Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations

Journal of Molecular Biology

Volumn 345, Issue 4, 2005, Pages 869-878

  Chong, Lillian T ^a   Snow, Christopher D ^a   Rhee, Young Min ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

molecular dynamics simulation; oligomerization; protein folding; protein interactions; tumor suppressor p53

Indexed keywords

PROTEIN P53;

ARTICLE; CALCULATION; DIMERIZATION; HIGH TEMPERATURE; MOLECULAR DYNAMICS; OLIGOMERIZATION; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; ROOM TEMPERATURE; STRUCTURE ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY;

EID: 10044265557     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.10.083     Document Type: Article

References (42)

1. H.J. Dyson, and P.E. Wright Coupling of folding and binding for unstructured proteins Curr. Opin. Struct. Biol. 12 2002 54 60
2. M.G. Mateu, M.M. Sanchez del Pino, and A.R. Fersht Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53 Nature Struct. Biol. 6 1999 191 198
3. G.M. Clore, J. Ernst, R. Clubb, J.G. Omichinski, W.M. Kennedy, and K. Sakaguchi Refined solution structure of the oligomerization domain of the tumour suppressor p53 Nature Struct. Biol. 1995 2
4. W. Lee, T.S. Harvey, Y. Yin, P. Yau, D. Litchfield, and C.H. Arrowsmith Solution structure of the tetrameric minimum transforming domain of p53 Nature Struct. Biol. 1 1994 877 890
5. P.D. Jeffrey, S. Gorina, and N.P. Pavletich Crystal structure of the tetramerization domain of the tumour suppressor p53 Science 267 1995 1498 1502
6. P.R. Mittl, P. Chene, and M.G. Grutter Crystallization and structure solution of p53 (residues 326-356) by molecular replacement using an NMR model as template Acta Crystallog. sect. D 54 1998 86 89
7. R.R. Gabdoulline, and R.C. Wade Biomolecular diffusional association Curr. Opin. Struct. Biol. 12 2002 204 213
8. Y. Levy, A. Caflisch, J.N. Onuchic, and P.G. Wolynes The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations J. Mol. Biol. 340 2004 67 79
9. Y. Levy, P.G. Wolynes, and J.N. Onuchic Protein topology determines binding mechanism Proc. Natl Acad. Sci. USA 101 2004 511 516
10. F. Ding, N.V. Dokholyan, S.V. Buldyrev, H.E. Stanley, and E.I. Shakhnovich Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism J. Mol. Biol. 324 2002 851 857
11. V.S. Pande, I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, and S.M. Larson Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing Biopolymers 1 2003 91 109
12. D. Chandler Introduction to Modern Statistical Mechanics 1987 Oxford University Press Oxford
13. V.S. Pande, and D.S. Rokhsar Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G Proc. Natl Acad. Sci. USA 96 1999 9062 9067
14. J. Gsponer, and A. Caflisch Molecular dynamics simulations of protein folding from the transition state Proc. Natl Acad. Sci. USA 99 2002 6719 6724
15. D.O. Alonso, and V. Daggett Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60% methanol and in water J. Mol. Biol. 247 1995 501 520
16. G.M. Verkhivker, D. Bouzida, D.K. Gehlhaar, P.A. Rejto, S.T. Freer, and P.W. Rose Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding Proc. Natl Acad. Sci. USA 100 2003 5148 5153
17. T.S. Davison, X. Nie, W. Ma, Y. Lin, C. Kay, S. Benchimol, and C.H. Arrowsmith Structure and functionality of a designed p53 dimer J. Mol. Biol. 307 2001 605 617
18. R. Du, V.S. Pande, A.Y. Grosberg, and T. Tanaka On the transition coordinate for protein folding J. Chem. Phys. 108 1998 334 350
19. R. Day, B.J. Bennion, S. Ham, and V. Daggett Increasing temperature accelerates protein unfolding without changing the pathway of unfolding J. Mol. Biol. 322 2002 189 203
20. A.R. Dinner, and M. Karplus Is protein unfolding the reverse of protein folding? A lattice simulation analysis J. Mol. Biol. 292 1999 403 419
21. A.R. Fersht, and S. Sato Phi-value analysis and the nature of protein-folding transition states Proc. Natl Acad. Sci. USA 101 2004 7976 7981
22. A.E. Garcia, and K.Y. Sanbonmatsu Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds Proc. Natl Acad. Sci. USA 99 2002 2782 2787
23. E. Lacroix, A.R. Viguera, and L. Serrano Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters J. Mol. Biol. 284 1998 173 191
24. A.R. Fersht Nucleation mechanisms in protein folding Curr. Opin. Struct. Biol. 7 1997 3 9
25. M.G. Mateu, and A.R. Fersht Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumor suppressor p53 tetramerization domain EMBO J. 17 1998 2748 2758
26. I.A. Hubner, M. Oliveberg, and E.I. Shakhnovich Simulation, experiment, and evolution: understanding nucleation in protein S6 folding Proc. Natl Acad. Sci. USA 101 2004 8354 8359
27. N. Cariello, L. Cui, C. Beroud, and T. Soussi Database and software for the analysis of mutations in the human p53 gene Cancer Res. 54 1994 4454 4460
28. C.D. Nicholls, K.G. McLure, M.A. Shields, and P.W.K. Lee Biogenesis of p53 involves cotranslational dimerization of monomers and posttranslational dimerization of dimers J. Biol. Chem. 277 2002 12937 12945
29. E. Lindahl, B. Hess, and D. van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7 2001 306 317
30. W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
31. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, and D.M. Ferguson A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
32. M. Beachy, D. Chasman, R. Murphy, T. Halgren, and R. Friesner Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields J. Am. Chem. Soc. 119 1997 5908 5920
33. M. Neumann, and O. Steinhauser The influence of boundary conditions used in machine simulations on the structure of polar systems Mol. Phys. 39 1980
34. B. Hess, H. Bekker, H. Berendsen, and J. Fraaije LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472
35. H. Berendsen, J. Postma, W. van Gunsteren, A. DiNola, and J. Haak Molecular dynamics with coupling to an external bath J. Comput. Phys. 81 1984 3684 3690
36. A.D. McLachlan Rapid comparison of protein structures Acta Crystallog. A 38 1982 871 873
37. B. Zagrovic, C.D. Snow, S. Khaliq, M.R. Shirts, and V.S. Pande Native-like mean structure in the unfolded ensemble of small proteins J. Mol. Biol. 323 2002 153 164
38. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
39. G.M. Downs, P. Willett, and W. Fisanick Similarity searching and clustering of chemical-structure databases using molecular property data J. Chem. Inf. Comput. Sci. 34 1994 1094 1102
40. M. Vendruscolo, E. Paci, C.M. Dobson, and M. Karplus Three key residues form a critical contact network in a protein folding transition state Nature 409 2001 641 645
41. A. Li, and V. Daggett Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2 Proc. Natl Acad. Sci. USA 91 1994 10430 10434
42. F. Ding, N.V. Dokholyan, S.V. Buldyrev, H.E. Stanley, and E.I. Shakhnovich Direct molecular dynamics observation of protein folding transition state ensemble Biophys. J. 83 2002 3525 3532