Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations

Biochemical and Biophysical Research Communications

Volumn 390, Issue 3, 2009, Pages 608-612

  Wang, Jing Fang ^a,b,c   Chou, Kuo Chen ^c  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^c GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

GTP binding; Internal motion; Molecular switch; P loop region; Water network rearrangement

Indexed keywords

ALANINE; GUANOSINE TRIPHOSPHATE; MAGNESIUM ION; PROLINE; RAB PROTEIN; RAB5A PROTEIN; UNCLASSIFIED DRUG; WATER;

ARTICLE; CRYSTAL STRUCTURE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION;

ARGININE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GUANOSINE TRIPHOSPHATE; HUMANS; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROLINE; PROTEIN STRUCTURE, SECONDARY; RAB5 GTP-BINDING PROTEINS;

EID: 70450224653     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.10.014     Document Type: Article

References (53)

1. Pereira-Leal J.B., and Seabra M.C. Evolution of the Rab family of small GTP-binding proteins. J. Mol. Biol. 313 (2001) 889-901
2. Pereira-Leal J.B., Hume A.N., and Seabra M.C. Prenylation of Rab GTPases: molecular mechanisms and involvement in genetic disease. FEBS Lett. 498 (2001) 197-200
3. Deacon S.W., and Gelfand V.I. Of yeast, mice, and men. Rab proteins and organelle transport. J. Cell Biol. 152 (2001) F21-24
4. Deacon S.W., Serpinskaya A.S., Vaughan P.S., Lopez Fanarraga M., Vernos I., Vaughan K.T., and Gelfand V.I. Dynactin is required for bidirectional organelle transport. J. Cell Biol. 160 (2003) 297-301
5. Waters M.G., and Pfeffer S.R. Membrane tethering in intracellular transport. Curr. Opin. Cell. Biol. 11 (1999) 453-459
6. Bock J.B., Matern H.T., Peden A.A., and Scheller R.H. A genomic perspective on membrane compartment organization. Nature 409 (2001) 839-841
7. Kahn R.A., Der C.J., and Bokoch G.M. The ras superfamily of GTP-binding proteins: guidelines on nomenclature. FASEB J. 6 (1992) 2512-2513
8. Carroll K.S., Hanna J., Simon I., Krise J., Barbero P., and Pfeffer S.R. Role of Rab9 GTPase in facilitating receptor recruitment by TIP47. Science 292 (2001) 1373-1376
9. Karcher R.L., Deacon S.W., and Gelfand V.I. Motor-cargo interactions: the key to transport specificity. Trends Cell. Biol. 12 (2002) 21-27
10. Salminen A., and Novick P.J. A ras-like protein is required for a post-Golgi event in yeast secretion. Cell 49 (1987) 527-538
11. Pereira-Leal J.B., and Seabra M.C. The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily. J. Mol. Biol. 301 (2000) 1077-1087
12. Milburn M.V., Tong L., deVos A.M., Brunger A., Yamaizumi Z., Nishimura S., and Kim S.H. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science 247 (1990) 939-945
13. Brunger A.T., Milburn M.V., Tong L., deVos A.M., Jancarik J., Yamaizumi Z., Nishimura S., Ohtsuka E., Kim S.H., and protein C.s.o.a.a.f.o.R. a complex of a GTP analog and the HRAS p21 catalytic domain. Proc. Natl. Acad. Sci. USA 87 (1990) 4849-4853
14. Merithew E., Hatherly S., Dumas J.J., Lawe D.C., Heller-Harrison R., and Lambright D.G. Structural plasticity of an invariant hydrophobic triad in the switch regions of Rab GTPases is a determinant of effector recognition. J. Biol. Chem. 276 (2001) 13982-13988
15. Stroupe C., and Brunger A.T. Crystal structures of a Rab protein in its inactive and active conformations. J. Mol. Biol. 304 (2000) 585-598
16. Boguski M.S., and McCormick F. Proteins regulating Ras and its relatives. Nature 366 (1993) 643-654
17. Fukui K., Sasaki T., Imazumi K., Matsuura Y., Nakanishi H., and Takai Y. Isolation and characterization of a GTPase activating protein specific for the Rab3 subfamily of small G proteins. J. Biol. Chem. 272 (1997) 4655-4658
18. Du L.L., Collins R.N., and Novick P.J. Identification of a Sec4p GTPase-activating protein (GAP) as a novel member of a Rab GAP family. J. Biol. Chem. 273 (1998) 3253-3256
19. Strom M., Vollmer P., Tan T.J., and Gallwitz D. A yeast GTPase-activating protein that interacts specifically with a member of the Ypt/Rab family. Nature 361 (1993) 736-739
20. Nagano F., Sasaki T., Fukui K., Asakura T., Imazumi K., and Takai Y. Molecular cloning and characterization of the noncatalytic subunit of the Rab3 subfamily-specific GTPase-activating protein. J. Biol. Chem. 273 (1998) 24781-24785
21. Albert S., and Gallwitz D. Two new members of a family of Ypt/Rab GTPase activating proteins, promiscuity of substrate recognition. J. Biol. Chem. 274 (1999) 33186-33189
22. Burton J.L., Burns M.E., Gatti E., Augustine G.J., and De Camilli P. Specific interactions of Mss4 with members of the Rab GTPase subfamily. EMBO J. 13 (1994) 5547-5558
23. Worthylake D.K., Rossman K.L., and Sondek J. Crystal structure of Rac1 in complex with the guanine nucleotide exchange region of Tiam1. Nature 408 (2000) 682-688
24. Pfeffer S.R., Dirac-Svejstrup A.B., and Soldati T. Rab GDP dissociation inhibitor: putting rab GTPases in the right place. J. Biol. Chem. 270 (1995) 17057-17059
25. Bucci C., Parton R.G., Mather I.H., Stunnenberg H., Simons K., Hoflack B., and Zerial M. The small GTPase rab5 functions as a regulatory factor in the early endocytic pathway. Cell 70 (1992) 715-728
26. Gorvel J.P., Chavrier P., Zerial M., and Gruenberg J. Rab5 controls early endosome fusion in vitro. Cell 64 (1991) 915-925
27. Barbieri M.A., Li G., Mayorga L.S., and Stahl P.D. Characterization of Rab5:Q79L-stimulated endosome fusion. Arch. Biochem. Biophys. 326 (1996) 64-72
28. Li G., and Stahl P.D. Structure-function relationship of the small GTPase rab5. J. Biol. Chem. 268 (1993) 24475-24480
29. McLauchlan H., Newell J., Morrice N., Osborne A., West M., and Smythe E. A novel role for Rab5-GDI in ligand sequestration into clathrin-coated pits. Curr. Biol. 8 (1998) 34-45
30. Li G., and Liang Z. Phosphate-binding loop and Rab GTPase function: mutations at Ser29 and Ala30 of Rab5 lead to loss-of-function as well as gain-of-function phenotype. Biochem. J. 355 (2001) 681-689
31. Liang Z., Mather T., and Li G. GTPase mechanism and function: new insights from systematic mutational analysis of the phosphate-binding loop residue Ala30 of Rab5. Biochem. J. 346 Pt 2 (2000) 501-508
32. Li G., Barbieri M.A., Colombo M.I., and Stahl P.D. Structural features of the GTP-binding defective Rab5 mutants required for their inhibitory activity on endocytosis. J. Biol. Chem. 269 (1994) 14631-14635
33. Coleman D.E., Berghuis A.M., Lee E., Linder M.E., Gilman A.G., and Sprang S.R. Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis. Science 265 (1994) 1405-1412
34. Sondek J., Lambright D.G., Noel J.P., Hamm H.E., and Sigler P.B. GTPase mechanism of Gproteins from the 1.7-A crystal structure of transducin alpha-GDP-AIF-4. Nature 372 (1994) 276-279
35. Scheffzek K., Ahmadian M.R., Kabsch W., Wiesmuller L., Lautwein A., Schmitz F., and Wittinghofer A. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277 (1997) 333-338
36. Scheffzek K., Lautwein A., Kabsch W., Ahmadian M.R., and Wittinghofer A. Crystal structure of the GTPase-activating domain of human p120GAP and implications for the interaction with Ras. Nature 384 (1996) 591-596
37. Chou K.C. Review: low-frequency collective motion in biomacromolecules and its biological functions. Biophys. Chem. 30 (1988) 3-48
38. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
39. Chou K.C. The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophys. J. 45 (1984) 881-890
40. Chou K.C. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem. Sci. 14 (1989) 212
41. Chou K.C. The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition. Biophys. Chem. 20 (1984) 61-71
42. Chou K.C. The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers 26 (1987) 285-295
43. Chou K.C., and Mao B. Collective motion in DNA and its role in drug intercalation. Biopolymers 27 (1988) 1795-1815
44. Chou K.C., Zhang C.T., and Maggiora G.M. Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers 34 (1994) 143-153
45. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Onufriev A., Simmerling C., Wang B., and Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
46. Ponder J.W., and Case D.A. Force fields for protein simulations. Adv. Protein Chem. 66 (2003) 27-85
47. Darden T., York D., and Pedersen L. Particle mesh ewald: an N - log(N) method for ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
48. W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, J. Mol. Graph. 14 (1996) 33-38, 27-38.
49. Chou K.C. Energy-optimized structure of antifreeze protein and its binding mechanism. J. Mol. Biol. 223 (1992) 509-517
50. Chou K.C. Review: structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11 (2004) 2105-2134
51. Miller A.F., Papastavros M.Z., and Redfield A.G. NMR studies of the conformational change in human N-p21ras produced by replacement of bound GDP with the GTP analog GTP gamma S. Biochemistry 31 (1992) 10208-10216
52. Maegley K.A., Admiraal S.J., and Herschlag D. Ras-catalyzed hydrolysis of GTP: a new perspective from model studies. Proc. Natl. Acad. Sci. USA 93 (1996) 8160-8166
53. Zhu G., Liu J., Terzyan S., Zhai P., Li G., and Zhang X.C. High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop. J. Biol. Chem. 278 (2003) 2452-2460