Length-dependent compaction of intrinsically disordered proteins

FEBS Letters

Volumn 586, Issue 1, 2012, Pages 70-73

  Uversky, Vladimir N ^a,b   Santambrogio, Carlo ^c   Brocca, Stefania ^c   Grandori, Rita ^c  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

^c UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

Compaction index; Functional misfolding; Hydrodynamic radius; Induced folding; Sic1; Structural disorder

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; GEL PERMEATION CHROMATOGRAPHY; HYDRODYNAMICS; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN COMPACTION; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN FUNCTION;

MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 84655167815     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.11.026     Document Type: Article

References (32)

1. V.N. Uversky Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes Chem. Soc. Rev. 40 2011 1623 1634
2. T. Mittag, S. Orlicky, W.Y. Choy, X. Tang, H. Lin, F. Sicheri, L.E. Kay, M. Tyers, and J.D. Forman-Kay Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor Proc. Natl. Acad. Sci. USA 105 2008 17772 17777
3. A.K. Dunker, M.S. Cortese, P. Romero, L.M. Iakoucheva, and V.N. Uversky Flexible nets. The roles of intrinsic disorder in protein interaction networks FEBS J. 272 2005 5129 5148 (Pubitemid 41503146)
4. V.N. Uversky Natively unfolded proteins: a point where biology waits for physics Protein Sci. 11 2002 739 756 (Pubitemid 34241284)
5. V.N. Uversky What does it mean to be natively unfolded? Eur. J. Biochem. 269 2002 2 12 (Pubitemid 34107333)
6. M.R. Jensen, P.R. Markwick, S. Meier, C. Griesinger, M. Zweckstetter, S. Grzesiek, P. Bernadó, and M. Blackledge Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings Structure 17 2009 1169 1185
7. M.R. Jensen, G. Communie, E.A.J. Ribeiro, N. Martinez, A. Desfosses, L. Salmon, L. Mollica, F. Gabel, M. Jamin, S. Longhi, R.W. Ruigrok, and M. Blackledge Intrinsic disorder in measles virus nucleocapsids Proc. Natl. Acad. Sci. USA 108 2011 9839 9844
8. Schneider, R., Huang, J.R., Yao, M., Communie, G., Ozenne, V., Mollica, L., Salmon, L., Jensen, M.R. and Blackledge, M. (2011). Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy. Mol. Biosyst. doi: 10.1039/C1MB05291H.
9. O. Tcherkasskaya, E.A. Davidson, and V.N. Uversky Biophysical constraints for protein structure prediction J. Proteome Res. 2 2003 37 42 (Pubitemid 36207188)
10. A.H. Mao, S.L. Crick, A. Vitalis, C.L. Chicoine, and R.V. Pappu Net charge per residue modulates conformational ensembles of intrinsically disordered proteins Proc. Natl. Acad. Sci. USA 107 2010 8183 8188
11. J. Yamada, J.L. Phillips, S. Patel, G. Goldfien, A. Calestagne-Morelli, H. Huang, R. Reza, J. Acheson, V.V. Krishnan, S. Newsam, A. Gopinathan, E.Y. Lau, M.E. Colvin, V.N. Uversky, and M.F. Rexach A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins Mol. Cell. Proteomics 9 2010 2205 2224
12. J.A. Marsh, and J.D. Forman-Kay Sequence determinants of compaction in intrinsically disordered proteins Biophys. J. 98 2010 2383 2390
13. V.N. Uversky, J.R. Gillespie, and A.L. Fink Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41 2000 415 427
14. L. Dougan, J. Li, C.L. Badilla, B.J. Berne, and J.M. Fernandez Single homopolypeptide chains collapse into mechanically rigid conformations Proc. Natl. Acad. Sci. USA 106 2009 12605 12610
15. R.H. Walters, and R.M. Murphy Examining polyglutamine peptide length: a connection between collapsed conformations and increased aggregation J. Mol. Biol. 393 2009 978 992
16. X. Wang, A. Vitalis, M.A. Wyczalkowski, and R.V. Pappu Characterizing the conformational ensemble of monomeric polyglutamine Proteins 63 2006 297 311
17. H.T. Tran, A. Mao, and R.V. Pappu Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins J. Am. Chem. Soc. 130 2008 7380 7392 (Pubitemid 351813231)
18. H.S. Ashbaugh, and H.W. Hatch Natively unfolded protein stability as a coil-to-globule transition in charge/hydropathy space J. Am. Chem. Soc. 130 2008 9536 9542 (Pubitemid 352031165)
19. O. Tcherkasskaya, and V.N. Uversky Polymeric aspects of protein folding: a brief overview Protein Pept. Lett. 10 2003 239 245 (Pubitemid 36614848)
20. V.N. Uversky Protein folding revisited. A polypeptide chain at the folding-misfolding-non-folding cross-roads: which way to go? Cell. Mol. Life Sci. 60 2003 1852 1871 (Pubitemid 37222583)
21. S. Brocca, L. Testa, F. Sobott, M. Šamalikova, A. Natalello, E. Papaleo, M. Lotti, L. De Gioia, S.M. Doglia, L. Alberghina, and R. Grandori Compaction properties of an intrinsically disordered protein: sic1 and its kinase-inhibitor domain Biophys. J. 100 2011 2243 2252
22. D.K. Wilkins, S.B. Grimshaw, V. Receveur, C.M. Dobson, J.A. Jones, and L.J. Smith Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques 38 1999 16424 16431
23. S. Müller-Späth, A. Soranno, V. Hirschfeld, H. Hofmann, S. Rüegger, L. Reymond, D. Nettels, and B. Schuler Charge interactions can dominate the dimensions of intrinsically disordered proteins Proc. Natl. Acad. Sci. USA 107 2010 14609 14614
24. C.J. Oldfield, M.S. Cortese, C.J. Brown, V.N. Uversky, and A.K. Dunker Comparing and combining predictors of mostly disordered proteins Biochemistry 44 2005 1989 2000 (Pubitemid 40227474)
25. A. Vitalis, X. Wang, and R.V. Pappu Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization J. Mol. Biol. 384 2008 279 297
26. D.P. Goldenberg Computational simulation of the statistical properties of unfolded proteins J. Mol. Biol. 326 2003 1615 1633 (Pubitemid 36269097)
27. C.J. Oldfield, Y. Cheng, M.S. Cortese, P. Romero, V.N. Uversky, and A.K. Dunker Coupled folding and binding with alpha-helix-forming molecular recognition elements Biochemistry 44 2005 12454 12470 (Pubitemid 41324337)
28. J.A. Marsh, B. Dancheck, M.J. Ragusa, M. Allaire, J.D. Forman-Kay, and W. Peti Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators Structure 18 2010 1094 1103
29. V.N. Uversky Intrinsically disordered proteins may escape unwanted interactions via functional misfolding Biochim. Biophys. Acta 1814 2011 693 712
30. S. Brocca, M. Šamalikova, V.N. Uversky, M. Lotti, M. Vanoni, L. Alberghina, and R. Grandori Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1 Proteins 76 2009 731 746
31. L. Testa, S. Brocca, M. Šamalikova, C. Santambrogio, L. Alberghina, and R. Grandori Electrospray ionization-mass spectrometry conformational analysis of isolated domains of an intrinsically disordered protein Biotechnol. J. 6 2011 96 100
32. S. Brocca, L. Testa, M. Šamalikova, R. Grandori, and M. Lotti Defining structural domains of an intrinsically disordered protein: Sic1, the cyclin-dependent kinase inhibitor of Saccharomyces cerevisiae Mol. Biotechnol. 47 2011 34 42