Integrating three views of Arf1 activation dynamics

Journal of Molecular Biology

Volumn 337, Issue 4, 2004, Pages 969-983

  Robert, Charles H ^a   Cherfils, Jacqueline ^b   Mouawad, Liliane ^c   Perahia, David ^a  

^a INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^b LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^c INSTITUT CURIE   (France)

Author keywords

Arf, ADP ribosylation factor; Arf1; Arno; BFA, Brefeldin A; Gea2; GEFs, guanine nucleotide exchange factors; Normal modes; Sec7d, Sec7 domain; Small G proteins

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; GUANINE NUCLEOTIDE BINDING PROTEIN; M PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHEMICAL REACTION; CRYSTAL STRUCTURE; GENE INSERTION; MEMBRANE TRANSPORT; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN TRANSPORT; SEQUENCE HOMOLOGY;

INSERTION SEQUENCES;

EID: 1642408704     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.01.052     Document Type: Article

References (41)

1. Rothman J.E., Wieland F.T. Protein sorting by transport vesicles. Science. 272:1996;227-234.
2. Antonny B., Béraud-Dufour S., Chardin P., Chabre M. N-terminal hydrophobic residues of the G-protein ADP-ribosylation factor-1 insert into membrane phospholipids upon GDP to GTP exchange. Biochemistry. 36:1997;4675-4684.
3. 2+ and the beta-phosphate to destabilize GDP on ARF1. EMBO J. 17:1998;3651-3659.
4. Béraud-DuFour S., Paris S., Chabre M., Antonny B. Dual interaction of ADP ribosylation factor 1 with Sec7 domain and with lipid membranes during catalysis of guanine nucleotide exchange. J. Biol. Chem. 274:1999;37629-37636.
5. Amor J.C., Harrison D.H., Kahn R.A., Ringe D. Structure of the human ADP-ribosylation factor 1 complexed with GDP. Nature. 372:1994;704-708.
6. Pasqualato S., Renault L., Cherfils J. The GDP/GTP cycle of Arf proteins: structural and biochemical aspects. Kahn R. Arf Family GTPases. 2003;Kluwer Academic Publishers, Dordrecht, The Netherlands.
7. Franco M., Chardin P., Chabre M., Paris S. Myristoylation-facilitated binding of the G protein ARF1GDP to membrane phospholipids is required for its activation by a soluble nucleotide exchange factor. J. Biol. Chem. 271:1996;1573-1578.
8. Randazzo P.A., Terui T., Sturch S., Fales H.M., Ferrige A.G., Kahn R.A. The myristoylated amino terminus of ADP-ribosylation factor 1 is a phospholipid- and GTP-sensitive switch. J. Biol. Chem. 270:1995;14809-14815.
9. Goldberg J. Structural activation of ARF GTPase: mechanisms of guanine-nucleotide exchange and GTP-Myristoyl switching. Cell. 95:1998;237-248.
10. Cherfils J., Menetrey J., Mathieu M., LeBras G., Robineau S., Béraud-Dufour S., et al. Structure of the Sec7 domain of the Arf exchange factor ARNO. Nature. 392:1998;101-105.
11. Mossessova E., Gulbis J.M., Goldberg J. Structure of the guanine nucleotide exchange factor Sec7 domain of human Arno and analysis of the interaction with ARF GTPase. Cell. 92:1998;415-423.
12. Renault L., Christova P., Guilbert B., Pasqualato S., Cherfils J. Mechanism of domain closure of Sec7 domains and role in BFA sensitivity. Biochemistry. 41:2002;3605-3612.
13. Peyroche A., Antonny B., Robineau S., Acker J., Cherfils J., Jackson C.L. Brefeldin A acts to stabilize an abortive ARF-GDP-Sec7 domain protein complex: involvement of specific residues of the Sec7 domain. Mol. Cell. 3:1999;275-285.
14. Robineau S., Chabre M., Antonny B. Binding site of brefeldin A at the interface between the small G protein ADP-ribosylation factor 1 (ARF1) and the nucleotide-exchange factor Sec7 domain. Proc. Natl Acad. Sci. USA. 97:2000;9913-9918.
15. Diaz J.F., Wroblowski B., Schlitter J., Engelborghs Y. Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins: Struct. Funct. Genet. 28:1997;434-451.
16. Kosztin I., Bruinsma R., O'Lague P., Schulten; K. Mechanical force generation by G-proteins. Proc. Natl Acad. Sci. USA. 99:2002;3575-3580.
17. Ma J., Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc. Natl Acad. Sci. USA. 95:1998;8502-8507.
18. Tama F., Valle M., Frank J., Brooks C.L. III. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryoelectron microscopy. Proc. Natl Acad. Sci. USA. 100:2003;9319-9323.
19. Ma J., Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:1997;114-131.
20. Guilbert C., Pecorari F., Perahia D., Mouawad L. Low frequency motions in phosphoglycerate kinase. A normal mode analysis. Chem. Phys. 204:1996;327-336.
21. Hayward S., Berendsen H.J.C. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins: Struct. Funct. Genet. 30:1998;144-154.
22. Hayward S., Kitao A., Go N. Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis. Protein Sci. 3:1994;936-943.
23. Brooks B.R., Janezic D., Karplus M.J. Harmonic analysis of large systems I. Methodology. J. Comput. Chem. 16:1995;1522-1542.
24. Wriggers W., Schulten K. Protein domain movements: detection of rigid domains and visualization of effective rotations in comparisons of atomic coordinates. Proteins: Struct. Funct. Genet. 29:1997;1-14.
25. Chou K.C. Prediction of tight turns and their types in proteins. Anal. Biochem. 286:2000;1-16.
26. Greasley S.E., Jhoti H., Teahan C., Solari R., Fensome A., Thomas G.M., et al. The structure of rat ADP-ribosylation factor-1 (ARF-1) complexed to GDP determined from two different crystal forms. Nature Struct. Biol. 2:1995;797-806.
27. Menetrey J., Macia E., Pasqualato S., Franco M., Cherfils J. Structure of Arf6-Gdp suggests a basis for guanine nucleotide exchange factors specificity. Nature Struct. Biol. 7:2000;466-469.
28. Robert C.H., Ho P.S. Significance of bound water to local chain conformations in protein crystals. Proc. Natl Acad. Sci. USA. 92:1995;7600-7604.
29. Sekharudu C.Y., Sundaralingam M. Hydration of protein secondary structures: the role in protein folding. Westhof E. Water and Biological Macromolecules. 1993;CRC Press, Boca Raton.
30. Sundaralingam M., Sekharudu Y.C. Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. Science. 244:1989;1333-1337.
31. Paris S., Béraud-Dufour S., Robineau S., Bigay J., Antonny B., Chabre M., Chardin P. Role of protein-phospholipid interactions in the activation of Arf1 by the guanine-nucleotide exchange factor Arno. J. Biol. Chem. 272:1997;22221-22226.
32. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Letters. 77:1996;1905-1908.
33. 2+-ATPase. Biophys. J. 83:2002;2457-2474.
34. Doruker P., Jernigan R.L., Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:2002;119-127.
35. Tama F., Sanejouand Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:2001;1-6.
36. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
37. MacKerell A.D. Jr, Bashford D., Bellot M., Dunbrack R.L., Evanseck J.D., Field S., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:1998;3586-3616.
38. Steinbach P.J., Brooks P.R. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl Acad. Sci. USA. 90:1993;9135-9139.
39. van Vlijman H.W.T., Karplus M. Analysis of calculated normal modes of a set of native and partially unfolded proteins. J. Phys. Chem. 103:1999;3009-3021.
40. Humphrey W., Dalke A., Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14:1996;33-38.
41. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.