Effect of Ser392 phosphorylation on the structure and dynamics of the polybasic domain of ADP ribosylation factor nucleotide site opener protein: A molecular simulation study

Biochemistry

Volumn 52, Issue 41, 2013, Pages 7339-7349

  Srinivasaraghavan, Kannan ^a,b   Nacro, Kassoum ^b   Grüber, Gerhard ^a,c   Verma, Chandra S ^a,c,d  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b Agency for Science   (Singapore)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ADP-RIBOSYLATION FACTORS; CONFORMATIONAL SAMPLINGS; GUANINE NUCLEOTIDE EXCHANGE FACTORS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; REPLICA EXCHANGE METHOD; STRUCTURAL REARRANGEMENT; STRUCTURE AND DYNAMICS;

MOLECULAR DYNAMICS; NUCLEOTIDES; ORDER DISORDER TRANSITIONS; PEPTIDES; STRUCTURAL DYNAMICS;

PHOSPHORYLATION;

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR; GUANINE NUCLEOTIDE EXCHANGE FACTOR; SERINE;

ARTICLE; AUTOREGULATION; CARBOXY TERMINAL SEQUENCE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE;

AMINO ACID MOTIFS; GTPASE-ACTIVATING PROTEINS; HELA CELLS; HUMANS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PHOSPHORYLATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SERINE;

EID: 84886072298     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400912e     Document Type: Article

References (37)

1. Casanova, J. E. (2007) Regulation of Arf activation: The Sec7 family of guanine nucleotide exchange factors Traffic 8, 1476-1485
2. Bourne, H. R., Sanders, D. A., and McCormick, F. (1990) The GTPase superfamily: A conserved switch for diverse cell functions Nature 348, 125-132
3. Donaldson, J. G. and Klausner, R. D. (1994) ARF: A key regulatory switch in membrane traffic and organelle structure Curr. Opin. Cell Biol. 6, 527-532
4. D'Souza-Schorey, C. and Chavrier, P. (2006) ARF proteins: Roles in membrane traffic and beyond Nat. Rev. Mol. Cell Biol. 7, 347-358
5. Hurtado-Lorenzo, A., Skinner, M., El Annan, J., Futai, M., Sun-Wada, G. H., Bourgoin, S., Casanova, J., Wildeman, A., Bechoua, S., Ausiello, D. A., Brown, D., and Marshansky, V. (2006) V-ATPase interacts with ARNO and Arf6 in early endosomes and regulates the protein degradative pathway Nat. Cell Biol. 8, 124-136
6. Marshansky, V. (2007) The V-ATPase a2-subunit as a putative endosomal pH-sensor Biochem. Soc. Trans. 35, 1092-1099
7. +-ATPase (V-ATPase) and cytohesin-2 J. Biol. Chem. 288, 5896-5913
8. Merkulova, M., Bakulina, A., Thaker, Y. R., Grüber, G., and Marshansky, V. (2010) Specific motifs of the V-ATPase a2-subunit isoform interact with catalytic and regulatory domains of ARNO Biochim. Biophys. Acta 1797, 1398-1409
9. DiNitto, J. P., Delprato, A., Gabe Lee, M. T., Cronin, T. C., Huang, S., Guilherme, A., Czech, M. P., and Lambright, D. G. (2007) Structural basis and mechanism of autoregulation in 3-phosphoinositide-dependent Grp1 family Arf GTPase exchange factors Mol. Cell 28, 569-583
10. Smart, J. L. and McCammon, J. A. (1999) Phosphorylation stabilizes the N-termini of α-helices Biopolymers 49, 225-233
11. Espinoza-Fonseca, L. M., Kast, D., and Thomas, D. D. (2007) Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin Biophys. J. 93, 2083-2090
12. Kast, D., Espinoza-Fonseca, L. M., Yi, C., and Thomas, D. D. (2010) Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain Proc. Natl. Acad. Sci. U.S.A. 107, 8207-8212
13. Metcalfe, E. E., Traaseth, N. J., and Veglia, G. (2005) Serine 16 phosphorylation induces an order-to-disorder transition in monomeric phospholamban Biochemistry 44, 4386-4396
14. Karim, C. B., Zhang, Z., Howard, E. C., Torgersen, K. D., and Thomas, D. D. (2006) Phosphorylation-dependent conformational switch in spin-labeled phospholamban bound to SERCA J. Mol. Biol. 358, 1032-1040
15. Paterlini, M. G. and Thomas, D. D. (2005) The α-helical propensity of the cytoplasmic domain of phospholamban: A molecular dynamics simulation of the effect of phosphorylation and mutation Biophys. J. 88, 3243-3251
16. Steinmetz, M. O., Jahnke, W., Towbin, H., Garcia-Echeverria, C., Voshol, H., Müller, D., and van Oostrum, J. (2001) Phosphorylation disrupts the central helix in Op18/stathmin and suppresses binding to tubulin EMBO Rep. 2, 505-510
17. Missimer, J. H., Steinmetz, M. O., van Gunsteren, W. F., and Dolenc, J. (2012) Influence of 63Ser Phosphorylation and Dephosphorylation on the Structure of the Stathmin Helical Nucleation Sequence: A Molecular Dynamics Study Biochemistry 51, 8455-8463
18. Santy, L. C., Frank, S. R., Hatfield, J. C., and Casanova, J. E. (1999) Regulation of ARNO nucleotide exchange by a PH domain electrostatic switch Curr. Biol. 9, 1173-1176
19. Kannan, S. and Zacharias, M. (2007) Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential Proteins 66, 697-706
20. Kannan, S. and Zacharias, M. (2009) Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica Exchange Molecular Dynamics Simulations Int. J. Mol. Sci. 10, 1121-1137
21. Kannan, S. and Zacharias, M. (2009) Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations Proteins 76, 448-460
22. Frickenhaus, S., Kannan, S., and Zacharias, M. (2009) Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping J. Comput. Chem. 30, 479-492
23. Kannan, S. and Zacharias, M. (2010) Application of biasing potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent Proteins 78, 2809-2819
24. Case, D., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. (2010) Amber 9, University of California, San Francisco.
25. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79, 926-935
26. Duan, Y., Wu, A., Chowdhury, C. S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. A. (2003) Pointcharge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24, 1999-2012
27. Homeyer, N., Horn, A. H. C., Lanig, H., and Sticht, H. (2006) AMBER force field parameters for phosphorylated amino acids in different protonation states: Phosphoserine, phosphothreonine, phosphotyrosine and phosphohistidine J. Mol. Model. 12, 281-289
28. Okamoto, Y. (2004) Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations J. Mol. Graphics Modell. 22, 425-439
29. Sali, A. and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234, 779-815
30. DiNitto, J. P., Delprato, A., Gabe Lee, M. T., Cronin, T. C., Huang, S., Guilherme, A., Czech, M. P., and Lambright, D. G. (2007) Structural basis and mechanism of autoregulation in 3-phosphoinositide-dependent Grp1 family Arf GTPase exchange factors Mol. Cell 28, 569-583
31. Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems J. Chem. Phys. 98, 10089-10092
32. Miyamoto, S. and Kollman, P. A. (1992) Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 13, 952-962
33. Han, B., Liu, Y., Ginzinger, S., and Wishart, D. (2011) SHIFTX2: Significantly improved protein chemical shift prediction J. Biomol. NMR 50, 43-57
34. Wishart, D. S., Sykes, B. D., and Richards, F. M. (1992) The Chemical Shift Index: A Fast and Simple Method for the Assignment of Protein Secondary Structure through NMR Spectroscopy Biochemistry 31, 1647-1651
35. Feig, M., Karanicolas, J., and Brooks, C. L. (2004) MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology J. Mol. Graphics Modell. 22, 377-395
36. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics J. Mol. Graphics 14, 33-38
37. De Lano, W. (2002) The PyMOL molecular graphics system, De Lano Scientific, San Carlos CA.