Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 1, 2011, Pages 282-293

  Madala, Satish K ^a,c,d   Dolan, Michael A ^a   Sharma, Deepak ^b   Ramalingam, Thirumalai R ^a   Wilson, Mark S ^a   Mentink Kane, Margaret M ^a   Masison, Daniel C ^a   Wynn, Thomas A ^a  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^c CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^d Natl Institute for Medical Research   (United States)

Author keywords

Cytokine receptors; Peptide arrays; Protein protein interactions; Structure and protein modeling

Indexed keywords

INTERLEUKIN 13 RECEPTOR; INTERLEUKIN 13 RECEPTOR ALPHA2; INTERLEUKIN 4 RECEPTOR; INTERLEUKIN 4 RECEPTOR ALPHA; MONOCLONAL ANTIBODY;

AMINO ACID SEQUENCE; ANTIBODY PRODUCTION; ANTIGEN BINDING; ARTICLE; BINDING SITE; HUMAN; MICROARRAY ANALYSIS; MOLECULAR DOCKING; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; COMPUTER SIMULATION; HUMANS; INTERLEUKIN-13; INTERLEUKIN-13 RECEPTOR ALPHA1 SUBUNIT; INTERLEUKIN-13 RECEPTOR ALPHA2 SUBUNIT; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

VERMES;

EID: 78649788867     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22881     Document Type: Article

References (25)

1. Wynn TA. IL-13 effector functions. Annu Rev Immunol 2003; 21: 425-456.
2. Wills-Karp M. Interleukin-13 in asthma pathogenesis. Immunol Rev 2004; 202: 175-190.
3. Wilson MS, Wynn TA. Pulmonary fibrosis: pathogenesis, etiology and regulation. Mucosal Immunol 2009; 2: 103-121.
4. Beghe B, Hall IP, Parker SG, Moffatt MF, Wardlaw A, Connolly MJ, Fabbri LM, Ruse C, Sayers I. Polymorphisms in IL13 pathway genes in asthma and chronic obstructive pulmonary disease. Allergy 2010; 65: 474-481.
5. LaPorte SL, Juo ZS, Vaclavikova J, Colf LA, Qi X, Heller NM, Keegan AD, Garcia KC. Molecular and structural basis of cytokine receptor pleiotropy in the interleukin-4/13 system. Cell 2008; 132: 259-272.
6. Wills-Karp M, Luyimbazi J, Xu X, Schofield B, Neben TY, Karp CL, Donaldson DD. Interleukin-13: central mediator of allergic asthma. Science 1998; 282: 2258-2261.
7. Ramalingam TR, Pesce JT, Sheikh F, Cheever AW, Mentink-Kane MM, Wilson MS, Stevens S, Valenzuela DM, Murphy AJ, Yancopoulos GD, Urban JFJr, Donnelly RP, Wynn TA. Unique functions of the type II interleukin 4 receptor identified in mice lacking the interleukin 13 receptor alpha1 chain. Nat Immunol 2008; 9: 25-33.
8. Morimoto M, Zhao A, Sun R, Stiltz J, Madden KB, Mentink-Kane M, Ramalingam T, Wynn TA, Urban JFJr, Shea-Donohue T. IL-13 receptor alpha2 regulates the immune and functional response to Nippostrongylus brasiliensis infection. J Immunol 2009; 183: 1934-1939.
9. Grunig G, Warnock M, Wakil AE, Venkayya R, Brombacher F, Rennick DM, Sheppard D, Mohrs M, Donaldson DD, Locksley RM, Corry DB. Requirement for IL-13 independently of IL-4 in experimental asthma. Science 1998; 282: 2261-2263.
10. Ito T, Suzuki S, Kanaji S, Shiraishi H, Ohta S, Arima K, Tanaka G, Tamada T, Honjo E, Garcia KC, Kuroki R, Izuhara K. Distinct structural requirements for interleukin-4 (IL-4) and IL-13 binding to the shared IL-13 receptor facilitate cellular tuning of cytokine responsiveness. J Biol Chem 2009; 284: 24289-24296.
11. Chiaramonte MG, Donaldson DD, Cheever AW, Wynn TA. An IL-13 inhibitor blocks the development of hepatic fibrosis during a T-helper type 2-dominated inflammatory response. J Clin Invest 1999; 104: 777-785.
12. Lupardus PJ, Birnbaum ME, Garcia KC. Molecular basis for shared cytokine recognition revealed in the structure of an unusually high affinity complex between IL-13 and IL-13Ralpha2. Structure 2010; 18: 332-342.
13. Andrews AL, Holloway JW, Puddicombe SM, Holgate ST, Davies DE. Kinetic analysis of the interleukin-13 receptor complex. J Biol Chem 2002; 277: 46073-46078.
14. Mentink-Kane MM, Wynn TA. Opposing roles for IL-13 and IL-13 receptor alpha 2 in health and disease. Immunol Rev 2004; 202: 191-202.
15. Fichtner-Feigl S, Strober W, Kawakami K, Puri RK, Kitani A. IL-13 signaling through the IL-13alpha2 receptor is involved in induction of TGF-beta1 production and fibrosis. Nat Med 2006; 12: 99-106.
16. Andrews AL, Nasir T, Bucchieri F, Holloway JW, Holgate ST, Davies DE. IL-13 receptor alpha 2: a regulator of IL-13 and IL-4 signal transduction in primary human fibroblasts. J Allergy Clin Immunol 2006; 118: 858-865.
17. Wilson MS, Elnekave E, Mentink-Kane MM, Hodges MG, Pesce JT, Ramalingam TR, Thompson RW, Kamanaka M, Flavell RA, Keane-Myers A, Cheever AW, Wynn TA. IL-13Ralpha2 and IL-10 coordinately suppress airway inflammation, airway-hyperreactivity, and fibrosis in mice. J Clin Invest 2007; 117: 2941-2951.
18. Nahtman T, Jernberg A, Mahdavifar S, Zerweck J, Schutkowski M, Maeurer M, Reilly M. Validation of peptide epitope microarray experiments and extraction of quality data. J Immunol Methods 2007; 328: 1-13.
19. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007; 35: 3375-3382.
20. Laskowski RA, Moss DS, Thornton JM. Main-chain bond lengths and bond angles in protein structures. J Mol Biol 1993; 231: 1049-1067.
21. Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 503-519.
22. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 2001; 98: 10037-10041.
23. Bazan JF. Structural design and molecular evolution of a cytokine receptor superfamily. Proc Natl Acad Sci U S A 1990; 87: 6934-6938.
24. de Vos AM, Ultsch M, Kossiakoff AA. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 1992; 255: 306-312.
25. Arima K, Sato K, Tanaka G, Kanaji S, Terada T, Honjo E, Kuroki R, Matsuo Y, Izuhara K. Characterization of the interaction between interleukin-13 and interleukin-13 receptors. J Biol Chem 2005; 280: 24915-24922.