151
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Stone MJ, Hayward JA, Huang C, E Huma Z, Sanchez J. Mechanisms of Regulation of the Chemokine-Receptor Network. Int J Mol Sci 2017; 18:E342. [PMID: 28178200 PMCID: PMC5343877 DOI: 10.3390/ijms18020342] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/18/2017] [Accepted: 01/26/2017] [Indexed: 12/18/2022] Open
Abstract
The interactions of chemokines with their G protein-coupled receptors promote the migration of leukocytes during normal immune function and as a key aspect of the inflammatory response to tissue injury or infection. This review summarizes the major cellular and biochemical mechanisms by which the interactions of chemokines with chemokine receptors are regulated, including: selective and competitive binding interactions; genetic polymorphisms; mRNA splice variation; variation of expression, degradation and localization; down-regulation by atypical (decoy) receptors; interactions with cell-surface glycosaminoglycans; post-translational modifications; oligomerization; alternative signaling responses; and binding to natural or pharmacological inhibitors.
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Affiliation(s)
- Martin J Stone
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Jenni A Hayward
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Cheng Huang
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Zil E Huma
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Julie Sanchez
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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152
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Guo C, Hou G, Lu X, Polenova T. Mapping protein-protein interactions by double-REDOR-filtered magic angle spinning NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2017; 67:95-108. [PMID: 28120201 PMCID: PMC6258002 DOI: 10.1007/s10858-016-0086-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/25/2016] [Indexed: 05/03/2023]
Abstract
REDOR-based experiments with simultaneous 1H-13C and 1H-15N dipolar dephasing are explored for investigating intermolecular protein-protein interfaces in complexes formed by a U-13C,15N-labeled protein and its natural abundance binding partner. The application of a double-REDOR filter (dREDOR) results in a complete dephasing of proton magnetization in the U-13C,15N-enriched molecule while the proton magnetization of the unlabeled binding partner is not dephased. This retained proton magnetization is then transferred across the intermolecular interface by 1H-13C or 1H-15N cross polarization, permitting to establish the residues of the U-13C,15N-labeled protein, which constitute the binding interface. To assign the interface residues, this dREDOR-CPMAS element is incorporated as a building block into 13C-13C correlation experiments. We established the validity of this approach on U-13C,15N-histidine and on a structurally characterized complex of dynactin's U-13C,15N-CAP-Gly domain with end-binding protein 1 (EB1). The approach introduced here is broadly applicable to the analysis of intermolecular interfaces when one of the binding partners in a complex cannot be isotopically labeled.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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153
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Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs. Angew Chem Int Ed Engl 2017; 56:2508-2512. [PMID: 28128538 DOI: 10.1002/anie.201610441] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/13/2016] [Indexed: 12/30/2022]
Abstract
The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane-mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co-polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high-resolution solid-state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
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Affiliation(s)
- Beate Bersch
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Audrey Hessel
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Paul Schanda
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
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154
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Koop G, Vrieling M, Storisteanu DML, Lok LSC, Monie T, van Wigcheren G, Raisen C, Ba X, Gleadall N, Hadjirin N, Timmerman AJ, Wagenaar JA, Klunder HM, Fitzgerald JR, Zadoks R, Paterson GK, Torres C, Waller AS, Loeffler A, Loncaric I, Hoet AE, Bergström K, De Martino L, Pomba C, de Lencastre H, Ben Slama K, Gharsa H, Richardson EJ, Chilvers ER, de Haas C, van Kessel K, van Strijp JAG, Harrison EM, Holmes MA. Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus. Sci Rep 2017; 7:40660. [PMID: 28106142 PMCID: PMC5247767 DOI: 10.1038/srep40660] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/08/2016] [Indexed: 11/09/2022] Open
Abstract
Bicomponent pore-forming leukocidins are a family of potent toxins secreted by Staphylococcus aureus, which target white blood cells preferentially and consist of an S- and an F-component. The S-component recognizes a receptor on the host cell, enabling high-affinity binding to the cell surface, after which the toxins form a pore that penetrates the cell lipid bilayer. Until now, six different leukocidins have been described, some of which are host and cell specific. Here, we identify and characterise a novel S. aureus leukocidin; LukPQ. LukPQ is encoded on a 45 kb prophage (ΦSaeq1) found in six different clonal lineages, almost exclusively in strains cultured from equids. We show that LukPQ is a potent and specific killer of equine neutrophils and identify equine-CXCRA and CXCR2 as its target receptors. Although the S-component (LukP) is highly similar to the S-component of LukED, the species specificity of LukPQ and LukED differs. By forming non-canonical toxin pairs, we identify that the F-component contributes to the observed host tropism of LukPQ, thereby challenging the current paradigm that leukocidin specificity is driven solely by the S-component.
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Affiliation(s)
- Gerrit Koop
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Manouk Vrieling
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Daniel M. L. Storisteanu
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Laurence S. C. Lok
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Tom Monie
- Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge CB1 9NL, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Glenn van Wigcheren
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nicholas Gleadall
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
- Central Veterinary Institute of Wageningen UR, 8200 AB Lelystad, The Netherlands
| | - Heleen M. Klunder
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, United Kingdom
| | - Ruth Zadoks
- Moredun Research Institute, Bush Loan, Penicuik EH26 0PZ, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Gavin K. Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, Logroño 26006, Spain
| | - Andrew S. Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket CB8 7UU, United Kingdom
| | - Anette Loeffler
- Department of Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, North Mymms, Hertfordshire AL9 7TA, United Kingdom
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Armando E. Hoet
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
- Veterinary Public Health Program, College of Public Health, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
| | - Karin Bergström
- Department of Animal Health and Antimicrobial Strategies, SVA, SE-751 89 Uppsala, Sweden
| | - Luisa De Martino
- Department of Veterinary Medicine and Animal Production, Infectious Diseases Section, University of Naples “Federico II”, 80137 Naples, Italy
| | - Constança Pomba
- Interdisciplinary Centre of Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 LISBOA, Portugal
| | - Hermínia de Lencastre
- Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY10065, USA
| | - Karim Ben Slama
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Haythem Gharsa
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
| | - Emily J. Richardson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Edwin R. Chilvers
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Carla de Haas
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Kok van Kessel
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jos A. G. van Strijp
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
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155
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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156
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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157
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Ekanayake EV, Fu R, Cross TA. Structural Influences: Cholesterol, Drug, and Proton Binding to Full-Length Influenza A M2 Protein. Biophys J 2016; 110:1391-9. [PMID: 27028648 DOI: 10.1016/j.bpj.2015.11.3529] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022] Open
Abstract
The structure and functions of the M2 protein from Influenza A are sensitive to pH, cholesterol, and the antiinfluenza drug Amantadine. This is a tetrameric membrane protein of 97 amino-acid residues that has multiple functions, among them as a proton-selective channel and facilitator of viral budding, replacing the need for the ESCRT proteins that other viruses utilize. Here, various amino-acid-specific-labeled samples of the full-length protein were prepared and mixed, so that only interresidue (13)C-(13)C cross peaks between two differently labeled proteins representing interhelical interactions are observed. This channel is activated at slightly acidic pH values in the endosome when the His(37) residues in the middle of the transmembrane domain take on a +2 or +3 charged state. Changes observed here in interhelical distances in the N-terminus can be accounted for by modest structural changes, and no significant changes in structure were detected in the C-terminal portion of the channel upon activation of the channel. Amantadine, which blocks proton conductance by binding in the aqueous pore near the N-terminus, however, significantly modifies the tetrameric structure on the opposite side of the membrane. The interactions between the juxtamembrane amphipathic helix of one monomer and its neighboring monomer observed in the absence of drug are disrupted in its presence. However, the addition of cholesterol prevents this structural disruption. In fact, strong interactions are observed between cholesterol and residues in the amphipathic helix, accounting for cholesterol binding adjacent to a native palmitoylation site and near to an interhelix crevice that is typical of cholesterol binding sites. The resultant stabilization of the amphipathic helix deep in the bilayer interface facilitates the bilayer curvature that is essential for viral budding.
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Affiliation(s)
- E Vindana Ekanayake
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; National High Magnetic Field Lab, Florida State University, Tallahassee, Florida
| | - Riqiang Fu
- National High Magnetic Field Lab, Florida State University, Tallahassee, Florida
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida; National High Magnetic Field Lab, Florida State University, Tallahassee, Florida; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida.
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158
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Positive selection in cathelicidin host defense peptides: adaptation to exogenous pathogens or endogenous receptors? Heredity (Edinb) 2016; 118:453-465. [PMID: 27925615 PMCID: PMC5564380 DOI: 10.1038/hdy.2016.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022] Open
Abstract
The cause of adaptive protein evolution includes internal (for example, co-evolution of ligand-receptor pairs) and external (for example, adaptation to different ecological niches) mechanisms. Host defense peptides (HDPs) are a class of vertebrate-specific cationic antimicrobial peptides evolving under positive selection. Besides their antibiotic activity, HDPs also exert an effect on multiple host immune cells, thus providing an ideal model to study selective agents driving their evolution. On the basis of a combination of computational and experimental approaches, we studied the evolution of LL-37-type HDPs in mammals, the mature peptide of cathelicidin CAP18 (herein termed CAP18-MP) and investigated the driving force behind the evolution. Using codon-substitution maximum likelihood models, we analyzed CAP18-MPs in 40 species belonging to nine mammalian Orders and identified four positively selected sites (PSSs) that all are located on two terminal unordered regions of CAP18-MPs. Grafting the two positively selected regions of human or whale CAP18-MP to the α-helical scaffold of a rabbit homolog (substituting its corresponding parts) led to no alterations in antibacterial activity, spectrum and action mode. Likewise, further deletion of the two terminal regions did not alter its functional features. Evolutionary conservation analysis of mammalian FPR2, a receptor known to interact with the C-terminal positively selected region of LL-37, revealed high evolutionary variability in its ligand-binding extracellular loop domains, matching sequence diversity of the unordered regions in CAP18-MPs. This is the first report describing that the signature of positive selection of cathelicidins is not associated with their direct bactericidal activity, but rather with the evolutionary variability of their endogenous receptors.
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159
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Núñez Miguel R, Sanders J, Furmaniak J, Smith BR. Structure and activation of the TSH receptor transmembrane domain. AUTOIMMUNITY HIGHLIGHTS 2016; 8:2. [PMID: 27921237 PMCID: PMC5136658 DOI: 10.1007/s13317-016-0090-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/23/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE The thyroid-stimulating hormone receptor (TSHR) is the target autoantigen for TSHR-stimulating autoantibodies in Graves' disease. The TSHR is composed of: a leucine-rich repeat domain (LRD), a hinge region or cleavage domain (CD) and a transmembrane domain (TMD). The binding arrangements between the TSHR LRD and the thyroid-stimulating autoantibody M22 or TSH have become available from the crystal structure of the TSHR LRD-M22 complex and a comparative model of the TSHR LRD in complex with TSH, respectively. However, the mechanism by which the TMD of the TSHR and the other glycoprotein hormone receptors (GPHRs) becomes activated is unknown. METHODS We have generated comparative models of the structures of the inactive (TMD_In) and active (TMD_Ac) conformations of the TSHR, follicle-stimulating hormone receptor (FSHR) and luteinizing hormone receptor (LHR) TMDs. The structures of TMD_Ac and TMD_In were obtained using class A GPCR crystal structures for which fully active and inactive conformations were available. RESULTS Most conserved motifs observed in GPCR TMDs are also observed in the amino acid sequences of GPHR TMDs. Furthermore, most GPCR TMD conserved helix distortions are observed in our models of the structures of GPHR TMDs. Analysis of these structures has allowed us to propose a mechanism for activation of GPHR TMDs. CONCLUSIONS Insight into the mechanism of activation of the TSHR by both TSH and TSHR autoantibodies is likely to be useful in the development of new treatments for Graves' disease.
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Affiliation(s)
| | - Jane Sanders
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK
| | - Jadwiga Furmaniak
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK
| | - Bernard Rees Smith
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK.
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160
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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161
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Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors. Sci Rep 2016; 6:37290. [PMID: 27849063 PMCID: PMC5110974 DOI: 10.1038/srep37290] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/28/2016] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors are a large family of membrane proteins activated by a variety of structurally diverse ligands making them highly adaptable signaling molecules. Despite recent advances in the structural biology of this protein family, the mechanism by which ligands induce allosteric changes in protein structure and dynamics for its signaling function remains a mystery. Here, we propose the use of terahertz spectroscopy combined with molecular dynamics simulation and protein evolutionary network modeling to address the mechanism of activation by directly probing the concerted fluctuations of retinal ligand and transmembrane helices in rhodopsin. This approach allows us to examine the role of conformational heterogeneity in the selection and stabilization of specific signaling pathways in the photo-activation of the receptor. We demonstrate that ligand-induced shifts in the conformational equilibrium prompt vibrational resonances in the protein structure that link the dynamics of conserved interactions with fluctuations of the active-state ligand. The connection of vibrational modes creates an allosteric association of coupled fluctuations that forms a coherent signaling pathway from the receptor ligand-binding pocket to the G-protein activation region. Our evolutionary analysis of rhodopsin-like GPCRs suggest that specific allosteric sites play a pivotal role in activating structural fluctuations that allosterically modulate functional signals.
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162
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Metzemaekers M, Van Damme J, Mortier A, Proost P. Regulation of Chemokine Activity - A Focus on the Role of Dipeptidyl Peptidase IV/CD26. Front Immunol 2016; 7:483. [PMID: 27891127 PMCID: PMC5104965 DOI: 10.3389/fimmu.2016.00483] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022] Open
Abstract
Chemokines are small, chemotactic proteins that play a crucial role in leukocyte migration and are, therefore, essential for proper functioning of the immune system. Chemokines exert their chemotactic effect by activation of chemokine receptors, which are G protein-coupled receptors (GPCRs), and interaction with glycosaminoglycans (GAGs). Furthermore, the exact chemokine function is modulated at the level of posttranslational modifications. Among the different types of posttranslational modifications that were found to occur in vitro and in vivo, i.e., proteolysis, citrullination, glycosylation, and nitration, NH2-terminal proteolysis of chemokines has been described most intensively. Since the NH2-terminal chemokine domain mediates receptor interaction, NH2-terminal modification by limited proteolysis or amino acid side chain modification can drastically affect their biological activity. An enzyme that has been shown to provoke NH2-terminal proteolysis of various chemokines is dipeptidyl peptidase IV or CD26. This multifunctional protein is a serine protease that preferably cleaves dipeptides from the NH2-terminal region of peptides and proteins with a proline or alanine residue in the penultimate position. Various chemokines possess such a proline or alanine residue, and CD26-truncated forms of these chemokines have been identified in cell culture supernatant as well as in body fluids. The effects of CD26-mediated proteolysis in the context of chemokines turned out to be highly complex. Depending on the chemokine ligand, loss of these two NH2-terminal amino acids can result in either an increased or a decreased biological activity, enhanced receptor specificity, inactivation of the chemokine ligand, or generation of receptor antagonists. Since chemokines direct leukocyte migration in homeostatic as well as pathophysiologic conditions, CD26-mediated proteolytic processing of these chemotactic proteins may have significant consequences for appropriate functioning of the immune system. After introducing the chemokine family together with the GPCRs and GAGs, as main interaction partners of chemokines, and discussing the different forms of posttranslational modifications, this review will focus on the intriguing relationship of chemokines with the serine protease CD26.
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Affiliation(s)
- Mieke Metzemaekers
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, KU Leuven , Leuven , Belgium
| | - Jo Van Damme
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, KU Leuven , Leuven , Belgium
| | - Anneleen Mortier
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, KU Leuven , Leuven , Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, KU Leuven , Leuven , Belgium
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163
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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164
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Zhang R, Chen Y, Rodriguez-Hornedo N, Ramamoorthy A. Enhancing NMR Sensitivity of Natural-Abundance Low-γ Nuclei by Ultrafast Magic-Angle-Spinning Solid-State NMR Spectroscopy. Chemphyschem 2016; 17:2962-2966. [PMID: 27310287 PMCID: PMC5831690 DOI: 10.1002/cphc.201600637] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Indexed: 12/18/2022]
Abstract
Although magic-angle-spinning (MAS) solid-state NMR spectroscopy has been able to provide piercing atomic-level insights into the structure and dynamics of various solids, the poor sensitivity has limited its widespread application, especially when the sample amount is limited. Herein, we demonstrate the feasibility of acquiring high S/N ratio natural-abundance 13 C NMR spectrum of a small amount of sample (≈2.0 mg) by using multiple-contact cross polarization (MCP) under ultrafast MAS. As shown by our data from pharmaceutical compounds, the signal enhancement achieved depends on the number of CP contacts employed within a single scan, which depends on the T1ρ of protons. The use of MCP for fast 2D 1 H/13 C heteronuclear correlation experiments is also demonstrated. The significant signal enhancement can be greatly beneficial for the atomic-resolution characterization of many types of crystalline solids including polymorphic drugs and nanomaterials.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, 48109-1055, USA
| | - Yitian Chen
- Department of Pharmaceutical Science, The University of Michigan, Ann Arbor, Michigan, 48109-1055, USA
| | - Nair Rodriguez-Hornedo
- Department of Pharmaceutical Science, The University of Michigan, Ann Arbor, Michigan, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, 48109-1055, USA.
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165
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Kufareva I. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol 2016; 30:27-37. [PMID: 27459124 PMCID: PMC5071139 DOI: 10.1016/j.coph.2016.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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166
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Affiliation(s)
- Naomi R. Latorraca
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - A. J. Venkatakrishnan
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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167
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Gaieb Z, Lo DD, Morikis D. Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7. J Chem Inf Model 2016; 56:1808-22. [PMID: 27529431 DOI: 10.1021/acs.jcim.6b00367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biased ligand binding to G protein-coupled receptors enables functional selectivity of intracellular effectors to mediate cellular function. Despite the significant advances made in characterizing the conformational states (transmembrane helical arrangements) capable of discriminating between G protein and arrestin binding, the role of the ligand in stabilizing such conformations remains unclear. To address this issue, we simulate microsecond dynamics of CC chemokine receptor 7 (CCR7) bound to its native biased ligands, CCL19 and CCL21, and detect a series of molecular switches that are mediated by various ligand-induced allosteric events. These molecular switches involve three tyrosine residues (Y112(3.32), Y255(6.51), and Y288(7.39)), three phenylalanine residues (F116(3.36), F208(5.47), and F248(6.44)), and a polar interaction between Q252(6.48) and R294(7.45) in the transmembrane domain of CCR7. Conformational changes within these switches, particularly hydrogen bond formation between Y112(3.32) and Y255(6.51), lead to global helical movements in the receptor's transmembrane helices and contribute to the transitioning of the receptor to distinct states. Ligand-induced helical movements in the receptor highlight the ability of biased ligands to stabilize the receptor in different states through a dynamic network of allosteric events.
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Affiliation(s)
- Zied Gaieb
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
| | - David D Lo
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
| | - Dimitrios Morikis
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
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168
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Liu Q, Li A, Tian Y, Wu JD, Liu Y, Li T, Chen Y, Han X, Wu K. The CXCL8-CXCR1/2 pathways in cancer. Cytokine Growth Factor Rev 2016; 31:61-71. [PMID: 27578214 PMCID: PMC6142815 DOI: 10.1016/j.cytogfr.2016.08.002] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/13/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
Abstract
Persistent infection or chronic inflammation contributes significantly to tumourigenesis and tumour progression. C-X-C motif ligand 8 (CXCL8) is a chemokine that acts as an important multifunctional cytokine to modulate tumour proliferation, invasion and migration in an autocrine or paracrine manner. Studies have suggested that CXCL8 and its cognate receptors, C-X-C chemokine receptor 1 (CXCR1) and CX-C chemokine receptor 2 (CXCR2), mediate the initiation and development of various cancers including breast cancer, prostate cancer, lung cancer, colorectal carcinoma and melanoma. CXCL8 also integrates with multiple intracellular signalling pathways to produce coordinated effects. Neovascularisation, which provides a basis for fostering tumour growth and metastasis, is now recognised as a critical function of CXCL8 in the tumour microenvironment. In this review, we summarize the biological functions and ficlinical significance of the CXCL8 signalling axis in cancer. We also propose that CXCL8 may be a potential therapeutic target for cancer treatment
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Affiliation(s)
- Qian Liu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Anping Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yijun Tian
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jennifer D Wu
- Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Yu Liu
- Department of Geriatric, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tengfei Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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169
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Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
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170
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Harris MJ, Struppe JO, Wylie BJ, McDermott AE, Thompson LK. Multidimensional Solid-State Nuclear Magnetic Resonance of a Functional Multiprotein Chemoreceptor Array. Biochemistry 2016; 55:3616-24. [PMID: 27295350 PMCID: PMC5022360 DOI: 10.1021/acs.biochem.6b00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterial chemoreceptor complex governs signal detection and the upstream elements of chemotactic behavior, but the detailed molecular mechanism is still unclear. We have assembled nativelike functional arrays of an aspartate receptor cytoplasmic fragment (CF) with its two cytoplasmic protein partners (CheA and CheW) for solid-state nuclear magnetic resonance (NMR) studies of structural changes involved in signaling. In this initial study of the uniformly (13)C- and (15)N-enriched CF in these >13.8 MDa size arrays, residue-type assignments are made for amino acids that together make up 90% of the protein. We demonstrate that homo- and heteronuclear two-dimensional spectra are consistent with structure-based chemical shift predictions: a number of major assignable correlations are consistent with the predominantly α-helical secondary structure, and minor correlations are consistent with the disordered C-terminal tail. Sub-parts per million line widths and spectral changes upon freezing of samples suggest these arrays are structurally homogeneous and sufficiently immobilized for efficient solid-state NMR.
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Affiliation(s)
- Michael J. Harris
- Department of Chemistry, University of Massachusetts, 710 N Pleasant St, Amherst, Massachusetts 01003, USA
| | - Jochem O. Struppe
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Benjamin J. Wylie
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Lynmarie K. Thompson
- Department of Chemistry, University of Massachusetts, 710 N Pleasant St, Amherst, Massachusetts 01003, USA
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171
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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172
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Kaur H, Lakatos A, Spadaccini R, Vogel R, Hoffmann C, Becker-Baldus J, Ouari O, Tordo P, Mchaourab H, Glaubitz C. The ABC exporter MsbA probed by solid state NMR – challenges and opportunities. Biol Chem 2016; 396:1135-49. [PMID: 25849794 DOI: 10.1515/hsz-2015-0119] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/26/2015] [Indexed: 01/20/2023]
Abstract
ATP binding cassette (ABC) transporters form a superfamily of integral membrane proteins involved in translocation of substrates across the membrane driven by ATP hydrolysis. Despite available crystal structures and extensive biochemical data, many open questions regarding their transport mechanisms remain. Therefore, there is a need to explore spectroscopic techniques such as solid state NMR in order to bridge the gap between structural and mechanistic data. In this study, we investigate the feasibility of using Escherichia coli MsbA as a model ABC transporter for solid state NMR studies. We show that optimised solubilisation and reconstitution procedures enable preparing stable and homogenous protein samples. Depending on the duration of solubilisation, MsbA can be obtained in either an apo- or in a native lipid A bound form. Building onto these optimisations, the first promising MAS-NMR spectra with narrow lines have been recorded. However, further sensitivity improvements are required so that complex NMR experiments can be recorded within a reasonable amount of time. We therefore demonstrate the usability of paramagnetic doping for rapid data acquisition and explore dynamic nuclear polarisation as a method for general signal enhancement. Our results demonstrate that solid state NMR provides an opportunity to address important biological questions related to complex mechanisms of ABC transporters.
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173
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Barington L, Rummel PC, Lückmann M, Pihl H, Larsen O, Daugvilaite V, Johnsen AH, Frimurer TM, Karlshøj S, Rosenkilde MM. Role of Conserved Disulfide Bridges and Aromatic Residues in Extracellular Loop 2 of Chemokine Receptor CCR8 for Chemokine and Small Molecule Binding. J Biol Chem 2016; 291:16208-20. [PMID: 27226537 DOI: 10.1074/jbc.m115.706747] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 11/06/2022] Open
Abstract
Chemokine receptors play important roles in the immune system and are linked to several human diseases. The initial contact of chemokines with their receptors depends on highly specified extracellular receptor features. Here we investigate the importance of conserved extracellular disulfide bridges and aromatic residues in extracellular loop 2 (ECL-2) for ligand binding and activation in the chemokine receptor CCR8. We used inositol 1,4,5-trisphosphate accumulation and radioligand binding experiments to determine the impact of receptor mutagenesis on both chemokine and small molecule agonist and antagonist binding and action in CCR8. We find that the seven-transmembrane (TM) receptor conserved disulfide bridge (7TM bridge) linking transmembrane helix III (TMIII) and ECL-2 is crucial for chemokine and small molecule action, whereas the chemokine receptor conserved disulfide bridge between the N terminus and TMVII is needed only for chemokines. Furthermore, we find that two distinct aromatic residues in ECL-2, Tyr(184) (Cys + 1) and Tyr(187) (Cys + 4), are crucial for binding of the CC chemokines CCL1 (agonist) and MC148 (antagonist), respectively, but not for small molecule binding. Finally, using in silico modeling, we predict an aromatic cluster of interaction partners for Tyr(187) in TMIV (Phe(171)) and TMV (Trp(194)). We show in vitro that these residues are crucial for the binding and action of MC148, thus supporting their participation in an aromatic cluster with Tyr(187) This aromatic cluster appears to be present in a large number of CC chemokine receptors and thereby could play a more general role to be exploited in future drug development targeting these receptors.
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Affiliation(s)
| | - Pia C Rummel
- From the Department of Neuroscience and Pharmacology
| | - Michael Lückmann
- From the Department of Neuroscience and Pharmacology, the Novo Nordisk Foundation Center for Basic Metabolic Research, and
| | - Heidi Pihl
- From the Department of Neuroscience and Pharmacology
| | - Olav Larsen
- From the Department of Neuroscience and Pharmacology
| | | | - Anders H Johnsen
- the Department of Clinical Biochemistry, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Thomas M Frimurer
- the Novo Nordisk Foundation Center for Basic Metabolic Research, and the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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174
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Liu J, Liu C, Fan Y, Munro RA, Ladizhansky V, Brown LS, Wang S. Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 65:7-13. [PMID: 27121590 DOI: 10.1007/s10858-016-0033-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the expression medium. This strategy improves the spectral resolution by 1.5 fold, displays site-specific labelling patterns, and has advantages for collecting long-range distance restraints for structure determination of large eukaryotic membrane proteins by solid-state NMR.
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Affiliation(s)
- Jing Liu
- Beijing NMR Centre, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Beijing, China
| | - Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ying Fan
- The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Guelph, Guelph, ON, Canada
| | - Rachel A Munro
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Shenlin Wang
- Beijing NMR Centre, Peking University, Beijing, China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Beijing National Laboratory for Molecular Sciences, Beijing, China.
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175
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Cohen LS, Arshava B, Kauffman S, Mathew E, Fracchiolla KE, Ding FX, Dumont ME, Becker JM, Naider F. Guided reconstitution of membrane protein fragments. Biopolymers 2016; 102:16-29. [PMID: 23897574 DOI: 10.1002/bip.22349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/13/2013] [Accepted: 06/26/2013] [Indexed: 11/12/2022]
Abstract
Structural analysis by NMR of G protein-coupled receptors (GPCRs) has proven to be extremely challenging. To reduce the number of peaks in the NMR spectra by segmentally labeling a GPCR, we have developed a Guided Reconstitution method that includes the use of charged residues and Cys activation to drive heterodimeric disulfide bond formation. Three different cysteine-activating reagents: 5-5'-dithiobis(2-nitrobenzoic acid) [DTNB], 2,2'-dithiobis(5-nitropyridine) [DTNP], and 4,4'-dipyridyl disulfide [4-PDS] were analyzed to determine their efficiency in heterodimer formation at different pHs. Short peptides representing the N-terminal (NT) and C-terminal (CT) regions of the first extracellular loop (EL1) of Ste2p, the Saccharomyces cerevisiae alpha-factor mating receptor, were activated using these reagents and the efficiencies of activation and rates of heterodimerization were analyzed. Activation of NT peptides with DTNP and 4-PDS resulted in about 60% yield, but heterodimerization was rapid and nearly quantitative. Double transmembrane domain protein fragments were biosynthesized and used in Guided Reconstitution reactions. A 102-residue fragment, 2TM-tail [Ste2p(G31-I120C)], was heterodimerized with CT-EL1-tail(DTNP) at pH 4.6 with a yield of ∼75%. A 132-residue fragment, 2TMlong-tail [Ste2p(M1-I120C)], was expressed in both unlabeled and (15)N-labeled forms and used with a peptide comprising the third transmembrane domain, to generate a 180-residue segmentally labeled 3TM protein that was found to be segmentally labeled using [(15)N,(1)H]-HSQC analysis. Our data indicate that the Guided Reconstitution method would be applicable to the segmental labeling of a membrane protein with 3 transmembrane domains and may prove useful in the preparation of an intact reconstituted GPCR for use in biophysical analysis and structure determination.
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Affiliation(s)
- Leah S Cohen
- Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, NY, 10314
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176
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Kleist AB, Getschman AE, Ziarek JJ, Nevins AM, Gauthier PA, Chevigné A, Szpakowska M, Volkman BF. New paradigms in chemokine receptor signal transduction: Moving beyond the two-site model. Biochem Pharmacol 2016; 114:53-68. [PMID: 27106080 DOI: 10.1016/j.bcp.2016.04.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Abstract
Chemokine receptor (CKR) signaling forms the basis of essential immune cellular functions, and dysregulated CKR signaling underpins numerous disease processes of the immune system and beyond. CKRs, which belong to the seven transmembrane domain receptor (7TMR) superfamily, initiate signaling upon binding of endogenous, secreted chemokine ligands. Chemokine-CKR interactions are traditionally described by a two-step/two-site mechanism, in which the CKR N-terminus recognizes the chemokine globular core (i.e. site 1 interaction), followed by activation when the unstructured chemokine N-terminus is inserted into the receptor TM bundle (i.e. site 2 interaction). Several recent studies challenge the structural independence of sites 1 and 2 by demonstrating physical and allosteric links between these supposedly separate sites. Others contest the functional independence of these sites, identifying nuanced roles for site 1 and other interactions in CKR activation. These developments emerge within a rapidly changing landscape in which CKR signaling is influenced by receptor PTMs, chemokine and CKR dimerization, and endogenous non-chemokine ligands. Simultaneous advances in the structural and functional characterization of 7TMR biased signaling have altered how we understand promiscuous chemokine-CKR interactions. In this review, we explore new paradigms in CKR signal transduction by considering studies that depict a more intricate architecture governing the consequences of chemokine-CKR interactions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Pierre-Arnaud Gauthier
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Andy Chevigné
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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177
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Zhao J, Deng Y, Jiang Z, Qing H. G Protein-Coupled Receptors (GPCRs) in Alzheimer's Disease: A Focus on BACE1 Related GPCRs. Front Aging Neurosci 2016; 8:58. [PMID: 27047374 PMCID: PMC4805599 DOI: 10.3389/fnagi.2016.00058] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/08/2016] [Indexed: 12/22/2022] Open
Abstract
The G protein coupled receptors (GPCRs) have been considered as one of the largest families of validated drug targets, which involve in almost overall physiological functions and pathological processes. Meanwhile, Alzheimer’s disease (AD), the most common type of dementia, affects thinking, learning, memory and behavior of elderly people, that has become the hotspot nowadays for its increasing risks and incurability. The above fields have been intensively studied, and the link between the two has been demonstrated, whereas the way how GPCRs perturb AD progress are yet to be further explored given their complexities. In this review, we summarized recent progress regarding the GPCRs interacted with β-site APP cleaving enzyme 1 (BACE1), a key secretase in AD pathogenesis. Then we discussed the current findings on the regulatory roles of GPCRs on BACE1, and the possibility for pharmaceutical treatment of AD patients by the allosteric modulators and biased ligands of GPCRs. We hope this review can provide new insights into the understanding of mechanistic link between GPCRs and BACE1, and highlight the potential of GPCRs as therapeutic target for AD.
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Affiliation(s)
- Juan Zhao
- School of Life Science, Beijing Institute of Technology Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology Beijing, China
| | - Zhaotan Jiang
- School of Physics, Beijing Institute of Technology Beijing, China
| | - Hong Qing
- School of Life Science, Beijing Institute of Technology Beijing, China
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178
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Wang J, Hu W, Wu X, Wang K, Yu J, Luo B, Luo G, Wang W, Wang H, Li J, Wen J. CXCR1 promotes malignant behavior of gastric cancer cells in vitro and in vivo in AKT and ERK1/2 phosphorylation. Int J Oncol 2016; 48:2184-96. [PMID: 26983663 DOI: 10.3892/ijo.2016.3428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/24/2016] [Indexed: 02/07/2023] Open
Abstract
CXCR1 is a member of the chemokine receptor family, which was reported to play an important role in several cancers. The present study investigated the influence of CXCR1 stable knockdown or overexpression on the malignant behavior of gastric cancer cells in vitro and in vivo and the potential mechanisms. MKN45 and BGC823 cells were stably transfected with plasmid pYr-1.1-CXCR1-shRNA (knockdown) and pIRES2-ZsGreen1-CXCR1 (overexpression), respectively. Malignant behavior was evaluated in vitro for changes in proliferation by MTT and colony forming assays; cell cycle and apoptosis by flow cytometry; and migration and invasion using transwell and wound-healing assays. Proliferation, cell cycle, apoptosis, migration and invasion-related signaling molecule expression were measured by real-time RT-PCR and western blot analysis. CXCR1 knockdown and overexpressing xenografts were monitored for in vivo tumor growth. Stable knockdown of CXCR1 inhibited MKN45 cell proliferation, migration and invasion, but were reversed in BGC823 cells stably overexpressing CXCR1. In addition, MKN45 cells stably transfected with CXCR1 shRNA inhibited AKT and ERK1/2 phosphorylation, protein expression of cyclin D1, EGFR, VEGF, MMP-9, MMP-2 and Bcl-2, and increased protein expression of Bax and E-cadherin (all P<0.05). In vivo CXCR1-shRNA-MKN45 cells transplanted into nude mice formed smaller tumors than non-transfected or scrambled-shRNA cells (both P<0.05). In contrast BGC823 cells overexpressing CXCR1 formed larger tumors in mice than cells carrying an empty expression plasmid or non-transfected cells (both P<0.05). CXCR1 promoted gastric cancer cell proliferation, migration and invasion. The present study provides preclinical data to support CXCR1 as a novel therapeutic target for gastric cancer.
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Affiliation(s)
- Junpu Wang
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Wanming Hu
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan 410083, P.R. China
| | - Xiaoying Wu
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Kuansong Wang
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Jun Yu
- Department of Neurology, Third Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Baihua Luo
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Gengqiu Luo
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Weiyuan Wang
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan 410083, P.R. China
| | - Huiling Wang
- Department of Pathology, School of Basic Medicine, Central South University, Changsha, Hunan 410083, P.R. China
| | - Jinghe Li
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
| | - Jifang Wen
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha, Hunan 410083, P.R. China
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179
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Carevic M, Öz H, Fuchs K, Laval J, Schroth C, Frey N, Hector A, Bilich T, Haug M, Schmidt A, Autenrieth SE, Bucher K, Beer-Hammer S, Gaggar A, Kneilling M, Benarafa C, Gao JL, Murphy PM, Schwarz S, Moepps B, Hartl D. CXCR1 Regulates Pulmonary Anti-Pseudomonas Host Defense. J Innate Immun 2016; 8:362-73. [PMID: 26950764 DOI: 10.1159/000444125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is a key opportunistic pathogen causing disease in cystic fibrosis (CF) and other lung diseases such as chronic obstructive pulmonary disease (COPD). However, the pulmonary host defense mechanisms regulating anti-P. aeruginosa immunity remain incompletely understood. Here we demonstrate, by studying an airway P. aeruginosa infection model, in vivo bioluminescence imaging, neutrophil effector responses and human airway samples, that the chemokine receptor CXCR1 regulates pulmonary host defense against P. aeruginosa. Mechanistically, CXCR1 regulates anti-Pseudomonas neutrophil responses through modulation of reactive oxygen species and interference with Toll-like receptor 5 expression. These studies define CXCR1 as a novel, noncanonical chemokine receptor that regulates pulmonary anti-Pseudomonas host defense with broad implications for CF, COPD and other infectious lung diseases.
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Affiliation(s)
- M Carevic
- Children's Hospital and Interdisciplinary Center for Infectious Diseases, University of Tx00FC;bingen, Tx00FC;bingen, Germany
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180
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Kimura T, Jennings W, Epand RM. Roles of specific lipid species in the cell and their molecular mechanism. Prog Lipid Res 2016; 62:75-92. [PMID: 26875545 DOI: 10.1016/j.plipres.2016.02.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 12/19/2022]
Abstract
Thousands of different molecular species of lipids are present within a single cell, being involved in modulating the basic processes of life. The vast number of different lipid species can be organized into a number of different lipid classes, which may be defined as a group of lipids with a common chemical structure, such as the headgroup, apart from the nature of the hydrocarbon chains. Each lipid class has unique biological roles. In some cases, a relatively small change in the headgroup chemical structure can result in a drastic change in function. Such phenomena are well documented, and largely understood in terms of specific interactions with proteins. In contrast, there are observations that the entire structural specificity of a lipid molecule, including the hydrocarbon chains, is required for biological activity through specific interactions with membrane proteins. Understanding of these phenomena represents a fundamental change in our thinking of the functions of lipids in biology. There are an increasing number of diverse examples of roles for specific lipids in cellular processes including: Signal transduction; trafficking; morphological changes; cell division. We are gaining knowledge and understanding of the underlying molecular mechanisms. They are of growing importance in both basic and applied sciences.
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Affiliation(s)
- Tomohiro Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
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181
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Wang S, Matsuda I, Long F, Ishii Y. Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach. JOURNAL OF BIOMOLECULAR NMR 2016; 64:131-141. [PMID: 26781951 DOI: 10.1007/s10858-016-0014-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40-80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055-15058, 2015) combines the reverse (13)C, (15)N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of "highlighted" labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching (13)CO or (15)N signals for a pair of consecutively labeled residues by recoupling (13)CO-(15)N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ~15% loss of signals for the highlighted residues while quenching as much as ~90% of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D (15)N/(13)Cα correlation and 2D (13)Cα/(13)CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and (1)H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using (13)C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (~300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable means of signal assignments especially for larger proteins through reducing the number of resonance and clarifying multiple starting points in sequential assignment with enhanced sensitivity.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Isamu Matsuda
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Structural Biology, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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182
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Struts AV, Barmasov AV, Brown MF. CONDENSED-MATTER SPECTROSCOPY SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. II. MAGNETIC RESONANCE METHODS. OPTICS AND SPECTROSCOPY 2016; 120:286-293. [PMID: 28260816 PMCID: PMC5334789 DOI: 10.1134/s0030400x16010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This article continues our review of spectroscopic studies of G-protein-coupled receptors. Magnetic resonance methods including electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) provide specific structural and dynamical data for the protein in conjunction with optical methods (vibrational, electronic spectroscopy) as discussed in the accompanying article. An additional advantage is the opportunity to explore the receptor proteins in the natural membrane lipid environment. Solid-state 2H and 13C NMR methods yield information about the both local structure and dynamics of the cofactor bound to the protein and its light induced changes. Complementary site-directed spin labeling studies monitor the structural alterations over larger distances and correspondingly longer time scales. A multi-scale reaction mechanism describes how local changes of the retinal cofactor unlock the receptor to initiate large-scale conformational changes of rhodopsin. Activation of the G-protein-coupled receptor involves an ensemble of conformational substates within the rhodopsin manifold that characterize the dynamically active receptor.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia
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183
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Li Y, Liew LSY, Li Q, Kang C. Structure of the transmembrane domain of human nicastrin-a component of γ-secretase. Sci Rep 2016; 6:19522. [PMID: 26776682 PMCID: PMC4726005 DOI: 10.1038/srep19522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
Nicastrin is the largest component of γ-secretase that is an intramembrane protease important in the development of Alzheimer's disease. Nicastrin contains a large extracellular domain, a single transmembrane (TM) domain, and a short C-terminus. Its TM domain is important for the γ-secretase complex formation. Here we report nuclear magnetic resonance (NMR) studies of the TM and C-terminal regions of human nicastrin in both sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles. Structural study and dynamic analysis reveal that the TM domain is largely helical and stable under both SDS and DPC micelles with its N-terminal region undergoing intermediate time scale motion. The TM helix contains a hydrophilic patch that is important for TM-TM interactions. The short C-terminus is not structured in solution and a region formed by residues V697-A702 interacts with the membrane, suggesting that these residues may play a role in the γ-secretase complex formation. Our study provides structural insight into the function of the nicastrin TM domain and the C-terminus in γ-secretase complex.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Lynette Sin Yee Liew
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
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184
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NMR of Membrane Proteins: Beyond Crystals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:29-42. [DOI: 10.1007/978-3-319-35072-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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185
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Tamaki H, Egawa A, Kido K, Kameda T, Kamiya M, Kikukawa T, Aizawa T, Fujiwara T, Demura M. Structure determination of uniformly (13)C, (15)N labeled protein using qualitative distance restraints from MAS solid-state (13)C-NMR observed paramagnetic relaxation enhancement. JOURNAL OF BIOMOLECULAR NMR 2016; 64:87-101. [PMID: 26728076 DOI: 10.1007/s10858-015-0010-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/29/2015] [Indexed: 06/05/2023]
Abstract
Magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) is a powerful method for structure determination of insoluble biomolecules. However, structure determination by MAS solid-state NMR remains challenging because it is difficult to obtain a sufficient amount of distance restraints owing to spectral complexity. Collection of distance restraints from paramagnetic relaxation enhancement (PRE) is a promising approach to alleviate this barrier. However, the precision of distance restraints provided by PRE is limited in solid-state NMR because of incomplete averaged interactions and intermolecular PREs. In this report, the backbone structure of the B1 domain of streptococcal protein G (GB1) has been successfully determined by combining the CS-Rosetta protocol and qualitative PRE restraints. The derived structure has a Cα RMSD of 1.49 Å relative to the X-ray structure. It is noteworthy that our protocol can determine the correct structure from only three cysteine-EDTA-Mn(2+) mutants because this number of PRE sites is insufficient when using a conventional structure calculation method based on restrained molecular dynamics and simulated annealing. This study shows that qualitative PRE restraints can be employed effectively for protein structure determination from a limited conformational sampling space using a protein fragment library.
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Affiliation(s)
- Hajime Tamaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Ayako Egawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kouki Kido
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoshi Kameda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masakatsu Kamiya
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoyasu Aizawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | | | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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186
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Ward ME, Wang S, Munro R, Ritz E, Hung I, Gor'kov PL, Jiang Y, Liang H, Brown LS, Ladizhansky V. In situ structural studies of Anabaena sensory rhodopsin in the E. coli membrane. Biophys J 2016; 108:1683-1696. [PMID: 25863060 DOI: 10.1016/j.bpj.2015.02.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/18/2014] [Accepted: 02/12/2015] [Indexed: 01/06/2023] Open
Abstract
Magic-angle spinning nuclear magnetic resonance is well suited for the study of membrane proteins in the nativelike lipid environment. However, the natural cellular membrane is invariably more complex than the proteoliposomes most often used for solid-state NMR (SSNMR) studies, and differences may affect the structure and dynamics of the proteins under examination. In this work we use SSNMR and other biochemical and biophysical methods to probe the structure of a seven-transmembrane helical photoreceptor, Anabaena sensory rhodopsin (ASR), prepared in the Escherichia coli inner membrane, and compare it to that in a bilayer formed by DMPC/DMPA lipids. We find that ASR is organized into trimers in both environments but forms two-dimensional crystal lattices of different symmetries. It favors hexagonal packing in liposomes, but may form a square lattice in the E. coli membrane. To examine possible changes in structure site-specifically, we perform two- and three-dimensional SSNMR experiments and analyze the differences in chemical shifts and peak intensities. Overall, this analysis reveals that the structure of ASR is largely conserved in the inner membrane of E. coli, with many of the important structural features of rhodopsins previously observed in ASR in proteoliposomes being preserved. Small, site-specific perturbations in protein structure that occur as a result of the membrane changes indicate that the protein can subtly adapt to its environment without large structural rearrangement.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Shenlin Wang
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Rachel Munro
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Emily Ritz
- Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Yunjiang Jiang
- Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado
| | - Hongjun Liang
- Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, Ontario, Canada; Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada.
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187
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Sengupta D, Joshi M, Athale CA, Chattopadhyay A. What can simulations tell us about GPCRs. Methods Cell Biol 2016; 132:429-52. [DOI: 10.1016/bs.mcb.2015.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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188
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Snijder HJA, Hakulinen J. Membrane Protein Production in E. coli for Applications in Drug Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:59-77. [PMID: 27165319 DOI: 10.1007/978-3-319-27216-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Producing high quality purified membrane proteins for structure-based drug design and biophysical assays compatible with typical timelines in drug discovery is a significant challenge. Escherichia coli has been an expression host of the utmost importance for soluble proteins and has applications for membrane proteins as well. However, membrane protein overexpression in E. coli may lead to toxicity and low yields of functional product. Here, we review the challenges encountered with heterologous overproduction of α-helical membrane proteins in E. coli and a range of strategies to overcome them. A detailed protocol is also provided for expression and screening of membrane proteins in E. coli using a His-specific fluorescent probe and fluorescent size-exclusion chromatography.
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Affiliation(s)
| | - Jonna Hakulinen
- Discovery Sciences, AstraZeneca R&D, SE-43183, Mölndal, Sweden
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189
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Jiang SJ, Liou JW, Chang CC, Chung Y, Lin LF, Hsu HJ. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1. Sci Rep 2015; 5:18638. [PMID: 26689258 PMCID: PMC4686899 DOI: 10.1038/srep18638] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/23/2015] [Indexed: 12/11/2022] Open
Abstract
Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.
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Affiliation(s)
- Shinn-Jong Jiang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Je-Wen Liou
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Chun-Chun Chang
- Institute of Medical Sciences, Tzu Chi University, Hualien 97004, Taiwan
- Department of Laboratory Medicine, Tzu Chi Medical Center, Hualien 97004, Taiwan
| | - Yi Chung
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Lee-Fong Lin
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
| | - Hao-Jen Hsu
- Department of Life Sciences, Tzu Chi University, Hualien 97004, Taiwan
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190
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Gustavsson M, Zheng Y, Handel TM. Production of Chemokine/Chemokine Receptor Complexes for Structural Biophysical Studies. Methods Enzymol 2015; 570:233-60. [PMID: 26921949 DOI: 10.1016/bs.mie.2015.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The development of methods for expression and purification of seven-transmembrane receptors has led to an increase in structural and biophysical data and greatly improved the understanding of receptor structure and function. For chemokine receptors, this has been highlighted by the determination of crystal structures of CXCR4 and CCR5 in complex with small-molecule antagonists, followed recently by two receptor/chemokine complexes; CXCR4 in complex with vMIP-II and US28 in complex with the CX3CL1. However, these studies cover only a few of the many chemokines and chemokine receptors and production of stable receptor/chemokine complexes remains a challenging task. Here, we present a method for producing purified complexes between chemokine receptors and chemokines by coexpression in Sf9 cells. Using the complex between atypical chemokine receptor 3 and its native chemokine CXCL12 as an example, we describe the virus production, protein expression, and purification process as well as reconstitution into different membrane mimics. This method provides an efficient way of producing pure receptor/chemokine complexes and has been used to successfully produce receptor/chemokine complexes for CXC as well as CC receptors.
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Affiliation(s)
- Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Tracy M Handel
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
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191
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Responsiveness of G protein-coupled odorant receptors is partially attributed to the activation mechanism. Proc Natl Acad Sci U S A 2015; 112:14966-71. [PMID: 26627247 DOI: 10.1073/pnas.1517510112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammals detect and discriminate numerous odors via a large family of G protein-coupled odorant receptors (ORs). However, little is known about the molecular and structural basis underlying OR response properties. Using site-directed mutagenesis and computational modeling, we studied ORs sharing high sequence homology but with different response properties. When tested in heterologous cells by diverse odorants, MOR256-3 responded broadly to many odorants, whereas MOR256-8 responded weakly to a few odorants. Out of 36 mutant MOR256-3 ORs, the majority altered the responses to different odorants in a similar manner and the overall response of an OR was positively correlated with its basal activity, an indication of ligand-independent receptor activation. Strikingly, a single mutation in MOR256-8 was sufficient to confer both high basal activity and broad responsiveness to this receptor. These results suggest that broad responsiveness of an OR is at least partially attributed to its activation likelihood.
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192
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Jaenecke F, Friedrich-Epler B, Parthier C, Stubbs MT. Membrane composition influences the activity of in vitro refolded human vitamin K epoxide reductase. Biochemistry 2015; 54:6454-61. [PMID: 26435421 DOI: 10.1021/acs.biochem.5b00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human vitamin K epoxide reductase (hVKOR) is an integral membrane protein responsible for the maintenance of reduced vitamin K pools, a prerequisite for the action of γ-glutamyl carboxylase and hence for hemostasis. Here we describe the recombinant expression of hVKOR as an insoluble fusion protein in Escherichia coli, followed by purification and chemical cleavage under denaturing conditions. In vitro renaturation and reconstitution of purified solubilized hVKOR in phospholipids could be established to yield active protein. Crucially, the renatured enzyme is inhibited by the powerful coumarin anticoagulant warfarin, and we demonstrate that enzyme activity depends on lipid composition. The completely synthetic system for protein production allows a rational investigation of the multiple variables in membrane protein folding and paves the way for the provision of pure, active membrane protein for structural studies.
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Affiliation(s)
- Frank Jaenecke
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany.,ZIK HALOmem , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Beatrice Friedrich-Epler
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Milton T Stubbs
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany.,ZIK HALOmem , Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
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193
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Structural basis of receptor sulfotyrosine recognition by a CC chemokine: the N-terminal region of CCR3 bound to CCL11/eotaxin-1. Structure 2015; 22:1571-81. [PMID: 25450766 DOI: 10.1016/j.str.2014.08.023] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/31/2014] [Accepted: 08/21/2014] [Indexed: 02/06/2023]
Abstract
Trafficking of leukocytes in immune surveillance and inflammatory responses is activated by chemokines engaging their receptors. Sulfation of tyrosine residues in peptides derived from the eosinophil chemokine receptor CCR3 dramatically enhances binding to cognate chemokines. We report the structural basis of this recognition and affinity enhancement. We describe the structure of a CC chemokine (CCL11/eotaxin-1) bound to a fragment of a chemokine receptor: residues 8–23 of CCR3, including two sulfotyrosine residues. We also show that intact CCR3 is sulfated and sulfation enhances receptor activity. The CCR3 sulfotyrosine residues form hydrophobic, salt bridge and cation-p interactions with residues that are highly conserved in CC chemokines. However, the orientation of the chemokine relative to the receptor N terminus differs substantially from those observed for two CXC chemokines, suggesting that initial binding of the receptor sulfotyrosine residues guides subsequent steps in receptor activation, thereby influencing the receptor conformational changes and signaling.
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194
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Courtney JM, Ye Q, Nesbitt AE, Tang M, Tuttle MD, Watt ED, Nuzzio KM, Sperling LJ, Comellas G, Peterson JR, Morrissey JH, Rienstra CM. Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum. Structure 2015; 23:1958-1966. [PMID: 26365800 PMCID: PMC4786943 DOI: 10.1016/j.str.2015.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/05/2023]
Abstract
Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure.
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Affiliation(s)
- Joseph M Courtney
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qing Ye
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna E Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcus D Tuttle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric D Watt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kristin M Nuzzio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lindsay J Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph R Peterson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James H Morrissey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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195
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Association between interleukin 8 receptor α gene (CXCR1) and mastitis in dairy cattle. Cent Eur J Immunol 2015; 40:153-8. [PMID: 26557028 PMCID: PMC4637389 DOI: 10.5114/ceji.2015.52828] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/03/2015] [Indexed: 11/26/2022] Open
Abstract
The innate immune response plays an important role in the course of bacterial infections. Innate immunity effectiveness relies on the expression of many genes, connected, among others, to the activity of neutrophils. Interleukin 8 (IL-8) receptor α, coded by the CXCR1 gene, is present on the neutrophil surface and binds pro-inflammatory IL-8 with high affinity. This is why the bovine CXCR1 gene carries a potential for use as a dairy cattle mastitis marker. To date, several studies on the CXCR1 polymorphism brought out contradictory results. The aim of this study was to analyse the association between two SNPs of the CXCR1 gene, which is potentially important for the protein function and animal phenotype for mastitis susceptibility. A total of 554 Polish Holsteins were genotyped, and 140 among them were bacteriologically tested. The differences between animals carrying different genotypes and haplotypes of CXCR1 in test day somatic cell count (SCC) and Staphylococcus aureus mastitis susceptibility were estimated. We found that test day SCC was significantly related to CXCR1+472 SNP but not to CXCR1+735 SNP. No statistically significant association between CXCR1 polymorphism and susceptibility to S. aureus mastitis was found in the studied herd.
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196
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Vyas VK, Ghate M, Patel K, Qureshi G, Shah S. Homology modeling, binding site identification and docking study of human angiotensin II type I (Ang II-AT1) receptor. Biomed Pharmacother 2015; 74:42-8. [DOI: 10.1016/j.biopha.2015.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023] Open
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197
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Schuler AD, Engles CA, Maeda DY, Quinn MT, Kirpotina LN, Wicomb WN, Mason SN, Auten RL, Zebala JA. Boronic acid-containing aminopyridine- and aminopyrimidinecarboxamide CXCR1/2 antagonists: Optimization of aqueous solubility and oral bioavailability. Bioorg Med Chem Lett 2015; 25:3793-7. [PMID: 26248802 DOI: 10.1016/j.bmcl.2015.07.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 07/27/2015] [Indexed: 12/12/2022]
Abstract
The chemokine receptors CXCR1 and CXCR2 are important pharmaceutical targets due to their key roles in inflammatory diseases and cancer progression. We have previously identified 2-[5-(4-fluoro-phenylcarbamoyl)-pyridin-2-ylsulfanylmethyl]-phenylboronic acid (SX-517) and 6-(2-boronic acid-5-trifluoromethoxy-benzylsulfanyl)-N-(4-fluoro-phenyl)-nicotinamide (SX-576) as potent non-competitive boronic acid-containing CXCR1/2 antagonists. Herein we report the synthesis and evaluation of aminopyridine and aminopyrimidine analogs of SX-517 and SX-576, identifying (2-{(benzyl)[(5-boronic acid-2-pyridyl)methyl]amino}-5-pyrimidinyl)(4-fluorophenylamino)formaldehyde as a potent chemokine antagonist with improved aqueous solubility and oral bioavailability.
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Affiliation(s)
- Aaron D Schuler
- Syntrix Biosystems, 215 Clay Street NW, Suite B-5, Auburn, WA 98001, United States.
| | - Courtney A Engles
- Syntrix Biosystems, 215 Clay Street NW, Suite B-5, Auburn, WA 98001, United States
| | - Dean Y Maeda
- Syntrix Biosystems, 215 Clay Street NW, Suite B-5, Auburn, WA 98001, United States
| | - Mark T Quinn
- Department of Microbiology and Immunology, Montana State University, 960 Technology Boulevard, Bozeman, MT 59717, United States
| | - Liliya N Kirpotina
- Department of Microbiology and Immunology, Montana State University, 960 Technology Boulevard, Bozeman, MT 59717, United States
| | - Winston N Wicomb
- Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, United States
| | - S Nicholas Mason
- Department of Pediatrics (Neonatal Medicine), DUMC Box 3373, Duke University, Durham, NC 27710, United States
| | - Richard L Auten
- Department of Pediatrics (Neonatal Medicine), DUMC Box 3373, Duke University, Durham, NC 27710, United States
| | - John A Zebala
- Syntrix Biosystems, 215 Clay Street NW, Suite B-5, Auburn, WA 98001, United States
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198
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de March CA, Yu Y, Ni MJ, Adipietro KA, Matsunami H, Ma M, Golebiowski J. Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. J Am Chem Soc 2015; 137:8611-8616. [PMID: 26090619 PMCID: PMC4497840 DOI: 10.1021/jacs.5b04659] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Odorant receptor (OR) genes and proteins represent more than 2% of our genome and 4% of our proteome and constitute the largest subgroup of G protein-coupled receptors (GPCRs). The mechanism underlying OR activation remains poorly understood, as they do not share some of the highly conserved motifs critical for activation of non-olfactory GPCRs. By combining site-directed mutagenesis, heterologous expression, and molecular dynamics simulations that capture the conformational change of constitutively active mutants, we tentatively identified crucial residues for the function of these receptors using the mouse MOR256-3 (Olfr124) as a model. The toggle switch for sensing agonists involves a highly conserved tyrosine residue in helix VI. The ionic lock is located between the "DRY" motif in helix III and a positively charged "R/K" residue in helix VI. This study provides an unprecedented model that captures the main mechanisms of odorant receptor activation.
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Affiliation(s)
- Claire A. de March
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
| | - Yiqun Yu
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mengjue J. Ni
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kaylin A. Adipietro
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Minghong Ma
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
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199
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200
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Maeda DY, Peck AM, Schuler AD, Quinn MT, Kirpotina LN, Wicomb WN, Auten RL, Gundla R, Zebala JA. Boronic acid-containing CXCR1/2 antagonists: Optimization of metabolic stability, in vivo evaluation, and a proposed receptor binding model. Bioorg Med Chem Lett 2015; 25:2280-4. [PMID: 25933594 PMCID: PMC4430358 DOI: 10.1016/j.bmcl.2015.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 12/14/2022]
Abstract
Blockade of undesired neutrophil migration to sites of inflammation remains an area of substantial pharmaceutical interest. To effect this blockade, a validated therapeutic target is antagonism of the chemokine receptor CXCR2. Herein we report the discovery of 6-(2-boronic acid-5-trifluoromethoxy-benzylsulfanyl)-N-(4-fluoro-phenyl)-nicotinamide 6, an antagonist with activity at both CXCR1 and CXCR2 receptors (IC50 values 31 and 21 nM, respectively). Compound 6 exhibited potent inhibition of neutrophil influx in a rat model of pulmonary inflammation, and is hypothesized to interact with a unique intracellular binding site on CXCR2. Compound 6 (SX-576) is undergoing further investigation as a potential therapy for pulmonary inflammation.
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Affiliation(s)
- Dean Y Maeda
- Syntrix Biosystems, 215 Clay Street Northwest, Suite B5, Auburn, WA 98001, United States.
| | - Angela M Peck
- Syntrix Biosystems, 215 Clay Street Northwest, Suite B5, Auburn, WA 98001, United States
| | - Aaron D Schuler
- Syntrix Biosystems, 215 Clay Street Northwest, Suite B5, Auburn, WA 98001, United States
| | - Mark T Quinn
- Department of Microbiology and Immunology, Montana State University, 960 Technology Boulevard, Bozeman, MT 59717, United States
| | - Liliya N Kirpotina
- Department of Microbiology and Immunology, Montana State University, 960 Technology Boulevard, Bozeman, MT 59717, United States
| | - Winston N Wicomb
- Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, United States
| | - Richard L Auten
- Division of Neonatal Medicine, Department of Pediatrics, Duke University Medical Center, 366 Sands Research Drive, Durham, NC 27710, United States
| | - Rambabu Gundla
- Integrated Drug Discovery Services, GVK Biosciences Private Limited, IDA Nacharam, Hyderabad 500 076, India
| | - John A Zebala
- Syntrix Biosystems, 215 Clay Street Northwest, Suite B5, Auburn, WA 98001, United States
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