical differences among the small molecules as well as among the hydrophilic monomeric pores and hydrophobic central pores of various AQPs. Preliminary work suggests that NH3 moves through the monomeric pores of AQP1, whereas CO2 moves through both monomeric and central pores. Initial work on AQP5 indicates that it is possible to create a metal-binding site on the central pore's extracellular face, thereby blocking CO2 movement. The trimeric Rh proteins have monomers with hydrophilic pores surrounding a hydrophobic central pore. Preliminary work on the bacterial Rh homologue AmtB suggests that gas can diffuse through the central pore and three sets of interfacial clefts between monomers. Finally, initial work indicates that CO2 diffuses through the electrogenic Na/HCO3 cotransporter NBCe1. At least in some cells, CO2-permeable proteins could provide important pathways for transmembrane CO2 movements. Such pathways could be amenable to cellular regulation and could become valuable drug targets.
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Affiliation(s)
- Marie Michenkova
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sara Taki
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Matthew C. Blosser
- Mork Family Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Hyea J. Hwang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Thomas Kowatz
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Fraser. J. Moss
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rossana Occhipinti
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Xue Qin
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Soumyo Sen
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Shinn
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dengke Wang
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Brian S. Zeise
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pan Zhao
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Noah Malmstadt
- Mork Family Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Ardeschir Vahedi-Faridi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Walter F. Boron
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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3
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Moss FJ, Mahinthichaichan P, Lodowski DT, Kowatz T, Tajkhorshid E, Engel A, Boron WF, Vahedi-Faridi A. Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF. Front Physiol 2020; 11:728. [PMID: 32695023 PMCID: PMC7339978 DOI: 10.3389/fphys.2020.00728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/04/2020] [Indexed: 12/27/2022] Open
Abstract
Xenopus oocytes expressing human aquaporin-7 (AQP7) exhibit greater osmotic water permeability and 3H-glycerol uptake vs. those expressing the bacterial glycerol facilitator GlpF. AQP7-expressing oocytes exposed to increasing extracellular [glycerol] under isosmolal conditions exhibit increasing swelling rates, whereas GlpF-expressing oocytes do not swell at all. To provide a structural basis for these observed physiological differences, we performed X-ray crystallographic structure determination of AQP7 and molecular-dynamics simulations on AQP7 and GlpF. The structure reveals AQP7 tetramers containing two monomers with 3 glycerols, and two monomers with 2 glycerols in the pore. In contrast to GlpF, no glycerol is bound at the AQP7 selectivity filter (SF), comprising residues F74, G222, Y223, and R229. The AQP7 SF is resolved in its closed state because F74 blocks the passage of small solutes. Molecular dynamics simulations demonstrate that F74 undergoes large and rapid conformational changes, allowing glycerol molecules to permeate without orientational restriction. The more rigid GlpF imposes orientational constraints on glycerol molecules passing through the SF. Moreover, GlpF-W48 (analogous to AQP7-F74) undergoes rare but long-lasting conformational changes that block the pore to H2O and glycerol.
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Affiliation(s)
- Fraser J. Moss
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Paween Mahinthichaichan
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - David T. Lodowski
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Thomas Kowatz
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Andreas Engel
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Walter F. Boron
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Ardeschir Vahedi-Faridi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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Soler DC, Young AE, Vahedi-Faridi A, McCormick TS. Generation of Flp-in tm-ready DG44 and Lec 3.2.8.1 CHO cell lines for quick and easy constitutive protein expression. Biotechniques 2018; 65:41-46. [PMID: 30014730 DOI: 10.2144/btn-2018-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The well-characterized cell line Chinese hamster ovary (CHO) has been used to produce numerous biopharmaceuticals and is an important tool for basic research. However, introducing foreign DNA into specially modified CHO cells such as DG44 and Lec 3.2.8.1 can sometimes be an arduous process. Here we show that the Flp-intm plasmid can be modified to produce a fluorescent tracer protein tag (mCherrytm) as a fusion reporter, to allow for the rapid selection of single-cell sorted, isogenic Flp-intm-ready DG44 and Lec 3.2.8.1 cell lines. These two cell lines are stable and viable and may be useful for applications such as antibody production and crystallographic studies. Here we provide key details on how the modified pFRT/CherryZeo plasmid may be used to incorporate Flp-intm technology into virtually any desired target cell line in a fast, safe and reliable manner.
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Affiliation(s)
- D C Soler
- The Department of Neurosurgery, 2109 Adelbert Road, Cleveland, OH 44106, USA
- Case Western Reserve University School of Medicine, 2109 Adelbert Road, Cleveland, OH 44106, USA
| | - A E Young
- Case Western Reserve University School of Medicine, 2109 Adelbert Road, Cleveland, OH 44106, USA
- The Department of Dermatology, 2109 Adelbert Road, OH, USA
- The Skin Diseases Research Center, 2109 Adelbert Road, OH, USA
| | - A Vahedi-Faridi
- Department of Physiology & Biophysics, 2109 Adelbert Road, OH, USA
| | - T S McCormick
- Case Western Reserve University School of Medicine, 2109 Adelbert Road, Cleveland, OH 44106, USA
- The Department of Dermatology, 2109 Adelbert Road, OH, USA
- The Skin Diseases Research Center, 2109 Adelbert Road, OH, USA
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5
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Wedepohl S, Dernedde J, Vahedi-Faridi A, Tauber R, Saenger W, Bulut H. Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 Å Resolution. Chembiochem 2017; 18:1338-1345. [PMID: 28489325 DOI: 10.1002/cbic.201700220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/07/2023]
Abstract
L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. After we further removed microheterogeneity, we obtained crystals that diffracted X-rays up to 1.9 Å from a variant (LE010) with exchanges N22Q and N139Q and one GlcNAc2 Man5 N-glycan chain attached to Asn66. Crystal-structure analysis showed that the terminal mannose of GlcNAc2 Man5 of one LE010 molecule was coordinated to Ca2+ in the binding site of a symmetry-related LE010. The orientation of the lectin and EGF-like domain was similar to the described "bent" conformation of E- and P-selectins. The Ca2+ -binding site reflects the binding mode seen in E- and P-selectin structures co-crystallised with ligands.
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Affiliation(s)
- Stefanie Wedepohl
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jens Dernedde
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
| | - Rudolf Tauber
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
| | - Haydar Bulut
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Ding F, Lee KJ, Vahedi-Faridi A, Yoneyama H, Osgood CJ, Xu XHN. Design and study of the efflux function of the EGFP fused MexAB-OprM membrane transporter in Pseudomonas aeruginosa using fluorescence spectroscopy. Analyst 2014; 139:3088-96. [PMID: 24781334 DOI: 10.1039/c4an00108g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidrug membrane transporters (efflux pumps) can selectively extrude a variety of structurally and functionally diverse substrates (e.g., chemotoxics, antibiotics), leading to multidrug resistance (MDR) and ineffective treatment of a wide variety of diseases. In this study, we have designed and constructed a fusion gene (egfp-mexB) of N-terminal mexB with C-terminal egfp, inserted it into a plasmid vector (pMMB67EH), and successfully expressed it in the ΔMexB (MexB deletion) strain of Pseudomonas aeruginosa to create a new strain that expresses MexA-(EGFP-MexB)-OprM. We characterized the fusion gene using gel electrophoresis and DNA sequencing, and determined its expression in live cells by measuring the fluorescence of EGFP in single live cells using fluorescence microscopy. Efflux function of the new strain was studied by measuring its accumulation kinetics of ethidium bromide (EtBr, a pump substrate) using fluorescence spectroscopy, which was compared with cells (WT, ΔMexM, ΔABM, and nalB1) with various expression levels of MexAB-OprM. The new strain shows 6-fold lower accumulation rates of EtBr (15 μM) than ΔABM, 4-fold lower than ΔMexB, but only 1.1-fold higher than WT. As the EtBr concentration increases to 40 μM, the new strain has nearly the same accumulation rate of EtBr as ΔMexB, but 1.4-fold higher than WT. We observed the nearly same level of inhibitory effect of CCCP (carbonyl cyanide-m-chlorophenylhydrazone) on the efflux of EtBr by the new strain and WT. Antibiotic susceptibility study shows that the minimum inhibitory concentrations (MICs) of aztreonam (AZT) and chloramphenicol (CP) for the new strain are 6-fold or 3-fold lower than WT, respectively, and 2-fold higher than those of ΔMexB. Taken together, the results suggest that the fusion protein partially retains the efflux function of MexAB-OprM. The modeled structure of the fusion protein shows that the position and orientation of the N-terminal fused EGFP domain may either partially block the translocation pore or restrict the movement of the individual pump domains, which may lead to partially restricted efflux activity.
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Affiliation(s)
- Feng Ding
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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Vahedi-Faridi A, Jastrzebska B, Palczewski K, Engel A. 3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy. Microscopy (Oxf) 2012; 62:95-107. [PMID: 23267047 DOI: 10.1093/jmicro/dfs091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Inherently unstable, detergent-solubilized membrane protein complexes can often not be crystallized. For complexes that have a mass of >300 kDa, cryo-electron microscopy (EM) allows their three-dimensional (3D) structure to be assessed to a resolution that makes secondary structure elements visible in the best case. However, many interesting complexes exist whose mass is below 300 kDa and thus need alternative approaches. Two methods are reviewed: (i) Mass measurement in a scanning transmission electron microscope, which has provided important information on the stoichiometry of membrane protein complexes. This technique is applicable to particulate, filamentous and sheet-like structures. (ii) 3D-EM of negatively stained samples, which determines the molecular envelope of small membrane protein complexes. Staining and dehydration artifacts may corrupt the quality of the 3D map. Staining conditions thus need to be optimized. 3D maps of plant aquaporin SoPIP2;1 tetramers solubilized in different detergents illustrate that the flattening artifact can be partially prevented and that the detergent itself contributes significantly. Another example discussed is the complex of G protein-coupled receptor rhodopsin with its cognate G protein transducin.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106-4965, USA
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Bulut H, Ma Q, Moniot S, Saenger W, Schneider E, Vahedi-Faridi A. Crystal structures of receptors involved in small molecule transport across membranes. Eur J Cell Biol 2012; 91:318-25. [PMID: 22341528 DOI: 10.1016/j.ejcb.2011.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 12/15/2011] [Accepted: 12/15/2011] [Indexed: 10/28/2022] Open
Abstract
This paper briefly reviews contemporary protein crystallography and focuses on six receptor proteins of membrane-intrinsic ATP binding cassette (ABC) transporters. Three of these receptors are specific for carbohydrates and three for amino acids. The receptor GacH of the transporter GacFGH from Streptomyces glaucescens is specific for acarbose and its homologs, and MalE of Salmonella typhimurium is specific for maltose but also forms a complex with acarbose, and the third receptor is the highly specific d-galactose receptor AcbH of the transporter AcbFGH from Actinoplanes sp. Concerning the receptors for amino acids, ArtJ belongs to the ArtJ-(MP)(2) transporter of Geobacillus stearotermophilus and recognizes and binds to positively charged arginine, lysine, and histidine with different sizes of side chains, contrasting the receptors Ngo0372 and Ngo2014 from Neisseria gonorrhaeae that are highly specific for cystine and cysteine, respectively. The differences in the rather unspecific receptors GacH, MalE and ArtJ are compared with the highly specific receptors AcbH, Ngo0372 and Ngo2014.
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Affiliation(s)
- Haydar Bulut
- Institut für Chemie und Biochemie, Abteilung Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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Porta J, Vahedi-Faridi A, Borgstahl GE. Structural Analysis of Peroxide-Soaked MnSOD Crystals Reveals Side-On Binding of Peroxide to Active-Site Manganese. J Mol Biol 2010; 399:377-84. [DOI: 10.1016/j.jmb.2010.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/24/2010] [Accepted: 04/18/2010] [Indexed: 10/19/2022]
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Vahedi-Faridi A, Licht A, Bulut H, Scheffel F, Keller S, Wehmeier UF, Saenger W, Schneider E. Crystal structures of the solute receptor GacH of Streptomyces glaucescens in complex with acarbose and an acarbose homolog: comparison with the acarbose-loaded maltose-binding protein of Salmonella typhimurium. J Mol Biol 2010; 397:709-23. [PMID: 20132828 DOI: 10.1016/j.jmb.2010.01.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/22/2010] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
Abstract
GacH is the solute binding protein (receptor) of the putative oligosaccharide ATP-binding cassette transporter GacFG, encoded in the acarbose biosynthetic gene cluster (gac) from Streptomyces glaucescens GLA.O. In the context of the proposed function of acarbose (acarviosyl-1,4-maltose) as a 'carbophor,' the transporter, in complex with a yet to be identified ATPase subunit, is supposed to mediate the uptake of longer acarbose homologs and acarbose for recycling purposes. Binding assays using isothermal titration calorimetry identified GacH as a maltose/maltodextrin-binding protein with a low affinity for acarbose but with considerable binding activity for its homolog, component 5C (acarviosyl-1,4-maltose-1,4-glucose-1,1-glucose). In contrast, the maltose-binding protein of Salmonella typhimurium (MalE) displays high-affinity acarbose binding. We determined the crystal structures of GacH in complex with acarbose, component 5C, and maltotetraose, as well as in unliganded form. As found for other solute receptors, the polypeptide chain of GacH is folded into two distinct domains (lobes) connected by a hinge, with the interface between the lobes forming the substrate-binding pocket. GacH does not specifically bind the acarviosyl group, but displays specificity for binding of the maltose moiety in the inner part of its binding pocket. The crystal structure of acarbose-loaded MalE showed that two glucose units of acarbose are bound at the same region and position as maltose. A comparative analysis revealed that in GacH, acarbose is buried deeper into the binding pocket than in MalE by exactly one glucose ring shift, resulting in a total of 18 hydrogen-bond interactions versus 21 hydrogen-bond interactions for MalE(acarbose). Since the substrate specificity of ATP-binding cassette import systems is determined by the cognate binding protein, our results provide the first biochemical and structural evidence for the proposed role of GacHFG in acarbose metabolism.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Berlin, Germany
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Kahlfeldt N, Vahedi-Faridi A, Koo SJ, Schäfer JG, Krainer G, Keller S, Saenger W, Krauss M, Haucke V. Molecular basis for association of PIPKI gamma-p90 with clathrin adaptor AP-2. J Biol Chem 2010; 285:2734-49. [PMID: 19903820 PMCID: PMC2807329 DOI: 10.1074/jbc.m109.074906] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 11/06/2009] [Indexed: 12/21/2022] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) is an essential determinant in clathrin-mediated endocytosis (CME). In mammals three type I phosphatidylinositol-4-phosphate 5-kinase (PIPK) enzymes are expressed, with the I gamma-p90 isoform being highly expressed in the brain where it regulates synaptic vesicle (SV) exo-/endocytosis at nerve terminals. How precisely PI(4,5)P(2) metabolism is controlled spatially and temporally is still uncertain, but recent data indicate that direct interactions between type I PIPK and components of the endocytic machinery, in particular the AP-2 adaptor complex, are involved. Here we demonstrated that PIPKI gamma-p90 associates with both the mu and beta2 subunits of AP-2 via multiple sites. Crystallographic data show that a peptide derived from the splice insert of the human PIPKI gamma-p90 tail binds to a cognate recognition site on the sandwich subdomain of the beta2 appendage. Partly overlapping aromatic and hydrophobic residues within the same peptide also can engage the C-terminal sorting signal binding domain of AP-2mu, thereby potentially competing with the sorting of conventional YXXØ motif-containing cargo. Biochemical and structure-based mutagenesis analysis revealed that association of the tail domain of PIPKI gamma-p90 with AP-2 involves both of these sites. Accordingly the ability of overexpressed PIPKI gamma tail to impair endocytosis of SVs in primary neurons largely depends on its association with AP-2 beta and AP-2mu. Our data also suggest that interactions between AP-2 and the tail domain of PIPKI gamma-p90 may serve to regulate complex formation and enzymatic activity. We postulate a model according to which multiple interactions between PIPKI gamma-p90 and AP-2 lead to spatiotemporally controlled PI(4,5)P(2) synthesis during clathrin-mediated SV endocytosis.
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Affiliation(s)
- Nina Kahlfeldt
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Seong Joo Koo
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Johannes G. Schäfer
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Georg Krainer
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
- the Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Sandro Keller
- the Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Wolfram Saenger
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Krauss
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
| | - Volker Haucke
- From the Institute of Chemistry and Biochemistry, Departments of Membrane Biochemistry and Protein Crystallography, Freie Universität Berlin, 14195 Berlin, Germany
- the Charité Universitätsmedizin Berlin, 14195 Berlin, Germany, and
- the Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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Kumar P, Vahedi-Faridi A, Saenger W, Merino E, López de Castro JA, Uchanska-Ziegler B, Ziegler A. Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens. J Biol Chem 2009; 284:29784-97. [PMID: 19617632 PMCID: PMC2785609 DOI: 10.1074/jbc.m109.038497] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 07/09/2009] [Indexed: 01/07/2023] Open
Abstract
The existence of cytotoxic T cells (CTL) cross-reacting with the human major histocompatibility antigens HLA-B14 and HLA-B27 suggests that their alloreactivity could be due to presentation of shared peptides in similar binding modes by these molecules. We therefore determined the crystal structures of the subtypes HLA-B*1402, HLA-B*2705, and HLA-B*2709 in complex with a proven self-ligand, pCatA (peptide with the sequence IRAAPPPLF derived from cathepsin A (residues 2-10)), and of HLA-B*1402 in complex with a viral peptide, pLMP2 (RRRWRRLTV, derived from latent membrane protein 2 (residues 236-244) of Epstein-Barr virus). Despite the exchange of 18 residues within the binding grooves of HLA-B*1402 and HLA-B*2705 or HLA-B*2709, the pCatA peptide is presented in nearly identical conformations. However, pLMP2 is displayed by HLA-B*1402 in a conformation distinct from those previously found in the two HLA-B27 subtypes. In addition, the complexes of HLA-B*1402 with the two peptides reveal a nonstandard, tetragonal mode of the peptide N terminus anchoring in the binding groove because of the exchange of the common Tyr-171 by His-171 of the HLA-B*1402 heavy chain. This exchange appears also responsible for reduced stability of HLA-B14-peptide complexes in vivo and slow assembly in vitro. The studies with the pCatA peptide uncover that CTL cross-reactive between HLA-B14 and HLA-B27 might primarily recognize the common structural features of the bound peptide, thus neglecting amino acid replacements within the rim of the binding grooves. In contrast, structural alterations between the three complexes with the pLMP2 peptide indicate how heavy chain polymorphisms can influence peptide display and prevent CTL cross-reactivity between HLA-B14 and HLA-B27 antigens.
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Affiliation(s)
- Pravin Kumar
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- the Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany, and
| | - Wolfram Saenger
- the Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany, and
| | - Elena Merino
- the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas and Universidad Autónoma de Madrid, Nicolás Cabrera, N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - José A. López de Castro
- the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas and Universidad Autónoma de Madrid, Nicolás Cabrera, N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - Barbara Uchanska-Ziegler
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Andreas Ziegler
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
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14
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Kumar P, Vahedi-Faridi A, Saenger W, Ziegler A, Uchanska-Ziegler B. Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity. Protein Sci 2009; 18:37-49. [PMID: 19177349 DOI: 10.1002/pro.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although there is X-ray crystallographic evidence that the interaction between major histocompatibility complex (MHC, in humans HLA) class I molecules and T cell receptors (TCR) or killer cell Ig-like receptors (KIR) may be accompanied by considerable changes in the conformation of selected residues or even entire loops within TCR or KIR, conformational changes between receptor-bound and -unbound MHC class I molecules of comparable magnitude have not been observed so far. We have previously determined the structure of the MHC class I molecule HLA-A1 bound to a melanoma antigen-encoding gene (MAGE)-A1-derived peptide in complex with a recombinant antibody fragment with TCR-like specificity, Fab-Hyb3. Here, we compare the X-ray structure of HLA-A1:MAGE-A1 with that complexed with Fab-Hyb3 to gain insight into structural changes of the MHC molecule that might be induced by the interaction with the antibody fragment. Apart from the expulsion of several water molecules from the interface, Fab-Hyb3 binding results in major rearrangements (up to 5.5 A) of heavy chain residues Arg65, Gln72, Arg145, and Lys146. Residue 65 is frequently and residues 72 and 146 are occasionally involved in TCR binding-induced conformational changes, as revealed by a comparison with MHC class I structures in TCR-liganded and -unliganded forms. On the other hand, residue 145 is subject to a reorientation following engagement of HLA-Cw4 and KIR2DL1. Therefore, conformational changes within the HLA-A1:MAGE-A1:Fab-Hyb3 complex include MHC residues that are also involved in reorientations in complexes with natural ligands, pointing to their central importance for the peptide-dependent recognition of MHC molecules.
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Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, Berlin 14195, Germany
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15
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Kittler JT, Chen G, Kukhtina V, Vahedi-Faridi A, Gu Z, Tretter V, Smith KR, McAinsh K, Arancibia-Carcamo IL, Saenger W, Haucke V, Yan Z, Moss SJ. Regulation of synaptic inhibition by phospho-dependent binding of the AP2 complex to a YECL motif in the GABAA receptor gamma2 subunit. Proc Natl Acad Sci U S A 2008; 105:3616-21. [PMID: 18305175 PMCID: PMC2265186 DOI: 10.1073/pnas.0707920105] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Indexed: 11/18/2022] Open
Abstract
The regulation of the number of gamma2-subunit-containing GABA(A) receptors (GABA(A)Rs) present at synapses is critical for correct synaptic inhibition and animal behavior. This regulation occurs, in part, by the controlled removal of receptors from the membrane in clathrin-coated vesicles, but it remains unclear how clathrin recruitment to surface gamma2-subunit-containing GABA(A)Rs is regulated. Here, we identify a gamma2-subunit-specific Yxxvarphi-type-binding motif for the clathrin adaptor protein, AP2, which is located within a site for gamma2-subunit tyrosine phosphorylation. Blocking GABA(A)R-AP2 interactions via this motif increases synaptic responses within minutes. Crystallographic and biochemical studies reveal that phosphorylation of the Yxxvarphi motif inhibits AP2 binding, leading to increased surface receptor number. In addition, the crystal structure provides an explanation for the high affinity of this motif for AP2 and suggests that gamma2-subunit-containing heteromeric GABA(A)Rs may be internalized as dimers or multimers. These data define a mechanism for tyrosine kinase regulation of GABA(A)R surface levels and synaptic inhibition.
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Affiliation(s)
- Josef T Kittler
- Department of Physiology, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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16
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Vahedi-Faridi A, Eckey V, Scheffel F, Alings C, Landmesser H, Schneider E, Saenger W. Crystal structures and mutational analysis of the arginine-, lysine-, histidine-binding protein ArtJ from Geobacillus stearothermophilus. Implications for interactions of ArtJ with its cognate ATP-binding cassette transporter, Art(MP)2. J Mol Biol 2007; 375:448-59. [PMID: 18022195 DOI: 10.1016/j.jmb.2007.10.049] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 10/04/2007] [Indexed: 11/30/2022]
Abstract
ArtJ is the substrate-binding component (receptor) of the ATP-binding cassette (ABC) transport system ArtJ-(MP)(2) from the thermophilic bacterium Geobacillus stearothermophilus that is specific for arginine, lysine, and histidine. The highest affinity is found for arginine (K(d)=0.039(+/-0.014) microM), while the affinities for lysine and histidine are about tenfold lower. We have determined the X-ray structures of ArtJ liganded with each of these substrates at resolutions of 1.79 A (arginine), 1.79 A (lysine), and 2.35 A (histidine), respectively. As found for other solute receptors, the polypeptide chain is folded into two distinct domains (lobes) connected by a hinge. The interface between the lobes forms the substrate-binding pocket whose geometry is well preserved in all three ArtJ/amino acid complexes. Structure-derived mutational analyses indicated the crucial role of a region in the carboxy-terminal lobe of ArtJ in contacting the transport pore Art(MP)(2) and revealed the functional importance of Gln132 and Trp68. While variant Gln132Leu exhibited lower binding affinity for arginine but no binding of lysine and histidine, the variant Trp68Leu had lost binding activity for all three substrates. The results are discussed in comparison with known structures of homologous proteins from mesophilic bacteria.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universitaet Berlin, Takustr. 6, 14195 Berlin, Germany
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17
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Yikilmaz E, Porta J, Grove LE, Vahedi-Faridi A, Bronshteyn Y, Brunold TC, Borgstahl GEO, Miller AF. How Can a Single Second Sphere Amino Acid Substitution Cause Reduction Midpoint Potential Changes of Hundreds of Millivolts? J Am Chem Soc 2007; 129:9927-40. [PMID: 17628062 DOI: 10.1021/ja069224t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The active site metal ion of superoxide dismutase (SOD) is reduced and reoxidized as it disproportionates superoxide to dioxygen and hydrogen peroxide. Thus, the reduction midpoint potential (Em) is a critical determinant of catalytic activity. In E. coli Fe-containing SOD (FeSOD), reduction of Fe3+ is accompanied by protonation of a coordinated OH-, to produce Fe2+ coordinated by H2O. The coordinated solvent's only contact with the protein beyond the active site is a conserved Gln residue. Mutation of this Gln to His or Glu resulted in elevation of the Em by 220 mV and more than 660 mV, respectively [Yikilmaz et al., Biochemistry 2006, 45, 1151-1161], despite the fact that overall protein structure was preserved, His is a chemically conservative replacement for Gln, and neutral Glu is isostructural and isoelectronic with Gln. Therefore, we have investigated several possible bases for the elevated Em's, including altered Fe electronic structure, altered active site electrostatics, altered H-bonding and altered redox-coupled proton transfer. Using EPR, MCD, and NMR spectroscopies, we find that the active site electronic structures of the two mutants resemble that of the WT enzyme, for both oxidation states, and Q69E-FeSOD's apparent deviation from WT-like Fe3+ coordination in the oxidized state can be explained by increased affinity for a small anion. Spontaneous coordination of an exogenous anion can only stabilize oxidized Q69E-Fe3+SOD and, therefore, cannot account for the increased Em of Q69E FeSOD. WT-like anion binding affinities and active site pK's indicate that His69 of Q69H-FeSOD is neutral in both oxidation states, like Gln69 of WT-FeSOD, whereas Glu69 appears to be neutral in the oxidized state but ionized in the reduced state of Q69E-FeSOD. A 1.1 A resolution crystal structure of Q69E-Fe2+SOD indicates that Glu69 accepts a strong H-bond from coordinated solvent in the reduced state, in contrast to the case in WT-FeSOD where Gln69 donates an H-bond. These data and DFT calculations lead to the proposal that the elevated Em of Q69E-FeSOD can be substantially explained by (1) relief from enforced H-bond donation in the reduced state, (2) Glu69's capacity to provide a proton for proton-coupled Fe3+ reduction, and (3) strong hydrogen bond acceptance in the reduced state, which stabilizes coordinated H2O. Our results thus support the hypothesis that the protein matrix can apply significant redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.
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Affiliation(s)
- Emine Yikilmaz
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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18
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Kumar P, Vahedi-Faridi A, Merino E, López de Castro JA, Volz A, Ziegler A, Saenger W, Uchanska-Ziegler B. Expression, purification and preliminary X-ray crystallographic analysis of the human major histocompatibility antigen HLA-B*1402 in complex with a viral peptide and with a self-peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:631-4. [PMID: 17620730 PMCID: PMC2335130 DOI: 10.1107/s1744309107029077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 06/13/2007] [Indexed: 05/16/2023]
Abstract
The product of the human major histocompatibility (HLA) class I allele HLA-B*1402 only differs from that of allele HLA-B*1403 at amino-acid position 156 of the heavy chain (Leu in HLA-B*1402 and Arg in HLA-B*1403). However, both subtypes are known to be differentially associated with the inflammatory rheumatic disease ankylosing spondylitis (AS) in black populations in Cameroon and Togo. HLA-B*1402 is not associated with AS, in contrast to HLA-B*1403, which is associated with this disease in the Togolese population. The products of these alleles can present peptides with Arg at position 2, a feature shared by a small group of other HLA-B antigens, including HLA-B*2705, the prototypical AS-associated subtype. Complexes of HLA-B*1402 with a viral peptide (RRRWRRLTV, termed pLMP2) and a self-peptide (IRAAPPPLF, termed pCatA) were prepared and were crystallized using polyethylene glycol as precipitant. The complexes crystallized in space groups P2(1) (pLMP2) and P2(1)2(1)2(1) (pCatA) and diffracted synchrotron radiation to 2.55 and 1.86 A resolution, respectively. Unambiguous solutions for both data sets were obtained by molecular replacement using a peptide-complexed HLA-B*2705 molecule (PDB code 1jge) as a search model.
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Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Elena Merino
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Facultad de Ciencias, Universidad Autónoma, 28049 Madrid, Spain
| | - José A. López de Castro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Facultad de Ciencias, Universidad Autónoma, 28049 Madrid, Spain
| | - Armin Volz
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
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Stojanoff V, Vahedi-Faridi A, Yeh JI. Improvement of crystal quality by time controlled annealing. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305099629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Vahedi-Faridi A, Stojanoff V, Yeh JI. The effects of flash-annealing on glycerol kinase crystals. Acta Crystallogr D Biol Crystallogr 2005; 61:982-9. [PMID: 15983422 DOI: 10.1107/s0907444905012746] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Accepted: 04/22/2005] [Indexed: 11/10/2022]
Abstract
Reflection profiles from glycerol kinase crystals were analyzed to determine the effect of flash-cooling on mosaicity (eta) and peak intensity in order to reveal changes in mosaic domain structure and composition. The results showed that repeated flash-annealing causes a significant decrease in the averaged mosaicity along with an increase in the overall peak counts of reflections and an enhanced signal-to-noise ratio. Individual reflection-profile analysis revealed a mostly dual domain structure, showing the minimization of one domain as a result of flash-annealing.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- Brown University, Department of Molecular Biology, Cell Biology and Biochemistry, 70 Ship Street, Providence, RI 02903, USA
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Vahedi-Faridi A, Lovelace J, Bellamy HD, Snell EH, Borgstahl GEO. Physical and structural studies on the cryocooling of insulin crystals. Acta Crystallogr D Biol Crystallogr 2003; 59:2169-82. [PMID: 14646075 DOI: 10.1107/s0907444903019668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2003] [Accepted: 09/05/2003] [Indexed: 11/10/2022]
Abstract
Reflection profiles were analyzed from microgravity-grown ( micro g) and earth-grown insulin crystals to measure mosaicity (eta) and to reveal mosaic domain structure and composition. The effects of cryocooling on single-domain and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were of larger volume, were more homogeneous and were of higher quality than earth crystals. Several micro g crystals contained a single mosaic domain which encompassed all or nearly all of the crystal with an eta(avg) of 0.005 degrees. The earth crystals varied in quality and all contained multiple domains with an eta(avg) of 0.031 degrees. Cryocooling caused a 43-fold increase in eta for micro g crystals (eta(avg) = 0.217 degrees ) and an eightfold increase for earth crystals (eta(avg) = 0.246 degrees ). These results indicate that very well ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryocooling. Cryocooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryocooled single-domain crystals relative to cryocooled multi-domain crystals. The improved signal from micro g crystals, along with the increase in crystal size, facilitated the measurement of the weaker high-resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit-cell parameters, which may be linked to cryocooling-associated structural changes and disorder.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- The University of Toledo, Department of Chemistry, 2801 West Bancroft Street, Toledo, OH 43606, USA
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Vahedi-Faridi A, Porta J, Borgstahl GEO. Improved three-dimensional growth of manganese superoxide dismutase crystals on the International Space Station. Acta Crystallogr D Biol Crystallogr 2003; 59:385-8. [PMID: 12554961 DOI: 10.1107/s0907444902020310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 11/07/2002] [Indexed: 11/11/2022]
Abstract
Manganese superoxide dismutase was crystallized in microgravity with 35 PCAM experiments (Protein Crystallization Apparatus for Microgravity) on the ISS (International Space Station) from 5 December 2001 to 19 April 2002. Crystals were very large in size and could easily be seen by eye. Crystals with 0.45 x 0.45 mm cross-sections and of up to 3 mm in length were obtained in several drops: an 80-fold increase in crystal Volume compared with the largest earth-grown crystal. A smaller crystal (0.15 x 0.30 mm in cross-section and 1.6 mm in length) was soaked in cryoprotectant and placed in a cryoloop. Diffraction data were collected at 100 K at the BioCARS bending-magnet beamline. The space group was C222(1), with unit-cell parameters a = 100.64, b = 107.78, c = 179.82 A. Diffraction spots to 1.26 A resolution were observed. Unfortunately, the high-resolution diffraction degraded owing to radiation damage and the resolution limit for the complete data set was 1.35 A. It is anticipated that increasing the crystal Volume and diffraction limit through microgravity crystal growth will enable several types of technically challenging structure determinations.
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Affiliation(s)
- Ardeschir Vahedi-Faridi
- The University of Toledo, Department of Chemistry, 2801 West Bancroft Street, Toledo, OH 43606, USA
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Borgstahl GE, Vahedi-Faridi A, Lovelace J, Bellamy HD, Snell EH. A test of macromolecular crystallization in microgravity: large well ordered insulin crystals. Acta Crystallogr D Biol Crystallogr 2001; 57:1204-7. [PMID: 11468418 DOI: 10.1107/s0907444901007892] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2001] [Accepted: 05/11/2001] [Indexed: 11/11/2022]
Abstract
Crystals of insulin grown in microgravity on Space Shuttle Mission STS-95 were extremely well ordered and unusually large (many >2 mm). The physical characteristics of six microgravity and six earth-grown crystals were examined by X-ray analysis employing superfine phi slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined from each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had sevenfold lower mosaicity, had 54-fold higher reflection peak heights and diffracted to significantly higher resolution than their earth-grown counterparts. A single mosaic domain model could account for the observed reflection profiles in microgravity crystals, whereas data from earth crystals required a model with multiple mosaic domains. This statistically significant and unbiased characterization indicates that the microgravity environment was useful for the improvement of crystal growth and the resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.
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Affiliation(s)
- G E Borgstahl
- University of Toledo, Department of Chemistry, 2801 West Bancroft Street, Toledo, OH 43606, USA.
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