Molecular dynamics simulation of phosphorylated KID post-translational modification

PLoS ONE

Volumn 4, Issue 8, 2009, Pages

  Chen, Hai Feng ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; ASPARTIC ACID; GENE PRODUCT; KINASE INDUCIBLE DOMAIN PROTEIN; LEUCINE; UNCLASSIFIED DRUG; PHOSPHOTRANSFERASE;

ALPHA HELIX; ARTICLE; BINDING KINETICS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; CHEMICAL STRUCTURE; METABOLISM; PHOSPHORYLATION; TEMPERATURE;

MODELS, MOLECULAR; PHOSPHORYLATION; PHOSPHOTRANSFERASES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; TEMPERATURE;

EID: 68349133281     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006516     Document Type: Article

References (61)

1. Chrivia JC, Kwok RP, Lamb N, Hagiwara M, Montminy MR, et al. (1993) Phosphorylated CREB binds specifically to the nuclear protein CBP. Nature 365: 855-859.
2. Kwok RP, Laurance ME, Lundblad JR, Goldman PS, Shih H, et al. (1996) Control of cAMP-regulated enhancers by the viral transactivator Tax through CREB and the co-activator CBP. Nature 380: 642-646.
3. Zor T, Mayr BM, Dyson HJ, Montminy MR, Wright PE (2002) Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators. J Biol Chem 277: 42241-42248.
4. Solt I, Magyar C, Simon I, Tompa P, Fuxreiter M (2006) Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP. Proteins 64: 749-757.
5. Geiger TR, Sharma N, Kim YM, Nyborg JK (2008) The human T-cell leukemia virus type 1 tax protein confers CBP/p300 recruitment and transcriptional activation properties to phosphorylated CREB. Mol Cell Biol 28: 1383-1392.
6. Campbell KM, Lumb KJ (2002) Structurally distinct modes of recognition of the KIX domain of CBP by Jun and CREB. Biochemistry 41: 13956-13964.
7. Radhakrishnan I, Perez-Alvarado GC, Parker D, Dyson HJ, Montminy MR, et al. (1997) Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator: coactivator interactions. Cell 91: 741-752.
8. Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447: 1021-1025.
9. Henkels CH, Kurz JC, Fierke CA, Oas TG (2001) Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein. Biochemistry 40: 2777-2789.
10. Henkels CH, Oas TG (2006) Ligation-state hydrogen exchange: Coupled binding and folding equilibria in ribonuclease P protein. J Am Chem Soc 128: 7772-7781.
11. Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108: 573-582.
12. Baker D (1998) Metastable states and folding free energy barriers. Nat Struct Biol 5: 1021-1024.
13. Caflisch A, Karplus M (1994) Molecular-Dynamics Simulation Of Protein Denaturation - Solvation Of The Hydrophobic Cores And Secondary Structure Of Barnase. Proc Natl Acad Sci U S A 91: 1746-1750.
14. Caflisch A, Karplus M (1995) Acid And Thermal-Denaturation Of Barnase Investigated By Molecular-Dynamics Simulations. J Mol Biol 252: 672-708.
15. Daggett V, Li AJ, Itzhaki LS, Otzen DE, Fersht AR (1996) Structure of the transition state for folding of a protein derived from experiment and simulation. J Mol Biol 257: 430-440.
16. Ladurner AG, Itzhaki LS, Daggett V, Fersht AR (1998) Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc Natl Acad Sci U S A 95: 8473-8478.
17. Gsponer J, Caflisch A (2001) Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J Mol Biol 309: 285-298.
18. Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor U, et al. (2003) Unifying features in protein-folding mechanisms. Proc Natl Acad Sci U S A 100: 13286-13291.
19. Mayor U, Johnson CM, Daggett V, Fersht AR (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci U S A 97: 13518-13522.
20. Akanuma S, Miyagawa H, Kitamura K, Yamagishi A (2005) A detailed unfolding pathway of a (beta/alpha)8-barrel protein as studied by molecular dynamics simulations. Proteins 58: 538-546.
21. Scott KA, Randles LG, Moran SJ, Daggett V, Clarke J (2006) The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment. J Mol Biol 359: 159-173.
22. Oard S, Karki B (2006) Mechanism of beta-purothionin antimicrobial peptide inhibition by metal ions: molecular dynamics simulation study. Biophys Chem 121: 30-43.
23. Tsai J, Levitt M, Baker D (1999) Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol 291: 215-225.
24. Chen HF, Luo R (2007) Binding induced folding in p53-MDM2 complex. J Am Chem Soc 129: 2930-2937.
25. Esposito L, Daggett V (2005) Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations. Biochemistry 44: 3358-3368.
26. Chen HF (2008) Mechanism of Coupled Folding and Binding in the siRNAPAZ Complex. J Chem Theory Comput 4: 1360-1368.
27. Turjanski AG, Gutkind JS, Best RB, Hummer G (2008) Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol 4: e1000060.
28. Levy Y, Onuchic JN, Wolynes PG (2007) Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc 129: 738-739.
29. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
30. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
31. Case DA, Darden TA, Cheatham TE, Simmerling III CL, Wang J, et al. (2004) AMBER 8, University of California, San Francisco.
32. Pande VS, Rokhsar DS (1999) Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc Natl Acad Sci U S A 96: 9062-9067.
33. Gsponer J, Caflisch A (2002) Molecular dynamics simulations of protein folding from the transition state. Proc Natl Acad Sci U S A 99: 6719-6724.
34. Chong LT, Snow CD, Rhee YM, Pande VS (2005) Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. J Mol Biol 345: 869-878.
35. Chen HF (2009) Aggregation mechanism investigation of the GIFQINS crossbeta amyloid fibril. Comput Biol Chem 33: 41-45.
36. Kabsch W, Sander C (1983) Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
37. Li A, Daggett V (1994) Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A 91: 10430-10434.
38. Vendruscolo M, Paci E, Dobson CM, Karplus M (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
39. Radhakrishnan I, Perez-Alvarado GC, Dyson HJ, Wright PE (1998) Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB. FEBS Lett 430: 317-322.
40. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8: 127-134.
41. Parker D, Ferreri K, Nakajima T, LaMorte VJ, Evans R, et al. (1996) Phosphorylation of CREB at Ser-133 induces complex formation with CREB-binding protein via a direct mechanism. Mol Cell Biol 16: 694-703.
42. Day R, Daggett V (2005) Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent. Protein Sci 14: 1242-1252.
43. Petsko GA, Ringe D (2003) Protein Structure and Function. Chartper 2. From Structure to Function. London: New Science Press.
44. Fersht AR, Matouschek A, Serrano L (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224: 771-782.
45. Sato S, Fersht AR (2007) Searching for multiple folding pathways of a nearly symmetrical protein: temperature dependent phi-value analysis of the B domain of protein A. J Mol Biol 372: 254-267.
46. Fersht AR (2000) Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc Natl Acad Sci U S A 97: 1525-1529.
47. Fernandez-Escamilla AM, Cheung MS, Vega MC, Wilmanns M, Onuchic JN, et al. (2004) Solvation in protein folding analysis: combination of theoretical and experimental approaches. Proc Natl Acad Sci U S A 101: 2834-2839.
48. Day R, Daggett V (2005) Ensemble versus single-molecule protein unfolding. Proc Natl Acad Sci U S A 102: 13445-13450.
49. Day R, Daggett V (2007) Direct observation of microscopic reversibility in single-molecule protein folding. J Mol Biol 366: 677-686.
50. McCully ME, Beck DA, Daggett V (2008) Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. Biochemistry 47: 7079-7089.
51. Boehr DD, Wright PE (2008) Biochemistry. How do proteins interact? Science 320: 1429-1430.
52. Koshland DE (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A 44: 98-104.
53. Ma B, Kumar S, Tsai CJ, Nussinov R (1999) Folding funnels and binding mechanisms. Protein Eng 12: 713-720.
54. Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9: 10-19.
55. Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 11: 184-197.
56. Tsai CJ, Ma B, Nussinov R (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci U S A 96: 9970-9972.
57. Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R (2001) Structured disorder and conformational selection. Proteins 44: 418-427.
58. Weikl TR, von Deuster C (2009) Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 75: 104-110.
59. Lange OF, Lakomek NA, Fares C, Schroder GF, Walter KF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320: 1471-1475.
60. James LC, Roversi P, Tawfik DS (2003) Antibody multi-specificity mediated by conformational diversity. Science 299: 1362-1367.
61. Okazaki K, Takada S (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc Natl Acad Sci U S A 105: 11182-11187.