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Volumn 73, Issue 4, 2008, Pages 918-928

A robust approach for analyzing a heterogeneous structural ensemble

Author keywords

Contact map; Hierarchical clustering; Intrinsically unstructured protein; Principal component analysis; Surface potential; Tumor suppressor

Indexed keywords

GLOBULAR PROTEIN; INTRINSICALLY UNSTRUCTURED PROTEIN; PROTEIN P53; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 58149288617     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22117     Document Type: Article
Times cited : (10)

References (70)
  • 1
    • 0035096292 scopus 로고    scopus 로고
    • Recognition between flexible protein molecules: Induced and assisted folding
    • DOI 10.1002/1099-1352(200101/02)14:1<42::AID-JMR518>3.0.CO;2-8
    • Demchenko AP. Recognition between flexible protein molecules: induced and assisted folding. J Mol Recognit 2001;14:42-61. (Pubitemid 32205707)
    • (2001) Journal of Molecular Recognition , vol.14 , Issue.1 , pp. 42-61
    • Demchenko, A.P.1
  • 4
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005;6:197-208. (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 6
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci 2002;27:527-533.
    • (2002) Trends Biochem Sci , vol.27 , pp. 527-533
    • Tompa, P.1
  • 7
    • 0036153571 scopus 로고    scopus 로고
    • What does it mean to be natively unfolded?
    • Uversky VN. What does it mean to be natively unfolded? Eur J Biochem 2002;269:2-12.
    • (2002) Eur J Biochem , vol.269 , pp. 2-12
    • Uversky, V.N.1
  • 8
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: A point where biology waits for physics
    • DOI 10.1110/ps.4210102
    • Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002;11:739-756. (Pubitemid 34241284)
    • (2002) Protein Science , vol.11 , Issue.4 , pp. 739-756
    • Uversky, V.N.1
  • 9
    • 0034669882 scopus 로고    scopus 로고
    • Why are "natively unfolded" proteins unstructured under physiologic conditions?
    • Uversky VN, Gillespie JR, Fink AL. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 2000; 41:415-427.
    • (2000) Proteins , vol.41 , pp. 415-427
    • Uversky, V.N.1    Gillespie, J.R.2    Fink, A.L.3
  • 10
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • DOI 10.1006/jmbi.1999.3110
    • Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999;293: 321-331. (Pubitemid 29516173)
    • (1999) Journal of Molecular Biology , vol.293 , Issue.2 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 11
    • 34249282661 scopus 로고    scopus 로고
    • Functional anthology of intrinsic disorder. 2. cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions
    • DOI 10.1021/pr060393m
    • Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. II. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res 2007;6:1899-1916. (Pubitemid 46814513)
    • (2007) Journal of Proteome Research , vol.6 , Issue.5 , pp. 1899-1916
    • Vucetic, S.1    Xie, H.2    Iakoucheva, L.M.3    Oldfield, C.J.4    Dunker, A.K.5    Obradovic, Z.6    Uversky, V.N.7
  • 12
    • 33847783298 scopus 로고    scopus 로고
    • Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins
    • DOI 10.1021/pr060394e
    • Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. III. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res 2007;6: 1917-1932. (Pubitemid 46814514)
    • (2007) Journal of Proteome Research , vol.6 , Issue.5 , pp. 1917-1932
    • Xie, H.1    Vucetic, S.2    Iakoucheva, L.M.3    Oldfield, C.J.4    Dunker, A.K.5    Obradovic, Z.6    Uversky, V.N.7
  • 13
    • 33847768609 scopus 로고    scopus 로고
    • Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions
    • Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z. Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J Proteome Res 2007;6:1882-1898.
    • (2007) J Proteome Res , vol.6 , pp. 1882-1898
    • Xie, H.1    Vucetic, S.2    Iakoucheva, L.M.3    Oldfield, C.J.4    Dunker, A.K.5    Uversky, V.N.6    Obradovic, Z.7
  • 17
    • 0034912536 scopus 로고    scopus 로고
    • Nuclear magnetic resonance methods for elucidation of structure and dynamics in disordered states
    • DOI 10.1016/S0076-6879(01)39317-5
    • Dyson HJ, Wright PE. Nuclear magnetic resonance methods for elucidation of structure and dynamics in disordered states. Methods Enzymol 2001;339:258-270. (Pubitemid 32666564)
    • (2001) Methods in Enzymology , vol.339 , pp. 258-270
    • Dyson, H.J.1    Wright, P.E.2
  • 18
    • 0036400715 scopus 로고    scopus 로고
    • Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance
    • DOI 10.1016/S0065-3233(02)62012-1
    • Dyson HJ, Wright PE. Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. Adv Protein Chem 2002;62:311-340. (Pubitemid 35204875)
    • (2002) Advances in Protein Chemistry , vol.62 , pp. 311-340
    • Dyson, H.J.1    Wright, P.E.2
  • 19
    • 0031585992 scopus 로고    scopus 로고
    • Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures
    • DOI 10.1006/jmbi.1997.0953
    • Gillespie JR, Shortle D. Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. J Mol Biol 1997;268:170-184. (Pubitemid 27192687)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 170-184
    • Gillespie, J.R.1    Shortle, D.2
  • 20
    • 0031585990 scopus 로고    scopus 로고
    • Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels
    • Gillespie JR, Shortle D. Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. J Mol Biol 1997; 268:158-169.
    • (1997) J Mol Biol , Issue.268 , pp. 158-169
    • Gillespie, J.R.1    Shortle, D.2
  • 25
    • 33846939583 scopus 로고    scopus 로고
    • Determination of conformationally heterogeneous states of proteins
    • DOI 10.1016/j.sbi.2007.01.002, PII S0959440X07000036, Foldinf and Binding / Protein-Nucleic Interactions
    • Vendruscolo M. Determination of conformationally heterogeneous states of proteins. Curr Opin Struct Biol 2007;17:15-20. (Pubitemid 46240813)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.1 , pp. 15-20
    • Vendruscolo, M.1
  • 26
    • 0036468397 scopus 로고    scopus 로고
    • Coupling of folding and binding for unstructured proteins
    • DOI 10.1016/S0959-440X(02)00289-0
    • Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002;12:54-60. (Pubitemid 34142721)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 54-60
    • Dyson, H.J.1    Wright, P.E.2
  • 27
    • 20444376186 scopus 로고    scopus 로고
    • The interplay between structure and function in intrinsically unstructured proteins
    • DOI 10.1016/j.febslet.2005.03.072, PII S0014579305004242
    • Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 2005;579:3346-3354. (Pubitemid 40804685)
    • (2005) FEBS Letters , vol.579 , Issue.15 , pp. 3346-3354
    • Tompa, P.1
  • 33
    • 41149177142 scopus 로고    scopus 로고
    • Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53
    • Lowry DF, Stancik A, Shrestha RM, Daughdrill GW. Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53. Proteins 2007;71:587-598.
    • (2007) Proteins , vol.71 , pp. 587-598
    • Lowry, D.F.1    Stancik, A.2    Shrestha, R.M.3    Daughdrill, G.W.4
  • 36
    • 34250885891 scopus 로고    scopus 로고
    • An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins
    • DOI 10.1110/ps.072845607
    • Ohashi T, Galiacy SD, Briscoe G, Erickson HP. An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins. Protein Sci 2007;16:1429-1438. (Pubitemid 46984877)
    • (2007) Protein Science , vol.16 , Issue.7 , pp. 1429-1438
    • Ohashi, T.1    Galiacy, S.D.2    Briscoe, G.3    Erickson, H.P.4
  • 39
    • 33748268107 scopus 로고    scopus 로고
    • Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease
    • DOI 10.1002/prot.21077
    • Francis CJ, Lindorff-Larsen K, Best RB, Vendruscolo M. Characterization of the residual structure in the unfolded state of the Delta131Delta fragment of staphylococcal nuclease. Proteins 2006;65: 145-152. (Pubitemid 44320624)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.1 , pp. 145-152
    • Francis, C.J.1    Lindorff-Larsen, K.2    Best, R.B.3    Vendruscolo, M.4
  • 41
    • 2542430932 scopus 로고    scopus 로고
    • Singular value decomposition and principal component analysis
    • Berrar D, Dubitzky W, Granzow M, editors. Norwell, Massachusetts: Kluwer
    • Wall M, Rechsteiner A, Rocha L. Singular value decomposition and principal component analysis. In: Berrar D, Dubitzky W, Granzow M, editors. A practical approach to microarray data analysis. Norwell, Massachusetts: Kluwer; 2003. pp 91-109.
    • (2003) A Practical Approach to Microarray Data Analysis , pp. 91-109
    • Wall, M.1    Rechsteiner, A.2    Rocha, L.3
  • 49
    • 0002741413 scopus 로고
    • Large scale singular value computations
    • Berry M. Large scale singular value computations. Int J Supercomput Appl 1992;6:13-49.
    • (1992) Int J Supercomput Appl , vol.6 , pp. 13-49
    • Berry, M.1
  • 51
    • 0032561246 scopus 로고    scopus 로고
    • The transcriptional program of sporulation in budding yeast
    • DOI 10.1126/science.282.5389.699
    • Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science 1998;282:699-705. (Pubitemid 28489376)
    • (1998) Science , vol.282 , Issue.5389 , pp. 699-705
    • Chu, S.1    Derisi, J.2    Eisen, M.3    Mulholland, J.4    Botstein, D.5    Brown, P.O.6    Herskowitz, I.7
  • 52
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1976;32:922-923.
    • (1976) Acta Crystallogr A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 53
    • 0028878767 scopus 로고
    • EDPDB: A multifunctional tool for protein structure analysis
    • Zhang XJ, Matthews BW. EDPDB: a multifunctional tool for protein structure analysis. J Appl Crystallogr 1995;28:624-630.
    • (1995) J Appl Crystallogr , vol.28 , pp. 624-630
    • Zhang, X.J.1    Matthews, B.W.2
  • 55
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • DOI 10.1093/nar/gkh381
    • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 2004;32 (Web Server issue): W665-667. (Pubitemid 38997419)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 56
    • 0000525721 scopus 로고
    • Multigrid solution of the Poisson-Boltzmann equation
    • Holst M, Saied F. Multigrid solution of the Poisson-Boltzmann equation. J Comput Chem 1993;14:105-113.
    • (1993) J Comput Chem , vol.14 , pp. 105-113
    • Holst, M.1    Saied, F.2
  • 57
    • 84986437211 scopus 로고
    • Numerical solution of the nonlinear Poisson- Boltzmann equation: Developing more robust and efficient methods
    • Holst MJ, Saied F. Numerical solution of the nonlinear Poisson- Boltzmann equation: developing more robust and efficient methods. J Comput Chem 1995;16:337-364.
    • (1995) J Comput Chem , vol.16 , pp. 337-364
    • Holst, M.J.1    Saied, F.2
  • 58
    • 2142757231 scopus 로고    scopus 로고
    • Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
    • DOI 10.1016/j.jmb.2004.03.017, PII S0022283604003079
    • Fuxreiter M, Simon I, Friedrich P, Tompa P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 2004;338:1015-1026. (Pubitemid 38542830)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.5 , pp. 1015-1026
    • Fuxreiter, M.1    Simon, I.2    Friedrich, P.3    Tompa, P.4
  • 59
    • 14844361449 scopus 로고    scopus 로고
    • Primary contact sites in intrinsically unstructured proteins: The case of calpastatin and microtubule-associated protein 2
    • DOI 10.1021/bi047817f
    • Csizmok V, Bokor M, Banki P, Klement E, Medzihradszky KF, Friedrich P, Tompa K, Tompa P. Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. Biochemistry 2005;44:3955-3964. (Pubitemid 40358047)
    • (2005) Biochemistry , vol.44 , Issue.10 , pp. 3955-3964
    • Csizmok, V.1    Bokor, M.2    Banki, P.3    Klement, E.4    Medzihradszky, K.F.5    Friedrich, P.6    Tompa, K.7    Tompa, P.8
  • 60
    • 0030575937 scopus 로고    scopus 로고
    • Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain
    • DOI 10.1126/science.274.5289.948
    • Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 1996;274: 948-953. (Pubitemid 26398409)
    • (1996) Science , vol.274 , Issue.5289 , pp. 948-953
    • Kussie, P.H.1    Gorina, S.2    Marechal, V.3    Elenbaas, B.4    Moreau, J.5    Levine, A.J.6    Pavletich, N.P.7
  • 64
    • 0035955635 scopus 로고    scopus 로고
    • How Transcriptional Activators Bind Target Proteins
    • DOI 10.1074/jbc.M103793200
    • Hermann S, Berndt KD, Wright AP. How transcriptional activators bind target proteins. J Biol Chem 2001;276:40127-40132. (Pubitemid 37391431)
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.43 , pp. 40127-40132
    • Hermann, S.1    Berndt, K.D.2    Wright, A.P.3
  • 66
    • 34250821717 scopus 로고    scopus 로고
    • Mechanism of coupled folding and binding of an intrinsically disordered protein
    • DOI 10.1038/nature05858, PII NATURE05858
    • Sugase K, Dyson HJ, Wright PE. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 2007;447: 1021-1025. (Pubitemid 46975749)
    • (2007) Nature , vol.447 , Issue.7147 , pp. 1021-1025
    • Sugase, K.1    Dyson, H.J.2    Wright, P.E.3
  • 68
    • 0032836911 scopus 로고    scopus 로고
    • Human replication protein A: Global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker
    • DOI 10.1023/A:1008373009786
    • Jacobs DM, Lipton AS, Isern NG, Daughdrill GW, Lowry DF, Gomes X, Wold MS. Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible Cterminal linker. J Biomol NMR 1999;14:321-331. (Pubitemid 29469056)
    • (1999) Journal of Biomolecular NMR , vol.14 , Issue.4 , pp. 321-331
    • Jacobs, D.M.1    Lipton, A.S.2    Isern, N.G.3    Daughdrill, G.W.4    Lowry, D.F.5    Gomes, X.6    Wold, M.S.7
  • 70
    • 17544381252 scopus 로고    scopus 로고
    • NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain
    • DOI 10.1093/nar/gki336
    • Vise PD, Baral B, Latos AJ, Daughdrill GW. NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain. Nucleic Acids Res 2005;33:2061-2077. (Pubitemid 41439875)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2061-2077
    • Vise, P.D.1    Baral, B.2    Latos, A.J.3    Daughdrill, G.W.4


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