Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation

Journal of Molecular Biology

Volumn 353, Issue 5, 2005, Pages 1118-1128

  Sivakolundu, Sivashankar G ^a   Bashford, Donald ^a   Kriwacki, Richard W ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

Cyclin dependant kinase; Intrinsically unstructured; Molecular dynamics; NMR; p27

Indexed keywords

CYCLIN A; CYCLIN DEPENDENT KINASE 2; CYCLIN DEPENDENT KINASE INHIBITOR 1B; PROTEIN SUBUNIT;

ARTICLE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; THERMODYNAMICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING;

COMPUTER SIMULATION; CYCLIN A; CYCLIN-DEPENDENT KINASE 2; CYCLIN-DEPENDENT KINASE INHIBITOR P27; HUMANS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 27144528728     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.08.074     Document Type: Article

References (51)

1. C.J. Sherr, and J.M. Roberts Cdk inhibitors: positive and negative regulators of G1-phase progression Genes Dev. 13 1999 1501 1512
2. E.R. Lacy, I. Filippov, W.S. Lewis, S. Otieno, L. Xiao, and S. Weiss p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding Nature Struct. Mol. Biol. 11 2004 358 364
3. E.A. Bienkiewicz, J.N. Adkins, and K.J. Lumb Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1) Biochemistry 41 2002 752 759
4. A.A. Russo, P.D. Jeffrey, A.K. Patten, J. Massague, and N.P. Pavletich Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex Nature 382 1996 325 331
5. P.E. Wright, and H.J. Dyson Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm J. Mol. Biol. 293 1999 321 331
6. L.M. Iakoucheva, C.J. Brown, J.D. Lawson, Z. Obradovic, and A.K. Dunker Intrinsic disorder in cell-signaling and cancer-associated proteins J. Mol. Biol. 323 2002 573 584
7. J.J. Ward, J.S. Sodhi, L.J. McGuffin, B.F. Buxton, and D.T. Jones Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 635 645
8. H. Schwalbe, K.M. Fiebig, M. Buck, J.A. Jones, S.B. Grimshaw, and A. Spencer Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea Biochemistry 36 1997 8977 8981
9. C.J. Penkett, C. Redfield, J.A. Jones, I. Dodd, J. Hubbard, and R.A. Smith Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus Biochemistry 37 1998 17054 17067
10. X. Wu, and S. Wang Self-guided molecular dynamics simulation for efficient conformational search J. Phys. Chem. B 102 1998 7238 7250
11. S. Piana, P. Carloni, and M. Parrinello Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease J. Mol. Biol. 319 2002 567 583
12. G.M. Verkhivker Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: hierarchy of structural loss from all-atom Monte Carlo simulations of p27(Kip1) unfolding-unbinding and structural determinants of the binding mechanism Biopolymers 75 2004 420 433
13. 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
14. A. Onufriev, D.A. Case, and D. Bashford Structural details, pathways, and energetics of unfolding apomyoglobin J. Mol. Biol. 325 2003 555 567
15. E. Paci, L.J. Smith, C.M. Dobson, and M. Karplus Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation J. Mol. Biol. 306 2001 329 347
16. X. Wu, S. Wang, and B.R. Brooks Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation J. Am. Chem. Soc. 124 2002 5282 5283
17. L. Wang, Y. Duan, R. Shortle, B. Imperiali, and P.A. Kollman Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures Protein Sci. 8 1999 1292 1304
18. Y. Duan, L. Wang, and P.A. Kollman The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation Proc. Natl Acad. Sci. USA 95 1998 9897 9902
19. 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
20. K. Lindorff-Larsen, R.B. Best, M.A. Depristo, C.M. Dobson, and M. Vendruscolo Simultaneous determination of protein structure and dynamics Nature 433 2005 128 132
21. S. Kristjansdottir, K. Lindorff-Larsen, W. Fieber, C.M. Dobson, M. Vendruscolo, and F.M. Poulsen Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies J. Mol. Biol. 347 2005 1053 1062
22. M.M. Dedmon, K. Lindorff-Larsen, J. Christodoulou, M. Vendruscolo, and C.M. Dobson Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations J. Am. Chem. Soc. 127 2005 476 477
23. K. Wuthrich NMR of Proteins and Nucleic Acids 1986 Wiley New York
24. H.J. Dyson, and P.E. Wright Defining solution conformations of small linear peptides Annu. Rev. Biophys. Biophys. Chem. 20 1991 519 538
25. P.E. Wright, H.J. Dyson, and R.A. Lerner Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding Biochemistry 27 1988 7167 7175
26. M. Fuxreiter, I. Simon, P. Friedrich, and P. Tompa Preformed structural elements feature in partner recognition by intrinsically unstructured proteins J. Mol. Biol. 338 2004 1015 1026
27. L. Zhu, H.J. Dyson, and P.E. Wright A NOESY-HSQC simulation program, SPIRIT J. Biomol. NMR 11 1998 17 29
28. 15N edited 3D-NOESY-HSQC spectra using back calculated and experimental spectra J. Magn. Reson. 137 1999 39 45
29. A. Ried, W. Gronwald, J.M. Trenner, K. Brunner, K.P. Neidig, and H.R. Kalbitzer Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy J. Biomol. NMR 30 2004 121 131
30. A.T. Alexandrescu, and D. Shortle Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease J. Mol. Biol. 242 1994 527 546
31. D. Yang, Y.-K. Mok, J.D. Forman-Kay, N.A. Farrow, and L.E. Kay Contributions to protein entropy and heat capacity from bond vector motions measured by NMR spin relaxation J. Mol. Biol. 272 1997 790 804
32. J.M. Schurr, H.P. Babcock, and B.S. Fujimoto A test of the model free formulas. Effects of anisotropic rotational diffusion and dimerization J. Magn. Reson. ser. B 105 1994 211 224
33. 1H spectroscopy Biochemistry 29 1990 7387 7401
34. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
35. Y. Gu, C.W. Turck, and D.O. Morgan Inhibition of CDK2 activity in vivo by an associated 20K regulatory subunit Nature 366 1993 707 710
36. W. El-Deiry, T. Tokino, V.E. Velculescu, D.B. Levy, R. Parsons, and J.M. Trent WAF1, a potential mediator of p53 tumor suppression Cell 75 1993 817 825
37. J.W. Harper, G.R. Adami, N. Wei, K. Keyomarsi, and S.J. Elledge The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases Cell 75 1993 805 816
38. Y. Xiong, G.J. Hannon, H. Zhang, D. Casso, R. Kobayashi, and D. Beach p21 is a universal inhibitor of cyclin kinases Nature 366 1993 701 704
39. W. Shou, and W.G. Dunphy Cell cycle control by Xenopus p28Kix1, a developmentally regulated inhibitor of cyclin-dependent kinases Mol. Biol. Cell 7 1996 457 469
40. M.H. Lee, I. Reynisdóttir, and J. Massagué Cloning of p57KIP2, a cyclin-dependent kinase inhibitor with unique domain structure and tissue distribution Genes Dev. 9 1995 639 649
41. S. Matsuoka, M.C. Edwards, C. Bai, S. Parker, P. Zhang, and A. Baldini p57KIP2, a structurally distinct member of the p21CIP1 Cdk inhibitor family, is a candidate tumor suppressor gene Genes Dev. 9 1995 650 652
42. E.R. Lacy, Y. Wang, J. Post, A. Nourse, W. Webb, and M. Mapelli Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division J. Mol. Biol. 349 2005 764 773
43. R.S. Spolar, and M.T.J. Record Coupling of local folding to site-specific binding of proteins to DNA Science 263 1994 777 784
44. P. Tompa Intrinsically unstructured proteins Trends Biochem. Sci. 27 2002 527 533
45. V.N. Uversky Natively unfolded proteins: a point where biology waits for physics Protein Sci. 11 2002 739 756
46. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMR Pipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
47. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham III, J. Wang, and W.S. Ross AMBER 7 2002 University of California San Francisco
48. J. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculationg conformational energies of organic and biological molecules? J. Comp. Chem. 21 2000 1049 1074
49. 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
50. Leach, A. R. (2001). Molecular Modelling: Principles and Applications. 2nd edit., Prentice Hall, London.
51. R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 29 32