Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process

Proteins: Structure, Function and Genetics

Volumn 72, Issue 1, 2008, Pages 323-332

  Zou, Jun ^a,b   Wang, Yi Dong ^a   Ma, Fan Xin ^a,b   Xiang, Ming Li ^a   Shi, Bing ^a   Wei, Yu Quan ^a   Yang, Sheng Yong ^a  

^a SICHUAN UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

A loop; JMR; Molecular dynamics; Receptor tyrosine kinase; Stem cell factor receptor

Indexed keywords

STEM CELL FACTOR;

ALLOSTERISM; ARTICLE; BINDING SITE; CONFORMATION; DISSOCIATION; ENZYME ACTIVATION; ENZYME PHOSPHORYLATION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION; WATER SUPPLY;

CELL MEMBRANE; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ENZYME ACTIVATION; HUMANS; MODELS, MOLECULAR; PHOSPHORYLATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-KIT; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE; TIME FACTORS;

EID: 44949190466     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21928     Document Type: Article

References (45)

1. Yarden Y, Kuang WJ, Yang-Feng T, Coussens L, Munemitsu S, Dull TJ, Chen E, Schlessinger J, Francke U, Ullrich A. Human protooncogene c-Kit: a new cell surface receptor tyrosine kinase for an unidentified ligand. EMBO J 1987;6:3341-3351.
2. Yarden Y, Escobedo JA, Kuang W-J, Yang-Feng TL, Daniel TO, Tremble PM, Chen EY, Ando ME, Harkins RN, Francke U, Fried VA, Ullrich A, Williams LT. Structure of the receptor for platelet-derived growth factor helps define a family of closely related growth factor receptors. Nature 1986;323:226-232.
3. Ullrich A, Schlessinger J. Signal transduction by receptors with tyrosine kinase activity. Cell 1990;61:203-212.
4. Noble MEM, Endicott JA, Johnson LN. Protein kinase inhibitors: insights into drug design from structure. Science 2004;303:1800-1805.
5. Nagata H, Worobec AS, Oh CK, Chowdhury BA, Tannenbaum S, Suzuki Y, Metcalfe DD. Identification of a point mutation in the catalytic domain of the protooncogene c-Kit in peripheral blood mononuclear cells of patients who have mastocytosis with an associated hematologic disorder. Proc Natl Acad Sci USA 1995;92:10560-10564.
6. Longley BJ, Jr, Metcalfe DD, Tharp M, Wang X, Tyrrell L, Lu S-Z, Heitjan D, Ma Y. Activating and dominant inactivating c-KIT catalytic domain mutations in distinct clinical forms of human mastocytosis. Proc Natl Acad Sci USA 1999;96:1609-1614.
7. Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishiguro S, Kawano K, Hanada M, Kurata A, Takeda M, Tunio GM, Matsuzawa Y, Kanakura Y, Shinomura Y, Kitamura Y. Gain-of-function mutations of c-Kit in human gastrointestinal stromal tumors. Science 1998;279:577-580.
8. Rubin BP, Singer S, Tsao C, Duensing A, Lux ML, Ruiz R, Hibbard MK, Chen CJ, Xiao S, Tuveson DA, Demetri GD, Fletcher CDM, Fletcher JA. KIT activation is a ubiquitous feature of gastrointestinal stromal tumors. Cancer Res 2001;61:8118-8121.
9. Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen C-J, Joseph N, Singer S, Griffith DJ, Haley A, Town A, Demetri GD, Fletche CD, Fletcher JA. PDGFRA activating mutations in gastrointestinal stromal tumors. Science 2003;299:708-710.
10. Hubbard SR, Till JH. Protein tyrosine kinase structure and function. Annu Rev Biochem 2000;69:373-398.
11. Hubbard SR. Protein tyrosine kinases: autoregulation and small-molecule inhibition. Curr Opin Struc Biol 2002;12:735-741.
12. Nolen B, Taylor S, Ghosh G. Regulation of protein kinases: controlling activity through activation segment conformation. Mol Cell 2004;15:661-675.
13. Hubbard SR. Juxtamembrane autoinhibition in receptor tyrosine kinases. Nat Rev Mol Cell Biol 2004;5:464-470.
14. Jensen PB, Hunter T. Oncogenic kinase signalling. Nature 2001;411:355-365.
15. Ma Y, Cunningham ME, Wang X, Ghosh I, Regan L, Longley BJ. Inhibition of spontaneous receptor phosphorylation by residues in a putative α-helix in the KIT intracellular juxtamembrane region. J Biol Chem 1999;274:13399-13402.
16. Chan PM, Ilangumaran S, Rose JL, Chakrabartty A, Rottapel R. Autoinhibition of the Kit receptor tyrosine kinase by the cytosolic juxtamembrane region. Mol Cell Biol 2003;23:3067-3078.
17. Mol CD, Lim KB, Sridhar V, Zou H, Chien ET, Sang B-C, Nowakowski J, Kassel DB, Cronin CN, McRee DE. Structure of a c-Kit product complex reveals the basis for kinase transactivation. J Biol Chem 2003;278:31461-31464.
18. Mol CD, Dougan DR, Schneider TR, Skene RJ, Kraus ML, Scheibe DN, Snell GP, Zou H, Sang B-C, Wilson KP. Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J Biol Chem 2004;279:31655-31663.
19. Pargellis C, Tong L, Churchill L, Cirillo PF, Gilmore T, Graham AG, Grob PM, Hickey ER, Moss N, Pav S, Regan J. Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat Struct Biol 2002;9:268-272.
20. Liu Y, Gray NS. Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2006;2:358-364.
21. Dibb NJ, Dilworth SM, Mol CD. Switching on kinases: oncogenic activation of BRAF and the PDGFR family. Nat Rev Cancer 2004;4:718-727.
22. Roskoski R, Jr. Structure and regulation of Kit protein-tyrosine kinase-the stem cell factor receptor. Biochem Biophys Res Commun 2005;338:1307-1315.
23. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002;9:646-652.
24. Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005;102:6679-6685.
25. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
26. Šali A, Blundell TL. Definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 1990;212:403-428.
27. Šali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
28. Melo F, Feytmans E. Novel knowledge-based mean force potential at the atomic level. J Mol Biol 1997;267:207-222.
29. Šali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci 1994;3:1582-1596.
30. Schlitter J, Engels M, Kruger P, Jacoby E, Wollmer A. Targeted molecular dynamics simulation of conformational change-application to the T-R transition in insulin. Mol Simul 1993;10:291-308.
31. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-1802.
32. MacKerell AD, Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
33. Beglov D, Roux B. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J Chem Phys 1994;100:9050-9063.
34. Feng M-H, Philippopoulos M, MacKerell AD, Jr, Lim C. Structural characterization of the phosphotyrosine binding region of a high-affinity SH2 domain-phosphopeptide complex by molecular dynamics simulation and chemical shift calculations. J Am Chem Soc 1996;118:11265-11277.
35. Jorgensen WL, Chandrasekhar J, Madura JD. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1993;79:926-935.
36. Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 1995;103:4613-4621.
37. Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
38. Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 1992;13:952-962.
39. Darden TA, York DM, Pedersen LG. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
40. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-38.
41. Griffith J, Black J, Faerman C, Swenson L, Wynn M, Lu F, Lippke J, Saxena K. The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. Mol Cell 2004;13:169-178.
42. Lennartsson J, Blume-Jensen P, Hermanson M, Pontén E, Carlberg M, Rönnstrand L. Phosphorylation of Shc by Src family kinases is necessary for stem cell factor receptor/c-kit mediated activation of the Ras/MAP kinase pathway and c-fos induction. Oncogene 1999;18:5546-5553.
43. Huse M, Kuriyan J. The conformational plasticity of protein kinases. Cell 2002;109:275-282.
44. Baxter RM, Secrist JP, Vaillancourt RR, Kazlauskas A. Full activation of the platelet-derived growth factor β-reeeptor kinase involves multiple events. J Biol Chem 1998;273:17050-17055.
45. Wiesner S, Wybenga-Groot LE, Warner N, Lin H, Pawson T, Forman-Kay JD, Sicheri F. A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases. EMBO J 2006;25:4686-4696.