The Structural Biology of Chemokines

  • Elias Lolis
  • James W. Murphy
Part of the The Receptors book series (REC)

Abstract

This chapter provides an overview of the literature in the field of the structural biology of chemokines. The secondary, tertiary, and quaternary structures as determined by x-ray crystallography and nuclear magnetic resonance are compared among the four chemokine families. The biological significance of chemokine structures is explored through a discussion of additional molecules that interact with the chemokines. Specific interactions of chemokines and their receptors are discussed as are interactions between chemokines and glycosaminoglycans. Additionally, a set of tables and figures summarizes the structural information available in the databases.

Key Words

Chemokines oligomerization GPCR GAGs heparin crystallography NMR structure 

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References

  1. 1.
    Nagasawa T, Hirota S, Tachibana K, et al. Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1. Nature 1996;382:635–8.PubMedCrossRefGoogle Scholar
  2. 2.
    Tachibana K, Hirota S, Iizasa H, et al. The chemokine receptor CXCR4 is essential for vascularization of the gastrointestinal tract. Nature 1998;393:591–4.PubMedCrossRefGoogle Scholar
  3. 3.
    Zou YR, Kottmann AH, Kuroda M, Taniuchi I, Littman DR. Function of the chemokine receptor CXCR4 in haematopoiesis and in cerebellar development. Nature 1998;393:595–9.PubMedCrossRefGoogle Scholar
  4. 4.
    Forster R, Emrich T, Kremmer E, Lipp M. Expression of the G-protein-coupled receptor BLR1 defines mature, recirculating B cells and a subset of T-helper memory cells. Blood 1994;84:830–40.PubMedGoogle Scholar
  5. 5.
    Vicari AP, Figueroa DJ, Hedrick JA, et al. TECK: a novel CC chemokine specifically expressed by thymic dendritic cells and potentially involved in T cell development. Immunity 1997;7:291–301.PubMedCrossRefGoogle Scholar
  6. 6.
    Meucci O, Fatatis A, Simen AA, Bushell TJ, Gray PW, Miller RJ. Chemokines regulate hippocampal neuronal signaling and gp120 neurotoxicity. Proc Natl Acad Sci U S A 1998;95:14500–5.PubMedCrossRefGoogle Scholar
  7. 7.
    Flomenberg N, Devine SM, DiPersio JF, et al. The use of AMD3100 plus G-CSF for autologous hematopoietic progenitor cell mobilization is superior to G-CSF alone. Blood 2005;106:1867–74.PubMedCrossRefGoogle Scholar
  8. 8.
    Hernandez PA, Gorlin RJ, Lukens JN, et al. Mutations in the chemokine receptor gene CXCR4 are associated with WHIM syndrome, a combined immunodeficiency disease. Nat Genet 2003;34:70–4.PubMedCrossRefGoogle Scholar
  9. 9.
    Boring L, Gosling J, Cleary M, Charo IF. Decreased lesion formation in CCR2−/− mice reveals a role for chemokines in the initiation of atherosclerosis. Nature 1998;394:894–7.PubMedCrossRefGoogle Scholar
  10. 10.
    Gu L, Okada Y, Clinton SK, et al. Absence of monocyte chemoattractant protein-1 reduces atherosclerosis in low density lipoprotein receptor-deficient mice. Mol Cell 1998;2:275–81.PubMedCrossRefGoogle Scholar
  11. 11.
    Zhou Y, Larsen PH, Hao C, Yong VW. CXCR4 is a major chemokine receptor on glioma cells and mediates their survival. J Biol Chem 2002;277:49481–7.PubMedCrossRefGoogle Scholar
  12. 12.
    Rubin JB, Kung AL, Klein RS, et al. A small-molecule antagonist of CXCR4 inhibits intracranial growth of primary brain tumors. Proc Natl Acad Sci U S A 2003;100:13513–8.PubMedCrossRefGoogle Scholar
  13. 13.
    Zhang J, Sarkar S, Yong VW. The chemokine stromal cell derived factor-1 (CXCL12) promotes glioma invasiveness through MT2-matrix metalloproteinase. Carcinogenesis 2005;26:2069–77.PubMedCrossRefGoogle Scholar
  14. 14.
    Muller A, Homey B, Soto H, et al. Involvement of chemokine receptors in breast cancer metastasis. Nature 2001;410:50–6.PubMedCrossRefGoogle Scholar
  15. 15.
    Murphy PM, Baggiolini M, Charo IF, et al. International union of pharmacology. XXII. Nomenclature for chemokine receptors. Pharmacol Rev 2000;52:145–76.PubMedGoogle Scholar
  16. 16.
    Bazan JF, Bacon KB, Hardiman G, et al. A new class of membrane-bound chemokine with a CX3C motif. Nature 1997;385:640–4.PubMedCrossRefGoogle Scholar
  17. 17.
    Matloubian M, David A, Engel S, Ryan JE, Cyster JG. A transmembrane CXC chemokine is a ligand for HIV-coreceptor Bonzo. Nat Immunol 2000;1:298–304.PubMedCrossRefGoogle Scholar
  18. 18.
    Hoover DM, Boulegue C, Yang D, et al. The structure of human macrophage inflammatory protein-3alpha/CCL20. Linking antimicrobial and CC chemokine receptor-6-binding activities with human beta-defensins. J Biol Chem 2002;277:37647–54.PubMedCrossRefGoogle Scholar
  19. 19.
    Loetscher P, Pellegrino A, Gong J-H, et al. The ligands of CXC chemokine receptor 3, I-TAC, Mig, and IP10, are natural antagonists for CCR3. J Biol Chem 2001;276:2986–91.PubMedCrossRefGoogle Scholar
  20. 20.
    Xanthou G, Duchesnes CE, Williams TJ, Pease JE. CCR3 functional responses are regulated by both CXCR3 and its ligands CXCL9, CXCL10 and CXCL11. Eur J Immunol 2003;33:2241–50.PubMedCrossRefGoogle Scholar
  21. 21.
    Sozzani S, Luini W, Bianchi G, et al. The viral chemokine macrophage inflammatory protein-II is a selective Th2 chemoattractant. Blood 1998;92:4036–9.PubMedGoogle Scholar
  22. 22.
    Kledal TN, Rosenkilde MM, Coulin F, et al. A broad-spectrum chemokine antagonist encoded by Kaposi’s sarcoma-associated herpesvirus. Science 1997;277:1656–9.PubMedCrossRefGoogle Scholar
  23. 23.
    Chen S, Bacon KB, Li L, et al. In vivo inhibition of CC and CX3C chemokine-induced leukocyte infiltration and attenuation of glomerulonephritis in Wistar-Kyoto (WKY) rats by vMIP-II. J Exp Med 1998;188:193–8.PubMedCrossRefGoogle Scholar
  24. 24.
    Luttichau HR, Stine J, Boesen TP, et al. A highly selective CC chemokine receptor (CCR)8 antagonist encoded by the poxvirus molluscum contagiosum. J Exp Med 2000;191:171–80.PubMedCrossRefGoogle Scholar
  25. 25.
    Bleul CC, Fuhlbrigge RC, Casasnovas JM, Aiuti A, Springer TA. A highly efficacious lymphocyte chemoattractant, stromal cell-derived factor 1 (SDF-1). J Exp Med 1996;184:1101–9.PubMedCrossRefGoogle Scholar
  26. 26.
    Clore GM, Appella E, Yamada M, Matsushima K, Gronenborn AM. Three-dimensional structure of interleukin 8 in solution. Biochemistry 1990;29:1689–96.PubMedCrossRefGoogle Scholar
  27. 27.
    Baldwin ET, Weber IT, St Charles R, et al. Crystal structure of interleukin 8: symbiosis of NMR and crystallography. Proc Natl Acad Sci U S A 1991;88:502–6.PubMedCrossRefGoogle Scholar
  28. 28.
    Booth V, Keizer DW, Kamphuis MB, Clark-Lewis I, Sykes BD. The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions. Biochemistry 2002;41:10418–25.PubMedCrossRefGoogle Scholar
  29. 29.
    Crump MP, Gong JH, Loetscher P, et al. Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1. EMBO J 1997;16:6996–7007.PubMedCrossRefGoogle Scholar
  30. 30.
    Veldkamp CT, Peterson FC, Pelzek AJ, Volkman BF. The monomer-dimer equilibrium of stromal cell-derived factor-1 (CXCL 12) is altered by pH, phosphate, sulfate, and heparin. Protein Sci 2005;14:1071–81.PubMedCrossRefGoogle Scholar
  31. 31.
    Dealwis C, Fernandez EJ, Thompson DA, Simon RJ, Siani MA, Lolis E. Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 “fusin” coreceptor. Proc Natl Acad Sci U S A 1998;95:6941–6.PubMedCrossRefGoogle Scholar
  32. 32.
    Swaminathan GJ, Holloway DE, Colvin RA, et al. Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine. Structure 2003;11:521–32.PubMedCrossRefGoogle Scholar
  33. 33.
    St Charles R, Walz DA, Edwards BF. The three-dimensional structure of bovine platelet factor 4 at 3.0-A resolution. J Biol Chem 1989;264:2092–9.PubMedGoogle Scholar
  34. 34.
    Lubkowski J, Bujacz G, Boque L, Domaille PJ, Handel TM, Wlodawer A. The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions. Nat Struct Biol 1997;4:64–9.PubMedCrossRefGoogle Scholar
  35. 35.
    Lau EK, Paavola CD, Johnson Z, et al. Identification of the glycosaminoglycan binding site of the CC chemokine, MCP-1: implications for structure and function in vivo. J Biol Chem 2004;279:22294–305.PubMedCrossRefGoogle Scholar
  36. 36.
    Perez-Canadillas JM, Zaballos A, Gutierrez J, et al. NMR solution structure of murine CCL20/MIP-3alpha, a chemokine that specifically chemoattracts immature dendritic cells and lymphocytes through its highly specific interaction with the beta-chemokine receptor CCR6. J Biol Chem 2001;276:28372–9.PubMedCrossRefGoogle Scholar
  37. 37.
    Mizoue LS, Bazan JF, Johnson EC, Handel TM. Solution structure and dynamics of the CX3C chemokine domain of fractalkine and its interaction with an N-terminal fragment of CX3CR1. Biochemistry 1999;38:1402–14.PubMedCrossRefGoogle Scholar
  38. 38.
    Hoover DM, Mizoue LS, Handel TM, Lubkowski J. The crystal structure of the chemokine domain of fractalkine shows a novel quaternary arrangement. J Biol Chem 2000;275:23187–93.PubMedCrossRefGoogle Scholar
  39. 39.
    Hedrick JA, Saylor V, Figueroa D, et al. Lymphotactin is produced by NK cells and attracts both NK cells and T cells in vivo. J Immunol 1997;158:1533–40.PubMedGoogle Scholar
  40. 40.
    Marcaurelle LA, Mizoue LS, Wilken J, et al. Chemical synthesis of lymphotactin: a glycosylated chemokine with a C-terminal mucin-like domain. Chemistry 2001;7:1129–32.PubMedCrossRefGoogle Scholar
  41. 41.
    Kuloglu ES, McCaslin DR, Kitabwalla M, Pauza CD, Markley JL, Volkman BF. Monomeric solution structure of the prototypical “C” chemokine lymphotactin. Biochemistry 2001;40:12486–96.PubMedCrossRefGoogle Scholar
  42. 42.
    Kuloglu ES, McCaslin DR, Markley JL, Volkman BF. Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions. J Biol Chem 2002;277:17863–70.PubMedCrossRefGoogle Scholar
  43. 43.
    Fernandez EJ, Lolis E. Structure, function, and inhibition of chemokines. Annu Rev Pharmacol Toxicol 2002;42:469–99.PubMedCrossRefGoogle Scholar
  44. 44.
    Fernandez EJ, Wilken J, Thompson DA, Peiper SC, Lolis E. Comparison of the structure of vMIP-II with eotaxin-1, RANTES, and MCP-3 suggests a unique mechanism for CCR3 activation. Biochemistry 2000;39:12837–44.PubMedCrossRefGoogle Scholar
  45. 45.
    Palczewski K, Kumasaka T, Hori T, et al. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 2000;289:739–45.PubMedCrossRefGoogle Scholar
  46. 46.
    Clubb RT, Omichinski JG, Clore GM, Gronenborn AM. Mapping the binding surface of interleukin-8 complexes with an N-terminal fragment of the type 1 human interleukin-8 receptor. FEBS Lett 1994;338:93–7.PubMedCrossRefGoogle Scholar
  47. 47.
    Skelton NJ, Quan C, Reilly D, Lowman H. Structure of a CXC chemokine-receptor fragment in complex with interleukin-8. Structure 1999;7:157–68.PubMedCrossRefGoogle Scholar
  48. 48.
    Ye J, Kohli LL, Stone MJ. Characterization of binding between the chemokine eotaxin and peptides derived from the chemokine receptor CCR3. J Biol Chem 2000;275:27250–7.PubMedCrossRefGoogle Scholar
  49. 49.
    Gozansky E, Louis J, Caffrey M, Clore G. Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1. J Mol Biol 2005;345:651–8.PubMedCrossRefGoogle Scholar
  50. 50.
    Datta A, Stone MJ. Soluble mimics of a chemokine receptor: chemokine binding by receptor elements juxtaposed on a soluble scaffold. Protein Sci 2003;12:2482–91.PubMedCrossRefGoogle Scholar
  51. 51.
    Datta-Mannan A, Stone MJ. Chemokine-binding specificity of soluble chemokine-receptor analogues: identification of interacting elements by chimera complementation. Biochemistry 2004;43:14602–11.PubMedCrossRefGoogle Scholar
  52. 52.
    Farzan M, Mirzabekov T, Kolchinsky P, et al. Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell 1999;96:667–76.PubMedCrossRefGoogle Scholar
  53. 53.
    Farzan M, Babcock GJ, Vasilieva N, et al. The role of post-translational modifications of the CXCR4 amino terminus in stromal-derived factor 1 alpha association and HIV-1 entry. J Biol Chem 2002;277:29484–9.PubMedCrossRefGoogle Scholar
  54. 54.
    Fong AM, Alam SM, Imai T, Haribabu B, Patel DD. CX3CR1 tyrosine sulfation enhances fractalkine-induced cell adhesion. J Biol Chem 2002;277:19418–23.PubMedCrossRefGoogle Scholar
  55. 55.
    Preobrazhensky AA, Dragan S, Kawano T, et al. Monocyte chemotactic protein-1 receptor CCR2B is a glycoprotein that has tyrosine sulfation in a conserved extracellular N-terminal region. J Immunol 2000;165:5295–303.PubMedGoogle Scholar
  56. 56.
    Hebert CA, Vitangcol RV, Baker JB. Scanning mutagenesis of interleukin-8 identifies a cluster of residues required for receptor binding. J Biol Chem 1991;266:18989–94.PubMedGoogle Scholar
  57. 57.
    Clark-Lewis I, Schumacher C, Baggiolini M, Moser B. Structure-activity relationships of interleukin-8 determined using chemically synthesized analogs. Critical role of NH2-terminal residues and evidence for uncoupling of neutrophil chemotaxis, exocytosis, and receptor binding activities. J Biol Chem 1991;266:23128–34.PubMedGoogle Scholar
  58. 58.
    Williams G, Borkakoti N, Bottomley GA, et al. Mutagenesis studies of interleukin-8. Identification of a second epitope involved in receptor binding. J Biol Chem 1996;271:9579–86.PubMedCrossRefGoogle Scholar
  59. 59.
    Monteclaro FS, Charo IF. The amino-terminal extracellular domain of the MCP-1 receptor, but not the RANTES/MIP-1alpha receptor, confers chemokine selectivity. Evidence for a two-step mechanism for MCP-1 receptor activation. J Biol Chem 1996;271:19084–92.PubMedCrossRefGoogle Scholar
  60. 60.
    Mayer KL, Stone MJ. NMR solution structure and receptor peptide binding of the CC chemokine eotaxin-2. Biochemistry 2000;39:8382–95.PubMedCrossRefGoogle Scholar
  61. 61.
    Pakianathan DR, Kuta EG, Artis DR, Skelton NJ, Hebert CA. Distinct but overlapping epitopes for the interaction of a CC-chemokine with CCR1, CCR3 and CCR5. Biochemistry 1997;36:9642–8.PubMedCrossRefGoogle Scholar
  62. 62.
    Middleton J, Patterson AM, Gardner L, Schmutz C, Ashton BA. Leukocyte extravasation: chemokine transport and presentation by the endothelium. Blood 2002;100:3853–60.PubMedCrossRefGoogle Scholar
  63. 63.
    Hoogewerf AJ, Kuschert GS, Proudfoot AE, et al. Glycosaminoglycans mediate cell surface oligomerization of chemokines. Biochemistry 1997;36:13570–8.PubMedCrossRefGoogle Scholar
  64. 64.
    Tanaka Y, Adams DH, Hubscher S, Hirano H, Siebenlist U, Shaw S. T-cell adhesion induced by proteoglycan-immobilized cytokine MIP-1 beta. Nature 1993;361:79–82.PubMedCrossRefGoogle Scholar
  65. 65.
    McCornack MA, Boren DM, LiWang PJ. Glycosaminoglycan disaccharide alters the dimer dissociation constant of the chemokine MIP-1 beta. Biochemistry 2004;43:10090–101.PubMedCrossRefGoogle Scholar
  66. 66.
    Proudfoot AE, Handel TM, Johnson Z, et al. Glycosaminoglycan binding and oligomerization are essential for the in vivo activity of certain chemokines. Proc Natl Acad Sci U S A 2003;100:1885–90.PubMedCrossRefGoogle Scholar
  67. 67.
    Johnson Z, Kosco-Vilbois MH, Herren S, et al. Interference with heparin binding and oligomerization creates a novel anti-inflammatory strategy targeting the chemokine system. J Immunol 2004;173:5776–85.PubMedGoogle Scholar
  68. 68.
    Mayo KH, Ilyina E, Roongta V, et al. Heparin binding to platelet factor-4. An NMR and site-directed mutagenesis study: arginine residues are crucial for binding. Biochem J 1995;312:357–65.PubMedGoogle Scholar
  69. 69.
    Kuschert GS, Hoogewerf AJ, Proudfoot AE, et al. Identification of a glycosaminoglycan binding surface on human interleukin-8. Biochemistry 1998;37:11193–201.PubMedCrossRefGoogle Scholar
  70. 70.
    McCornack MA, Cassidy CK, LiWang PJ. The binding surface and affinity of monomeric and dimeric chemokine macrophage inflammatory protein 1 beta for various glycosaminoglycan disaccharides. J Biol Chem 2003;278:1946–56.PubMedCrossRefGoogle Scholar
  71. 71.
    Shaw JP, Johnson Z, Borlat F, et al. The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors. Structure (Cambridge) 2004;12:2081–93.PubMedCrossRefGoogle Scholar
  72. 72.
    Stuckey JA, St Charles R, Edwards BF. A model of the platelet factor 4 complex with heparin. Proteins 1992;14:277–87.PubMedCrossRefGoogle Scholar
  73. 73.
    Amara A, Lorthioir O, Valenzuela A, et al. Stromal cell-derived factor-1alpha associates with heparan sulfates through the first beta-strand of the chemokine. J Biol Chem 1999;274:23916–25.PubMedCrossRefGoogle Scholar
  74. 74.
    Campanella GS, Lee EM, Sun J, Luster AD. CXCR3 and heparin binding sites of the chemokine IP-10 (CXCL10). J Biol Chem 2003;278:17066–74.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Elias Lolis
    • 1
  • James W. Murphy
    • 1
  1. 1.Department of PharmacologyYale University School of MedicineNew HavenUSA

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