Molecular dynamics simulations of transducin: Interdomain and front to back communication in activation and nucleotide exchange

Journal of Molecular Biology

Volumn 338, Issue 3, 2004, Pages 469-481

  Ceruso, Marc A ^a   Periole, Xavier ^a   Weinstein, Harel ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Allostery; Constitutively active mutants; ED, essential dynamics; GPCR; GPCRs; Rhodopsin; Signal transduction

Indexed keywords

GUANOSINE TRIPHOSPHATASE; MUTANT PROTEIN; NUCLEOTIDE; PROTEIN SUBUNIT; RECEPTOR; TRANSDUCIN;

ALPHA HELIX; ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DOMAIN; SIMULATION; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; TIME; WILD TYPE;

EID: 1842851911     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.064     Document Type: Article

References (53)

1. Neves S.R., Ram P.T., Iyengar R. G protein pathways. Science. 296:2002;1636-1639.
2. Marinissen M.J., Gutkind J.S. G-protein-coupled receptors and signaling networks: emerging paradigms. Trends Pharmacol. Sci. 22:2001;368-376.
3. Bourne H.R. How receptors talk to trimeric G proteins. Curr. Opin. Cell Biol. 9:1997;134-142.
4. Hamm H.E. How activated receptors couple to G proteins. Proc. Natl Acad. Sci. USA. 98:2001;4819-4821.
5. Hamm H.E. The many faces of G protein signaling. J. Biol. Chem. 273:1998;669-672.
6. Iiri T., Farfel Z., Bourne H.R. G-protein diseases furnish a model for the turn-on switch. Nature. 394:1998;35-38.
7. Ford C.E., Skiba N.P., Bae H., Daaka Y., Reuveny E., Shekter L.R., et al. Molecular basis for interactions of G protein betagamma subunits with effectors. Science. 280:1998;1271-1274.
8. Onrust R., Herzmark P., Chi P., Garcia P.D., Lichtarge O., Kingsley C., Bourne H.R. Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin. Science. 275:1997;381-384.
9. Rondard P., Iiri T., Srinivasan S., Meng E., Fujita T., Bourne H.R. Mutant G protein alpha subunit activated by Gbeta gamma: a model for receptor activation? Proc. Natl Acad. Sci. USA. 98:2001;6150-6155.
10. Cherfils J., Chabre M. Activation of G-protein Galpha subunits by receptors through Galpha-Gbeta and Galpha-Ggamma interactions. Trends Biochem. Sci. 28:2003;13-17.
11. Denker B.M., Schmidt C.J., Neer E.J. Promotion of the GTP-liganded state of the Go alpha protein by deletion of the C terminus. J. Biol. Chem. 267:1992;9998-10002.
12. Thomas T.C., Schmidt C.J., Neer E.J. G-protein alpha o subunit: mutation of conserved cysteines identifies a subunit contact surface and alters GDP affinity. Proc. Natl Acad. Sci. USA. 90:1993;10295-10298.
13. Iiri T., Herzmark P., Nakamoto J.M., van Dop C., Bourne H.R. Rapid GDP release from Gs alpha in patients with gain and loss of endocrine function. Nature. 371:1994;164-168.
14. Marin E.P., Krishna A.G., Sakmar T.P. Rapid activation of transducin by mutations distant from the nucleotide- binding site: evidence for a mechanistic model of receptor-catalyzed nucleotide exchange by G proteins. J. Biol. Chem. 276:2001;27400-27405.
15. Marin E.P., Krishna A.G., Sakmar T.P. Disruption of the alpha5 helix of transducin impairs rhodopsin- catalyzed nucleotide exchange. Biochemistry. 41:2002;6988-6994.
16. Posner B.A., Mixon M.B., Wall M.A., Sprang S.R., Gilman A.G. The A326S mutant of Gialpha1 as an approximation of the receptor-bound state. J. Biol. Chem. 273:1998;21752-21758.
17. Noel J.P., Hamm H.E., Sigler P.B. The 2.2 Å crystal structure of transducin-alpha complexed with GTP gamma S. Nature. 366:1993;654-663.
18. Lambright D.G., Noel J.P., Hamm H.E., Sigler P.B. Structural determinants for activation of the alpha-subunit of a heterotrimeric G protein. Nature. 369:1994;621-628.
19. Amadei A., Linssen A.B., Berendsen H.J. Essential dynamics of proteins. Proteins: Struct. Funct. Genet. 17:1993;412-425.
20. van Aalten D.M., Findlay J.B., Amadei A., Berendsen H.J. Essential dynamics of the cellular retinol-binding protein-evidence for ligand-induced conformational changes. Protein Eng. 8:1995;1129-1135.
21. van Aalten D.M., Amadei A., Linssen A.B., Eijsink V.G., Vriend G., Berendsen H.J. The essential dynamics of thermolysin: confirmation of the hinge- bending motion and comparison of simulations in vacuum and water. Proteins: Struct. Funct. Genet. 22:1995;45-54.
22. Coleman D.E., Berghuis A.M., Lee E., Linder M.E., Gilman A.G., Sprang S.R. Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis. Science. 265:1994;1405-1412.
23. Mixon M.B., Lee E., Coleman D.E., Berghuis A.M., Gilman A.G., Sprang S.R. Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science. 270:1995;954-960.
24. Sprang S.R. G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66:1997;639-678.
25. Skiba N.P., Yang C.S., Huang T., Bae H., Hamm H.E. The alpha-helical domain of Galphat determines specific interaction with regulator of G protein signaling 9. J. Biol. Chem. 274:1999;8770-8778.
26. Slep K.C., Kercher M.A., He W., Cowan C.W., Wensel T.G., Sigler P.B. Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 Å Nature. 409:2001;1071-1077.
27. Kimple R.J., Kimple M.E., Betts L., Sondek J., Siderovski D.P. Structural determinants for GoLoco-induced inhibition of nucleotide release by Galpha subunits. Nature. 416:2002;878-881.
28. Echeverria V., Hinrichs M.V., Torrejon M., Ropero S., Martinez J., Toro M.J., Olate J. Mutagenesis in the switch IV of the helical domain of the human Gsalpha reduces its GDP/GTP exchange rate. J. Cell. Biochem. 76:2000;368-375.
29. Mello L.V., van Aalten D.M., Findlay J.B. Dynamic properties of the guanine nucleotide binding protein alpha subunit and comparison of its guanosine triphosphate hydrolase domain with that of ras p21. Biochemistry. 37:1998;3137-3142.
30. Hayward S., Berendsen H.J. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:1998;144-154.
31. Hayward S. Structural principles governing domain motions in proteins. Proteins: Struct: Funct. Genet. 36:1999;425-435.
32. Yang C.S., Skiba N.P., Mazzoni M.R., Hamm H.E. Conformational changes at the carboxyl terminus of Galpha occur during G protein activation. J. Biol. Chem. 274:1999;2379-2385.
33. Natochin M., Moussaif M., Artemyev N.O. Probing the mechanism of rhodopsin-catalyzed transducin activation. J. Neurochem. 77:2001;202-210.
34. Denker B.M., Boutin P.M., Neer E.J. Interactions between the amino- and carboxyl-terminal regions of G alpha subunits: analysis of mutated G alpha o/G alpha i2 chimeras. Biochemistry. 34:1995;5544-5553.
35. Pasqualato S., Renault L., Cherfils J. Arf, Arl, Arp and Sar proteins: a family of GTP-binding proteins with a structural device for 'front-back' communication. EMBO Rep. 3:2002;1035-1041.
36. Hruby V.J., Balse P.M. Conformational and topographical considerations in designing agonist peptidomimetics from peptide leads. Curr. Med. Chem. 7:2000;945-970.
37. Hall B.E., Bar-Sagi D., Nassar N. The structural basis for the transition from Ras-GTP to Ras-GDP. Proc. Natl Acad. Sci. USA. 99:2002;12138-12142.
38. 35S]thio-triphosphate binding through M(1) muscarinic receptors in transfected Chinese hamster ovary cell membranes: 2. Testing the "two-states" model of receptor activation. Mol. Pharmacol. 59:2001;886-893.
39. 35S]thio-triphosphate binding through M(1) muscarinic receptors in transfected Chinese hamster ovary cell membranes; 1. Mathematical analysis of catalytic G protein activation. Mol. Pharmacol. 59:2001;875-885.
40. Renault L., Christova P., Guibert B., Pasqualato S., Cherfils J. Mechanism of domain closure of Sec7 domains and role in BFA sensitivity. Biochemistry. 41:2002;3605-3612.
41. Goldberg J. Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell. 95:1998;237-248.
42. Quilliam L.A., Zhong S., Rabun K.M., Carpenter J.W., South T.L., Der C.J., Campbell-Burk S. Biological and structural characterization of a Ras transforming mutation at the phenylalanine-156 residue, which is conserved in all members of the Ras superfamily. Proc. Natl Acad. Sci. USA. 92:1995;1272-1276.
43. Ceruso M.A., Amadei A., Di Nola A. Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein Sci. 8:1999;147-160.
44. Ceruso M.A., Grottesi A., Di Nola A. Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP. Proteins. 36:1999;436-446.
45. 551 from Pseudomonas aeruginosa. Proteins: Struct. Funct. Genet. 50:2003;222-229.
46. Roccatano D., Daidone I., Ceruso M.A., Bossa C., Nola A.D. Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys. J. 84:2003;1876-1883.
47. Berendsen H.J.C., van der Spoel D., van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Commun. 91:1995;43-56.
48. Essman U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103:1995;8577-8592.
49. Darden T., York D., Pedersen L. Particle mesh Ewald: An N(log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:1993;10089-10092.
50. Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput. Phys. 23:1977;327-341.
51. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Di Nola A., Haak J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 81:1984;3684-3690.
52. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J. Interactions models for water in relation to protein hydration. Pullman B. Intermolecular Forces. 1981;331-342 D. Reidel Publishing Company, Dordrecht.
53. Amadei A., Ceruso M.A., Di Nola A. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins: Struct. Funct. Genet. 36:1999;419-424.