An overview of the sequence features of N- and C-terminal segments of the human chemokine receptors

Cytokine

Volumn 70, Issue 2, 2014, Pages 141-150

  Raucci, Raffaele ^a   Costantini, Susan ^b   Castello, Giuseppe ^b   Colonna, Giovanni ^a  

^a SECOND UNIVERSITY OF NAPLES   (Italy)

^b NATIONAL CANCER INSTITUTE   (Italy)

Author keywords

Chemokine receptors evolution; Human chemokine receptors; Intrinsic protein disorder

Indexed keywords

CHEMOKINE RECEPTOR; POLYELECTROLYTE; INTRINSICALLY DISORDERED PROTEIN; PROTEIN KINASE;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; HUMAN; LIGAND BINDING; MODEL; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; PHYSICAL CHEMISTRY; PLASTICITY; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; ANIMAL; CHEMICAL PHENOMENA; CHEMISTRY; METABOLISM; PHYLOGENY; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INTRINSICALLY DISORDERED PROTEINS; PHYLOGENY; PROTEIN KINASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; RECEPTORS, CHEMOKINE; SEQUENCE ANALYSIS, PROTEIN;

EID: 84908368721     PISSN: 10434666     EISSN: 10960023     Source Type: Journal    
DOI: 10.1016/j.cyto.2014.07.257     Document Type: Article

References (62)

1. Olson T.S., Ley K. Chemokines and chemokine receptors in leukocyte trafficking. Am J Physiol Regul Integr Comp Physiol 2002, 283:7-28.
2. Clark-Lewis I., Kim K.S., Rajarathnam K., Gong J.H., Dewald B., Moser B., et al. Structure-activity relationships of chemokines. J Leukoc Biol 1995, 57:703-711.
3. Charo I.F., Ransohoff R.M. The many roles of chemokines and chemokine receptors in inflammation. MD N Engl J Med 2006, 354:610-621.
4. He B., Wang K., Liu Y., Xue B., Uversky V.N., Dunker A.K. Predicting intrinsic disorder in proteins: an overview. Cell Res 2009, 19:929-949.
5. Wright P.E., Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999, 293:321-331.
6. Iakoucheva L.M., Brown C.J., Lawson J.D., Obradovic Z., Dunker A.K. Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 2002, 323:573-584.
7. Costantini S., Sharma A., Raucci R., Costantini M., Autiero I., Colonna G. Genealogy of an ancient protein family: the Sirtuins, a family of disordered members. BMC Evol Biol 2013, 13:60.
8. Myung J.K., Banuelos A.C., Fernandez J.G., Mawji N.R., Wang J., Tien A.H., et al. An androgen receptor N-terminal domain antagonist for treating prostate cancer. J Clin Invest 2013, 123:2948-2960.
9. Hansen J.P., McDonald I.R. Theory of simple liquid 2006, Academic Press, Amsterdam, The Netherlands.
10. Iakoucheva L.M., Radivojac P., Brown C.J., O'Connor T.R., Sikes J.G., Obradovic Z., et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004, 32:1037-1049.
11. Sigalov A.B., Uversky V.N. Differential occurrence of protein intrinsic disorder in the cytoplasmic signaling domains of cell receptors. Self Nonself 2011, 2:55-72.
12. Das R.K., Mittal A., Pappu R.V. How is functional specificity achieved through disordered regions of proteins. BioEssays 2012, 35:17-22.
13. Pappu R.V., Wang X., Vitalis A., Crick S.L. A polymer physics perspective on driving forces and mechanisms for protein aggregation. Arch Biochem Biophys 2008, 469:132-141.
14. Dobrynin A.V. Theory and simulations of charged polymers: from solution properties to polymeric nanomaterials. Curr Opin Colloid Interface Sci 2008, 13:376-388.
15. Das R.K., Pappu R.V. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. PNAS 2013, 110:13392-13397.
16. Verkhivker G.M., Bouzida D., Gehlhaar D.K., Rejto P.A., Freer S.T., Rose P.W. Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding. PNAS 2003, 100:5148-5153.
17. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., et al. Protein identification and analysis tools on the ExPASy server 2005, Humana Press, Totowa, NJ.
18. Cole C., Barber J.D., Barton G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res 2008, 35:197-201.
19. Ragone R., Facchiano F., Facchiano A., Facchiano A.M., Colonna G. Flexibility plot of proteins. Protein Eng 1989, 2:497-504.
20. Vihinen M., Torkkila E., Riikonen P. Accuracy of protein flexibility predictions. Proteins 1994, 19:141-149.
21. Linding R., Jensen L.J., Diella F., Bork P., Gibson T.J., Russell R.B. Protein disorder prediction: implications for structural proteomics. Structure 2003, 11:1453-1459.
22. Peng K., Radivojac P., Vucetic S., Dunker A.K., Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 2006, 7:208.
23. Su C.T., Chen C.Y., Hsu C.M. IPDA: integrated protein disorder analyser. Nucleic Acids Res 2007, 35:465-472.
24. Cheng J., Sweredoski M., Baldi P. Accurate prediction of protein disordered regions by mining protein structure data. Data Min Knowl Disc 2005, 11:213-222.
25. Linding R., Russell R.B., Neduva V., Gibson T.J. GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acid Res 2003, 31:3701-3708.
26. Dosztányi Z., Csizmók V., Tompa P., Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 2005, 347:827-839.
27. Shimizu K., Hirose S., Noguchi T. POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics 2007, 23:2337-2338.
28. Hirose S., Shimizu K., Kanai S., Kuroda Y., Noguchi T. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 2007, 23:2046-2053.
29. Ishida T., Kinoshita K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 2007, 35:460-464.
30. Vullo A., Bortolami O., Pollastri G., Tosatto S. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res 2006, 34:164-168.
31. Yang Z.R., Thomson R., McNeil P., Esnouf R.M. RONN: the bio-basis function neural network technique applied to the detection of natively unordered regions in proteins. Bioinformatics 2005, 21:3369-3376.
32. Uversky V.N., Gillespie J.R., Fink A.L. Why are 'natively unfolded' proteins unstructured under physiologic conditions?. Proteins 2000, 41:415-427.
33. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
34. Blom N., Gammeltoft S., Brunak S. Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999, 294:1351-1362.
35. Xue Y., Ren J., Gao X., Jin C., Wen L., Yao X. GPS 20 a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics 2008, 7:1598-1608.
36. Blom N., Sicheritz-Ponten T., Gupta R., Gammeltoft S., Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4:1633-1649.
37. Monigatti F., Gasteiger E., Bairoch A., Jung E. The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics 2002, 18:769-770.
38. Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., et al. Precision mapping of the human O-GalNAcglycoproteome through SimpleCell technology. EMBO J 2013, 32:1478-1488.
39. Mao A.H., Crick S.L., Vitalis A., Chicoine C.L., Pappu R.V. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. PNAS 2010, 107:8183-8188.
40. Szilagyi A., Gyorffy D., Zavodszky P. The twilight zone between protein order and disorder. Biophys J 2008, 95:1612-1626.
41. Romero P., Obradovic Z., Li X., Garner E.C., Brown C.J., Dunker A.K. Sequence complexity of disordered protein. Proteins 2001, 42:38-48.
42. Tompa P. Intrinsically unstructured proteins. Trend Biochem Sci 2002, 27:527-533.
43. Dunker A.K., Obradovic Z., Romero P., Garner E.C., Brown C.J. Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 2000, 11:161-171.
44. Szpakowska M., Fievez V., Arumugan K., van Nuland N., Schmit J.C., Chevigné A. Function, diversity and therapeutic potential of the N-terminal domain of human chemokine receptors. Biochem Pharmacol 2012, 84:1366-1380.
45. Cohen P. Protein phosphorylation and hormone action. Proc R SocLond B BiolSci 1988, 234:115-144.
46. Busillo J.M., Armando S., Sengupta R., Meucci O., Bouvier M., Benovic J.L. Site-specific phosphorylation of CXCR4 is dynamically regulated by multiple kinases and results in differential modulation of CXCR4 signaling. J Biol Chem 2010, 285:7805-7817.
47. Schumacher J.A., Crockett D.K., Elenitoba-Johnson K.S., Lim M.S. Evaluation of enrichment techniques for mass spectrometry: identification of tyrosine phosphoproteins in cancer cells. J Mol Diagn 2007, 9:169-177.
48. Hartmann J., Tran T.V., Kaudeer J., Oberle K., Herrmann J., Quagliano I., et al. The stalk domain and the glycosylation status of the activating natural killer cell receptor NKp30 are important for ligand binding. J Biol Chem 2012, 287:31527-31539.
49. Tompa P., Fuxreiter M., Oldfield C.J., Simon I., Dunker A.K., Uversky V.N. Close encounters of the third kind: disordered domains and the interactions of proteins. BioEssays 2009, 31:328-335.
50. Lobanov M.Y., Furletova E.I., Bogatyreva N.S., Roytberg M.A., Galzitskaya O.V. Library of disordered patterns in 3D protein structures. PLoSComputBiol 2010, 6.
51. Lin M.F., Kheradpour P., Washietl S., Parker B.J., Pedersen J.S., Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 2011, 21:1916-1928.
52. Macossay-Castillo M., Kosol S., Tompa P., Pancsa R. Synonymous constraint elements show a tendency to encode intrinsically disordered protein segments. PLoS Comput Biol 2014, 10:e1003607.
53. Ludeman J.P., Stone M.J. The structural role of receptor tyrosine sulfation in chemokine recognition. Br J Pharmacol 2014, 171:1167-1179.
54. Siepmann M., Kumar S., Mayer G., Walter J. Casein kinase 2 dependent phosphorylation of neprilysin regulates receptor tyrosine kinase signaling to Akt. PLoS ONE 2010, 5:e13134.
55. Wu B., Chien E.Y., Mol C.D., Fenalti G., Liu W., Katritch V., et al. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 2010, 330:1066-1071.
56. Serebryany E., Zhu G.A., Yan E.C. Artificial membrane-like environments for in vitro studies of purified G-protein coupled receptors. Biochim Biophys Acta-Biomembr 2012, 1818:225-233.
57. Park S.H., Das B.B., Casagrande F., Tian Y., Nothnagel H.J., Chu M., et al. Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature 2012, 491:779-783.
58. De Clercq E. Recent advances on the use of the CXCR4 antagonist plerixafor (AMD3100, Mozobil) and potential of other CXCR4 antagonists as stem cell mobilizers. Pharmacol Ther 2010, 128:509-518.
59. Flory P.J. Principles of polymer chemistry 1953, Cornell University Press, Ithaca, NY and London, UK.
60. Grosberg A.Y., Khokhlov A.R. Statistical physics of macromolecules 1994, AIP Press, New York.
61. Meng W., Lyle N., Luan B., Raleigh D., Pappu R.V. Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure. PNAS 2013, 110:2123-2128.
62. Tran H.T., Mao A., Pappu R.V. Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. J Am Chem Soc 2008, 130:7380-7392.