Hostname: page-component-745bb68f8f-l4dxg Total loading time: 0 Render date: 2025-01-26T22:30:00.701Z Has data issue: false hasContentIssue false
  • English
  • Français

Expanding the proteome: disordered and alternatively folded proteins

Published online by Cambridge University Press:  01 July 2011

H. Jane Dyson
H. Jane Dyson*
Affiliation:
Department of Molecular Biology MB2, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
*
Author for correspondence: Dr H. J. Dyson, Department of Molecular Biology MB2, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.Tel.: 1-858-784-2223; Fax: 1-858-784-9822; Email: dyson@scripps.edu
Get access Rights & Permissions [Opens in a new window]

Abstract

Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question ‘why would a particular domain need to be unstructured?’ are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder–order continuum.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 44 , Issue 4 , November 2011 , pp. 467 - 518
Copyright
Copyright © Cambridge University Press 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

14. References

Adda, C. G., Murphy, V. J., Sunde, M., Waddington, L. J., Schloegel, J., Talbo, G. H., Vingas, K., Kienzle, V., Masciantonio, R., Howlett, G. J., Hodder, A. N., Foley, M. & Anders, R. F. (2009). Plasmodium falciparum merozoite surface protein 2 is unstructured and forms amyloid-like fibrils. Molecular and Biochemical Parasitology 166, 159–171.CrossRefGoogle ScholarPubMed
Alba, M. M., Tompa, P. & Veitia, R. A. (2007). Amino acid repeats and the structure and evolution of proteins. Genome Dynamics 3, 119–30, 119–130.CrossRefGoogle ScholarPubMed
Albert, R., Jeong, H. & Barabasi, A. L. (2000). Error and attack tolerance of complex networks. Nature 406, 378–382.CrossRefGoogle ScholarPubMed
Alberts, B. (1998). The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294.CrossRefGoogle ScholarPubMed
Ando, T., Kodera, N., Takai, E., Maruyama, D., Saito, K. & Toda, A. (2001). A high-speed atomic force microscope for studying biological macromolecules. Proceedings of the National Academy of Sciences of the United States of America 98, 12468–12472.CrossRefGoogle ScholarPubMed
Ando, T., Uchihashi, T., Kodera, N., Yamamoto, D., Taniguchi, M., Miyagi, A. & Yamashita, H. (2007). High-speed atomic force microscopy for observing dynamic biomolecular processes. Journal of Molecular Recognition 20, 448–458.CrossRefGoogle ScholarPubMed
Andrusier, N., Mashiach, E., Nussinov, R. & Wolfson, H. J. (2008). Principles of flexible protein–protein docking. Proteins 73, 271–289.CrossRefGoogle ScholarPubMed
Arumugam, S., Gao, G., Patton, B. L., Semenchenko, V., Brew, K. &Van Doren, S. R. (2003). Increased backbone mobility in β-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3. Journal of Molecular Biology 327, 719–734.CrossRefGoogle ScholarPubMed
Bae, S. H., Dyson, H. J. & Wright, P. E. (2009). Prediction of the rotational tumbling time for proteins with disordered segments. Journal of the American Chemical Society 131, 6814–6821.CrossRefGoogle ScholarPubMed
Bai, F., Branch, R. W., Nicolau, D. V. Jr., Pilizota, T., Steel, B. C., Maini, P. K. & Berry, R. M. (2010). Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science 327, 685–689.CrossRefGoogle ScholarPubMed
Baker, J. M., Hudson, R. P., Kanelis, V., Choy, W. Y., Thibodeau, P. H., Thomas, P. J. & Forman-Kay, J. D. (2007). CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices. Nature Structural and Molecular Biology 14, 738–745.CrossRefGoogle ScholarPubMed
Barrick, D. (2009). Biological regulation via ankyrin repeat folding. Acs Chemical Biology 4, 19–22.CrossRefGoogle ScholarPubMed
Bartels, T., Ahlstrom, L. S., Leftin, A., Kamp, F., Haass, C., Brown, M. F. & Beyer, K. (2010). The N-terminus of the intrinsically disordered protein α-synuclein triggers membrane binding and helix folding. Biophysical Journal 99, 2116–2124.CrossRefGoogle ScholarPubMed
Belle, V., Rouger, S., Costanzo, S., Liquiere, E., Strancar, J., Guigliarelli, B., Fournel, A. & Longhi, S. (2008). Mapping α-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy. Proteins 73, 973–988.CrossRefGoogle ScholarPubMed
Bergqvist, S., Alverdi, V., Mengel, B., Hoffmann, A., Ghosh, G. & Komives, E. A. (2009). Kinetic enhancement of NF-κB⋅DNA dissociation by IκBα. Proceedings of the National Academy of Sciences of the United States of America 106, 19328–19333.CrossRefGoogle ScholarPubMed
Bergqvist, S., Croy, C. H., Kjaergaard, M., Huxford, T., Ghosh, G. & Komives, E. A. (2006). Thermodynamics reveal that helix four in the NLS of NF-κB p65 anchors IκBα, forming a very stable complex. Journal of Molecular Biology 360, 421–434.CrossRefGoogle ScholarPubMed
Bergqvist, S., Ghosh, G. & Komives, E. A. (2008). The IκBα/NF-κB complex has two hot spots, one at either end of the interface. Protein Science 17, 2051–2058.CrossRefGoogle ScholarPubMed
Bernado, P., Blackledge, M. & Sancho, J. (2006). Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles. Biophysical Journal 91, 4536–4543.CrossRefGoogle ScholarPubMed
Bernado, P., Garcia, D. L. T. & Pons, M. (2004). Macromolecular crowding in biological systems: hydrodynamics and NMR methods. Journal of Molecular Recognition 17, 397–407.CrossRefGoogle ScholarPubMed
Bernado, P., Modig, K., Grela, P., Svergun, D. I., Tchorzewski, M., Pons, M. & Akke, M. (2010). Structure and dynamics of ribosomal protein L12: an ensemble model based on SAXS and NMR relaxation. Biophysical Journal 98, 2374–2382.CrossRefGoogle ScholarPubMed
Bernado, P., Mylonas, E., Petoukhov, M. V., Blackledge, M. & Svergun, D. I. (2007). Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the American Chemical Society 129, 5656–5664.CrossRefGoogle ScholarPubMed
Bernado, P., Perez, Y., Blobel, J., Fernandez-Recio, J., Svergun, D. I. & Pons, M. (2009). Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering. Protein Science 18, 716–726.CrossRefGoogle ScholarPubMed
Bernado, P., Perez, Y., Svergun, D. I. & Pons, M. (2008). Structural characterization of the active and inactive states of Src kinase in solution by small-angle X-ray scattering. Journal of Molecular Biology 376, 492–505.CrossRefGoogle ScholarPubMed
Bertagna, A., Toptygin, D., Brand, L. & Barrick, D. (2008). The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder. Biochemical Society Transactions 36, 157–166.CrossRefGoogle ScholarPubMed
Bertoncini, C. W., Jung, Y. S., Fernandez, C. O., Hoyer, W., Griesinger, C., Jovin, T. M. & Zweckstetter, M. (2005). Release of long-range tertiary interactions potentiates aggregation of natively unstructured α-synuclein. Proceedings of the National Academy of Sciences of the United States of America 102, 1430–1435.CrossRefGoogle ScholarPubMed
Bertoncini, C. W., Rasia, R. M., Lamberto, G. R., Binolfi, A., Zweckstetter, M., Griesinger, C. & Fernandez, C. O. (2007). Structural characterization of the intrinsically unfolded protein β-synuclein, a natural negative regulator of α-synuclein aggregation. Journal of Molecular Biology 372, 708–722.CrossRefGoogle ScholarPubMed
Bischak, C. G., Longhi, S., Snead, D. M., Costanzo, S., Terrer, E. & Londergan, C. H. (2010). Probing structural transitions in the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by vibrational spectroscopy of cyanylated cysteines. Biophysical Journal 99, 1676–1683.CrossRefGoogle ScholarPubMed
Blobel, J., Bernado, P., Svergun, D. I., Tauler, R. & Pons, M. (2009). Low-resolution structures of transient protein–protein complexes using small-angle X-ray scattering. Journal of the American Chemical Society 131, 4378–4386.CrossRefGoogle ScholarPubMed
Bochkareva, E., Kaustov, L., Ayed, A., Yi, G. S., Lu, Y., Pineda-Lucena, A., Liao, J. C. C., Okorokov, A. L., Milner, J., Arrowsmith, C. H. & Bochkarev, A. (2005). Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A. Proceedings of the National Academy of Sciences of the United States of America 102, 15412–15417.CrossRefGoogle ScholarPubMed
Bokor, M., Csizmok, V., Kovacs, D., Banki, P., Friedrich, P., Tompa, P. & Tompa, K. (2005). NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins. Biophysical Journal 88, 2030–2037.CrossRefGoogle ScholarPubMed
Bonsor, D. A., Meenan, N. A. & Kleanthous, C. (2008). Colicins exploit native disorder to gain cell entry: a hitchhiker's guide to translocation. Biochemical Society Transactions 36, 1409–1413.CrossRefGoogle ScholarPubMed
Borg, M., Mittag, T., Pawson, T., Tyers, M., Forman-Kay, J. D. & Chan, H. S. (2007). Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proceedings of the National Academy of Sciences of the United States of America 104, 9650–9655.CrossRefGoogle ScholarPubMed
Bork, P. & Sudol, M. (1994). The WW domain: a signalling site in dystrophin? Trends in Biochemical Sciences 19, 531–533.CrossRefGoogle ScholarPubMed
Bothner, B., Aubin, Y. & Kriwacki, R. W. (2003). Peptides derived from two dynamically disordered proteins self-assemble into amyloid-like fibrils. Journal of the American Chemical Society 125, 3200–3201.CrossRefGoogle ScholarPubMed
Bothner, B., Lewis, W. S., Digiammarino, E. L., Weber, J. D., Bothner, S. J. & Kriwacki, R. W. (2001). Defining the molecular basis of Arf and Hdm2 interactions. Journal of Molecular Biology 314, 263–277.CrossRefGoogle ScholarPubMed
Bowman, P., Galea, C. A., Lacy, E. & Kriwacki, R. W. (2006). Thermodynamic characterization of interactions between p27Kip1 and activated and non-activated Cdk2: intrinsically unstructured proteins as thermodynamic tethers. Biochimica et Biophysica Acta 1764, 182–189.CrossRefGoogle ScholarPubMed
Brown, C. J., Takayama, S., Campen, A. M., Vise, P., Marshall, T. W., Oldfield, C. J., Williams, C. J. & Dunker, A. K. (2002). Evolutionary rate heterogeneity in proteins with long disordered regions. Journal of Molecular Evolution 55, 104–110.CrossRefGoogle ScholarPubMed
Bryngelson, J. D., Onuchic, J. N., Socci, N. D. & Wolynes, P. G. (1995). Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21, 167–195.CrossRefGoogle ScholarPubMed
Burra, P. V., Kalmar, L. & Tompa, P. (2010). Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes. PLoS ONE 5, e12069.CrossRefGoogle ScholarPubMed
Campen, A., Williams, R. M., Brown, C. J., Meng, J., Uversky, V. N. & Dunker, A. K. (2008). TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein and Peptide Letters 15, 956–963.CrossRefGoogle ScholarPubMed
Carbonell, P., Nussinov, R. & Del Sol, A. (2009). Energetic determinants of protein binding specificity: Insights into protein interaction networks. Proteomics 9, 1744–1753.CrossRefGoogle ScholarPubMed
Cattoni, D. I., Kaufman, S. B. & Gonzalez Flecha, F. L. (2009). Kinetics and thermodynamics of the interaction of 1-anilino-naphthalene-8-sulfonate with proteins. Biochimica et Biophysica Acta 1794, 1700–1708.CrossRefGoogle ScholarPubMed
Cervantes, C. F., Bergqvist, S., Kjaergaard, M., Kroon, G., Sue, S. C., Dyson, H. J. & Komives, E. A. (2010). The RelA nuclear localization signal folds upon binding to IκBα. Journal of Molecular Biology.Google ScholarPubMed
Chakrabortee, S., Meersman, F., Kaminski Schierle, G. S., Bertoncini, C. W., Mcgee, B., Kaminski, C. F. & Tunnacliffe, A. (2010). Catalytic and chaperone-like functions in an intrinsically disordered protein associated with desiccation tolerance. Proceedings of the National Academy of Sciences of the United States of America 107, 16084–16089.CrossRefGoogle Scholar
Chang, Y. C. & Oas, T. G. (2010). Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand. Biochemistry 49, 5086–5096.CrossRefGoogle ScholarPubMed
Chatr-Aryamontri, A., Ceol, A., Licata, L. & Cesareni, G. (2008). Protein interactions: integration leads to belief. Trends in Biochemical Sciences 33, 241–242.CrossRefGoogle ScholarPubMed
Chen, B., Lowry, D. F., Mayer, M. U. & Squier, T. C. (2008). Helix A stabilization precedes amino-terminal lobe activation upon calcium binding to calmodulin. Biochemistry 47, 9220–9226.CrossRefGoogle ScholarPubMed
Chen, J. (2009). Intrinsically disordered p53 extreme C-terminus binds to S100B(ββ) through “fly-casting”. Journal of the American Chemical Society 131, 2088–2089.CrossRefGoogle ScholarPubMed
Chen, J. W., Romero, P., Uversky, V. N. & Dunker, A. K. (2006a). Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. Journal of Proteome Research 5, 879–887.CrossRefGoogle Scholar
Chen, J. W., Romero, P., Uversky, V. N. & Dunker, A. K. (2006b). Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder. Journal of Proteome Research 5, 888–898.CrossRefGoogle ScholarPubMed
Chenal, A., Guijarro, J. I., Raynal, B., Delepierre, M. & Ladant, D. (2009). RTX calcium binding motifs are intrinsically disordered in the absence of calcium. Journal of Biological Chemistry 284, 1781–1789.CrossRefGoogle ScholarPubMed
Cheng, Y., Legall, T., Oldfield, C. J., Mueller, J. P., Van, Y. Y., Romero, P., Cortese, M. S., Uversky, V. N. & Dunker, A. K. (2006). Rational drug design via intrinsically disordered protein. Trends in Biotechnology 24, 435–442.CrossRefGoogle ScholarPubMed
Clore, G. M. & Iwahara, J. (2009). Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chemical Reviews 109, 4108–4139.CrossRefGoogle Scholar
Cortese, M. S., Baird, J. P., Uversky, V. N. & Dunker, A. K. (2005). Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatment. Journal of Proteome Research 4, 1610–1618.CrossRefGoogle ScholarPubMed
Cortese, M. S., Uversky, V. N. & Dunker, A. K. (2008). Intrinsic disorder in scaffold proteins: getting more from less. Progress in Biophysics and Molecular Biology 98, 85–106.CrossRefGoogle ScholarPubMed
Cremeens, M. E., Zimmermann, J., Yu, W., Dawson, P. E. & Romesberg, F. E. (2009). Direct observation of structural heterogeneity in a β-sheet. Journal of the American Chemical Society 131, 5726–+.CrossRefGoogle ScholarPubMed
Croy, C. H., Bergqvist, S., Huxford, T., Ghosh, G. & Komives, E. A. (2004). Biophysical characterization of the free IκBα ankyrin repeat domain in solution. Protein Science 13, 1767–1777.CrossRefGoogle ScholarPubMed
Csermely, P., Palotai, R. & Nussinov, R. (2010). Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends in Biochemical Sciences 35, 539–546.CrossRefGoogle ScholarPubMed
Csizmok, V., Dosztanyi, Z., Simon, I. & Tompa, P. (2007). Towards proteomic approaches for the identification of structural disorder. Current Protein and Peptide Science 8, 173–179.CrossRefGoogle ScholarPubMed
Csizmok, V., Szollosi, E., Friedrich, P. & Tompa, P. (2006). A novel two-dimensional electrophoresis technique for the identification of intrinsically unstructured proteins. Molecular and Cellular Proteomics 5, 265–273.CrossRefGoogle ScholarPubMed
Dames, S. A., Aregger, R., Vajpai, N., Bernado, P., Blackledge, M. & Grzesiek, S. (2006). Residual dipolar couplings in short peptides reveal systematic conformational preferences of individual amino acids. Journal of the American Chemical Society 128, 13508–13514.CrossRefGoogle ScholarPubMed
Dames, S. A., Martinez-Yamout, M., De Guzman, R. N., Dyson, H. J. & Wright, P. E. (2002). Structural basis for Hif-1α/CBP recognition in the cellular hypoxic response. Proceedings of the National Academy of Sciences of the United States of America 99, 5271–5276.CrossRefGoogle Scholar
Das, R. (2009). Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Molecular Cell 34, 674–685.CrossRefGoogle ScholarPubMed
Daughdrill, G. W., Chadsey, M. S., Karlinsey, J. E., Hughes, K. T. & Dahlquist, F. W. (1997). The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, σ28. Nature Structural Biology 4, 285–291.CrossRefGoogle Scholar
Daughdrill, G. W., Hanely, L. J. & Dahlquist, F. W. (1998). The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations. Biochemistry 37, 1076–1082.CrossRefGoogle ScholarPubMed
Davey, N. E., Travé, G. & Gibson, T. J. (2011). How viruses hijack cell regulation. Trends in Biochemical Sciences 36, 159–169.CrossRefGoogle ScholarPubMed
De Guzman, R. N., Goto, N. K., Dyson, H. J. & Wright, P. E. (2006). Structural basis for cooperative transcription factor binding to the CBP coactivator. Journal of Molecular Biology 355, 1005–1013.CrossRefGoogle Scholar
De Guzman, R. N., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2004a). Interaction of the TAZ1 domain of the CREB-binding protein with the activation domain of CITED2: regulation by competition between intrinsically unstructured ligands for non-identical binding sites. Journal of Biological Chemistry 279, 3042–3049.CrossRefGoogle ScholarPubMed
De Guzman, R. N., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2004b). Structure and function of the CBP/p300 TAZ domains. In Zinc Finger Proteins: from Atomic Contact to Cellular Function (Eds. Iuchi, S. & Kuldell, N.), pp. 116–122. New York:Kluwer Academic/Plenum Publishers.Google Scholar
De Guzman, R. N., Wojciak, J. M., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2005). CBP/p300 TAZ1 domain forms a structured scaffold for ligand binding. Biochemistry 44, 490–497.CrossRefGoogle ScholarPubMed
De La Cruz, L., Bajaj, R., Becker, S. & Zweckstetter, M. (2010). The intermembrane space domain of Tim23 is intrinsically disordered with a distinct binding region for presequences. Protein Science 19, 2045–2054.CrossRefGoogle ScholarPubMed
Demarest, S. J., Martinez-Yamout, M., Chung, J., Chen, H., Xu, W., Dyson, H. J., Evans, R. M. & Wright, P. E. (2002). Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature 415, 549–553.CrossRefGoogle ScholarPubMed
Deryusheva, E. I., Galzitskaya, O. V. & Serdyuk, I. N. (2008). Prediction of short loops in intrinsically disordered proteins. Molecular Biology 42, 949–959.CrossRefGoogle Scholar
Di Lello, P., Jenkins, L. M. M., Jones, T. N., Nguyen, B. D., Hara, T., Yamaguchi, H., Dikeakos, J. D., Appella, E., Legault, P. & Omichinski, J. G. (2006). Structure of the Tfb1/p53 complex: insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53. Molecular Cell 22, 731–740.CrossRefGoogle ScholarPubMed
Donne, D. G., Viles, J. H., Groth, D., Mehlhorn, I., James, T. L., Cohen, F. E., Prusiner, S. B., Wright, P. E. & Dyson, H. J. (1997). Structure of the recombinant full-length hamster prion protein PrP(29–231): the N terminus is highly flexible. Proceedings of the National Academy of Sciences of the United States of America 94, 13452–13457.CrossRefGoogle Scholar
Dosztanyi, Z., Chen, J., Dunker, A. K., Simon, I. & Tompa, P. (2006). Disorder and sequence repeats in hub proteins and their implications for network evolution. Journal of Proteome Research 5, 2985–2995.CrossRefGoogle ScholarPubMed
Dosztanyi, Z., Csizmok, V., Tompa, P. & Simon, I. (2005). The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. Journal of Molecular Biology 347, 827–839.CrossRefGoogle ScholarPubMed
Drobnak, I., Korencic, A., Loris, R., Marianovsky, I., Glaser, G., Jamnik, A., Vesnaver, G. & Lah, J. (2009). Energetics of MazG unfolding in correlation with its structural features. Journal of Molecular Biology 392, 63–74.CrossRefGoogle ScholarPubMed
Duggan, B. M., Dyson, H. J. & Wright, P. E. (1999). Inherent flexibility in a potent inhibitor of blood coagulation, recombinant nematode anticoagulant protein c2. European Journal of Biochemistry 265, 539–548.CrossRefGoogle Scholar
Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M. & Obradovic, Z. (2002). Intrinsic disorder and protein function. Biochemistry 41, 6573–6582.CrossRefGoogle ScholarPubMed
Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M. & Uversky, V. N. (2005). Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS Journal 272, 5129–5148.CrossRefGoogle ScholarPubMed
Dunker, A. K., Garner, E., Guilliot, S., Romero, P., Albrecht, K., Hart, J., Obradovic, Z., Kissinger, C. & Villafranca, J. E. (1998). Protein disorder and the evolution of molecular recognition: theory, predictions and observations. Pacific Symposium on Biocomputing 3, 473–484.Google Scholar
Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., Oldfield, C. J., Campen, A. M., Ratliff, C. M., Hipps, K. W., Ausio, J., Nissen, M. S., Reeves, R., Kang, C., Kissinger, C. R., Bailey, R. W., Griswold, M. D., Chiu, W., Garner, E. C. & Obradovic, Z. (2001). Intrinsically disordered protein. Journal of Molecular Graphics and Modeling 19, 26–59.CrossRefGoogle ScholarPubMed
Dunker, A. K. & Obradovic, Z. (2001). The protein trinity–linking function and disorder. Nature Biotechnology 19, 805–806.CrossRefGoogle ScholarPubMed
Dunker, A. K., Obradovic, Z., Romero, P., Garner, E. C. & Brown, C. J. (2000). Intrinsic protein disorder in complete genomes. Genome Information Series Workshop on Genome Information 11, 161–171.Google ScholarPubMed
Dyson, H. J., Satterthwait, A. C., Lerner, R. A. & Wright, P. E. (1990). Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR. Biochemistry 29, 7828–7837.CrossRefGoogle ScholarPubMed
Dyson, H. J. & Wright, P. E. (2002). Coupling of folding and binding for unstructured proteins. Current Opinion in Structural Biology 12, 54–60.CrossRefGoogle ScholarPubMed
Dyson, H. J. & Wright, P. E. (2004). Unfolded proteins and protein folding studied by NMR. Chemical Reviews 104, 3607–3622.CrossRefGoogle ScholarPubMed
Dyson, H. J. & Wright, P. E. (2005). Intrinsically unstructured proteins and their functions. Nature Reviews in Molecular and Cellular Biology 6, 197–208.CrossRefGoogle ScholarPubMed
Edwards, Y. J., Lobley, A. E., Pentony, M. M. & Jones, D. T. (2009). Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biology 10, R50.CrossRefGoogle ScholarPubMed
Ehebauer, M. T., Chirgadze, D. Y., Hayward, P., Martinez, A. A. & Blundell, T. L. (2005). High-resolution crystal structure of the human Notch 1 ankyrin domain. Biochemical Journal 392, 13–20.CrossRefGoogle ScholarPubMed
Eliezer, D. (2009). Biophysical characterization of intrinsically disordered proteins. Current Opinion in Structural Biology 19, 23–30.CrossRefGoogle ScholarPubMed
Elkins, J. M., Hewitson, K. S., Mcneill, L. A., Seibel, J. F., Schlemminger, I., Pugh, C. W., Ratcliffe, P. J. & Schofield, C. J. (2003). Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 α. Journal of Biological Chemistry 278, 1802–1806.CrossRefGoogle ScholarPubMed
Espinoza-Fonseca, L. M. (2009a). Reconciling binding mechanisms of intrinsically disordered proteins. Biochemical and Biophysical Research Communications 382, 479–482.CrossRefGoogle ScholarPubMed
Espinoza-Fonseca, L. M. (2009b). Thermodynamic aspects of coupled binding and folding of an intrinsically disordered protein: a computational alanine scanning study. Biochemistry 48, 11332–11334.CrossRefGoogle ScholarPubMed
Estrada, J., Bernado, P., Blackledge, M. & Sancho, J. (2009). ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble. BMC Bioinformatics 10, 104.CrossRefGoogle ScholarPubMed
Feige, M. J., Groscurth, S., Marcinowski, M., Shimizu, Y., Kessler, H., Hendershot, L. M. & Buchner, J. (2009). An unfolded CH1 domain controls the assembly and secretion of IgG antibodies. Molecular Cell 34, 569–579.CrossRefGoogle ScholarPubMed
Feng, H., Jenkins, L. M. M., Durell, S. R., Hayashi, R., Mazur, S. J., Cherry, S., Tropea, J. E., Miller, M., Wlodawer, A., Appella, E. & Bai, Y. (2009). Structural basis for p300 Taz2-p53 TAD1 binding and modulation by phosphorylation. Structure 17, 202–210.CrossRefGoogle ScholarPubMed
Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M., Cho, S. S., Wolynes, P. G. & Komives, E. A. (2007). Stabilizing IκBα by “consensus” design. Journal of Molecular Biology 365, 1201–1216.CrossRefGoogle ScholarPubMed
Ferreon, A. C., Gambin, Y., Lemke, E. A. & Deniz, A. A. (2009a). Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence. Proceedings of the National Academy of Sciences of the United States of America 106, 5645–5650.CrossRefGoogle ScholarPubMed
Ferreon, J. C., Lee, C. W., Arai, M., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2009b). Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2. Proceedings of the National Academy of Sciences of the United States of America 106, 6591–6596.CrossRefGoogle ScholarPubMed
Ferreon, J. C., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2009c). Structural basis for subversion of cellular control mechanisms by the adenoviral E1A oncoprotein. Proceedings of the National Academy of Sciences of the United States of America 106, 13260–13265.CrossRefGoogle ScholarPubMed
Fischer, D., Mukrasch, M. D., Biernat, J., Bibow, S., Blackledge, M., Griesinger, C., Mandelkow, E. & Zweckstetter, M. (2009). Conformational changes specific for pseudophosphorylation at serine 262 selectively impair binding of tau to microtubules. Biochemistry 48, 10047–10055.CrossRefGoogle ScholarPubMed
Fisher, C. K., Huang, A. & Stultz, C. M. (2010). Modeling intrinsically disordered proteins with Bayesian statistics. Journal of the American Chemical Society 132, 14919–14927.CrossRefGoogle ScholarPubMed
Follis, A. V., Hammoudeh, D. I., Daab, A. T. & Metallo, S. J. (2009). Small-molecule perturbation of competing interactions between c-Myc and Max. Bioorganic & Medicinal Chemistry Letters 19, 807–810.CrossRefGoogle ScholarPubMed
Follis, A. V., Hammoudeh, D. I., Wang, H., Prochownik, E. V. & Metallo, S. J. (2008). Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules. Chemistry and Biology 15, 1149–1155.CrossRefGoogle ScholarPubMed
Fong, J. H., Shoemaker, B. A., Garbuzynskiy, S. O., Lobanov, M. Y., Galzitskaya, O. V. & Panchenko, A. R. (2009). Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. PLoS Computational Biology 5, e1000316.CrossRefGoogle ScholarPubMed
Forbes, J. G., Flaherty, D. B., Ma, K., Qadota, H., Benian, G. M. & Wang, K. (2010). Extensive and modular intrinsically disordered segments in C elegans TTN-1 and implications in filament binding, elasticity and oblique striation. Journal of Molecular Biology 398, 672–689.CrossRefGoogle Scholar
Frankel, A. D. & Kim, P. S. (1991). Modular structure of transcription factors: implications for gene regulation. Cell 65, 717–719.CrossRefGoogle ScholarPubMed
Freedman, S. J., Sun, Z. Y., Kung, A. L., France, D. S., Wagner, G. & Eck, M. J. (2003). Structural basis for negative regulation of hypoxia-inducible factor-1α by CITED2. Nature Structural Biology 10, 504–512.CrossRefGoogle ScholarPubMed
Freedman, S. J., Sun, Z. Y., Poy, F., Kung, A. L., Livingston, D. M., Wagner, G. & Eck, M. J. (2002). Structural basis for recruitment of CBP/p300 by hypoxia-inducible factor-1α. Proceedings of the National Academy of Sciences of the United States of America 99, 5367–5372.CrossRefGoogle Scholar
Frimpong, A. K., Abzalimov, R. R., Uversky, V. N. & Kaltashov, I. A. (2010). Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: conformational heterogeneity of α-synuclein. Proteins 78, 714–722.CrossRefGoogle ScholarPubMed
Fukuchi, S., Homma, K., Minezaki, Y., Gojobori, T. & Nishikawa, K. (2009). Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors. BMC Structural Biology 9, 26.CrossRefGoogle ScholarPubMed
Fuxreiter, M. & Tompa, P. (2009). Fuzzy interactome: the limitations of models in molecular biology. Trends in Biochemical Sciences 34, 3.CrossRefGoogle Scholar
Fuxreiter, M., Tompa, P., Simon, I., Uversky, V. N., Hansen, J. C. & Asturias, F. J. (2008). Malleable machines take shape in eukaryotic transcriptional regulation. Nature Chemical Biology 4, 728–737.CrossRefGoogle ScholarPubMed
Galea, C. A., High, A. A., Obenauer, J. C., Mishra, A., Park, C. G., Punta, M., Schlessinger, A., Ma, J., Rost, B., Slaughter, C. A. & Kriwacki, R. W. (2009). Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. Journal of Proteome Research 8, 211–226.CrossRefGoogle ScholarPubMed
Galea, C. A., Pagala, V. R., Obenauer, J. C., Park, C. G., Slaughter, C. A. & Kriwacki, R. W. (2006). Proteomic studies of the intrinsically unstructured mammalian proteome. Journal of Proteome Research 5, 2839–2848.CrossRefGoogle ScholarPubMed
Galzitskaya, O. V., Garbuzynskiy, S. O. & Lobanov, M. Y. (2006). Prediction of amyloidogenic and disordered regions in protein chains. PLoS Computational Biology 2, e177.CrossRefGoogle ScholarPubMed
Garcia-Pino, A., Balasubramanian, S., Wyns, L., Gazit, E., De, G. H., Magnuson, R. D., Charlier, D., Van Nuland, N. A. & Loris, R. (2010). Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell 142, 101–111.CrossRefGoogle ScholarPubMed
Garner, E., Cannon, P., Romero, P., Obradovic, Z. & Dunker, A. K. (1998). Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Information Series Workshop on Genome Information 9, 201–213.Google ScholarPubMed
Gaspar, A. M., Appavou, M. S., Busch, S., Unruh, T. & Doster, W. (2008). Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study. European Biophysics Journal with Biophysics Letters 37, 573–582.CrossRefGoogle ScholarPubMed
Gazi, A. D., Charova, S. N., Panopoulos, N. J. & Kokkinidis, M. (2009). Coiled-coils in type III secretion systems: structural flexibility, disorder and biological implications. Cellular Microbiology 11, 719–729.CrossRefGoogle ScholarPubMed
Gearhart, M. D., Holmbeck, S. M., Evans, R. M., Dyson, H. J. & Wright, P. E. (2003). Monomeric complex of human orphan estrogen related receptor-2 with DNA: a pseudo-dimer interface mediates extended half-site recognition. Journal of Molecular Biology 327, 819–832.CrossRefGoogle ScholarPubMed
Gibson, T. J. (2009). Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences 34, 471–482.CrossRefGoogle ScholarPubMed
Goh, G. K., Dunker, A. K. & Uversky, V. N. (2008). Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genomics 9 (Suppl. 2), S4.CrossRefGoogle ScholarPubMed
Goh, G. K., Dunker, A. K. & Uversky, V. N. (2009). Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses. Virology Journal 6, 1–12.CrossRefGoogle ScholarPubMed
Goto, N. K., Zor, T., Martinez-Yamout, M., Dyson, H. J. & Wright, P. E. (2002). Cooperativity in transcription factor binding to the coactivator CREB-binding protein (CBP). The mixed lineage leukemia protein (MLL) activation domain binds to an allosteric site on the KIX domain. Journal of Biological Chemistry 277, 43168–43174.CrossRefGoogle Scholar
Graf, P. C., Martinez-Yamout, M., Vanhaerents, S., Lilie, H., Dyson, H. J. & Jakob, U. (2004). Activation of the redox-regulated chaperone Hsp33 by domain unfolding. Journal of Biological Chemistry 279, 20529–20538.CrossRefGoogle ScholarPubMed
Grimmler, M., Wang, Y., Mund, T., Cilensek, Z., Keidel, E. M., Waddell, M. B., Jakel, H., Kullmann, M., Kriwacki, R. W. & Hengst, L. (2007). Cdk-inhibitory activity and stability of p27Kip1 are directly regulated by oncogenic tyrosine kinases. Cell 128, 269–280.CrossRefGoogle ScholarPubMed
Gsponer, J. & Babu, M. M. (2009). The rules of disorder or why disorder rules. Progress in Biophysics and Molecular Biology 99, 94–103.CrossRefGoogle ScholarPubMed
Gsponer, J., Futschik, M. E., Teichmann, S. A. & Babu, M. M. (2008). Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322, 1365–1368.CrossRefGoogle ScholarPubMed
Gu, W. & Helms, V. (2005). Dynamical binding of proline-rich peptides to their recognition domains. Biochimica et Biophysica Acta–Proteins and Proteomics 1754, 232–238.CrossRefGoogle ScholarPubMed
Gunasekaran, K., Tsai, C. J., Kumar, S., Zanuy, D. & Nussinov, R. (2003). Extended disordered proteins: targeting function with less scaffold. Trends in Biochemical Sciences 28, 81–85.CrossRefGoogle ScholarPubMed
Hamada, D., Kato, T., Ikegami, T., Suzuki, K. N., Hayashi, M., Murooka, Y., Honda, T. & Yanagihara, I. (2005). EspB from enterohaemorrhagic Escherichia coli is a natively partially folded protein. FEBS Journal 272, 756–768.CrossRefGoogle ScholarPubMed
Hammes, G. G., Chang, Y. C. & Oas, T. G. (2009). Conformational selection or induced fit: a flux description of reaction mechanism. Proceedings of the National Academy of Sciences of the United States of America 106, 13737–13741.CrossRefGoogle ScholarPubMed
Hammoudeh, D. I., Follis, A. V., Prochownik, E. V. & Metallo, S. J. (2009). Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. Journal of the American Chemical Society 131, 7390–7401.CrossRefGoogle ScholarPubMed
Han, J. D., Dupuy, D., Bertin, N., Cusick, M. E. & Vidal, M. (2005). Effect of sampling on topology predictions of protein-protein interaction networks. Nature Biotechnology 23, 839–844.CrossRefGoogle ScholarPubMed
Haynes, C. & Iakoucheva, L. M. (2006). Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins. Nucleic Acids Research 34, 305–312.CrossRefGoogle ScholarPubMed
Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M. & Iakoucheva, L. M. (2006). Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Computational Biology 2, e100.CrossRefGoogle ScholarPubMed
He, Y., Liwo, A., Weinstein, H. & Scheraga, H. A. (2011). PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. Journal of Molecular Biology 405, 298–314.CrossRefGoogle Scholar
Hegyi, H., Buday, L. & Tompa, P. (2009). Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PLoS Computational Biology 5, e1000552.CrossRefGoogle ScholarPubMed
Hegyi, H., Kalmar, L., Horvath, T. & Tompa, P. (2011). Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. Nucleic Acids Research 39, 1208–1219.CrossRefGoogle ScholarPubMed
Hegyi, H. & Tompa, P. (2008). Intrinsically disordered proteins display no preference for chaperone binding in vivo. PLoS Computational Biology 4, e1000017.CrossRefGoogle ScholarPubMed
Hill, K. K., Roemer, S. C., Jones, D. N., Churchill, M. E. & Edwards, D. P. (2009). A progesterone receptor co-activator (JDP2) mediates activity through interaction with residues in the carboxyl-terminal extension of the DNA binding domain. Journal of Biological Chemistry 284, 24415–24424.CrossRefGoogle ScholarPubMed
Hilser, V. J. (2010). An ensemble view of allostery. Science 327, 653–654.CrossRefGoogle ScholarPubMed
Hirota, K. & Semenza, G. L. (2005). Regulation of hypoxia-inducible factor 1 by prolyl and asparaginyl hydroxylases. Biochemical and Biophysical Research Communications 338, 610–616.CrossRefGoogle ScholarPubMed
Holmbeck, S. M., Foster, M. P., Casimiro, D. R., Sem, D. S., Dyson, H. J. & Wright, P. E. (1998). High-resolution solution structure of the retinoid X receptor DNA-binding domain. Journal of Molecular Biology 281, 271–284.CrossRefGoogle ScholarPubMed
Holt, C. & Sawyer, L. (1993). Caseins as rheomorphic proteins: interpretation of primary and secondary structures of the αS1, β and κ-caseins. Journal of the Chemical Society Faraday Transactions 89, 2683–2692.CrossRefGoogle Scholar
Hsu, S. T., Bertoncini, C. W. & Dobson, C. M. (2009). Use of protonless NMR spectroscopy to alleviate the loss of information resulting from exchange-broadening. Journal of the American Chemical Society 131, 7222–7223.CrossRefGoogle ScholarPubMed
Huang, F., Rajagopalan, S., Settanni, G., Marsh, R. J., Armoogum, D. A., Nicolaou, N., Bain, A. J., Lerner, E., Haas, E., Ying, L. & Fersht, A. R. (2009). Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer. Proceedings of the National Academy of Sciences of the United States of America 106, 20758–20763.CrossRefGoogle ScholarPubMed
Huang, Y. & Liu, Z. (2010a). Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins. PLoS ONE 5, e15375.CrossRefGoogle ScholarPubMed
Huang, Y. & Liu, Z. (2010b). Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins. Proteins 78, 3251–3259.CrossRefGoogle ScholarPubMed
Hughes, S. & Graether, S. P. (2010). Cryoprotective mechanism of a small intrinsically disordered dehydrin protein. Protein Science 20, 42–50.CrossRefGoogle Scholar
Iakoucheva, L. M., Brown, C. J., Lawson, J. D., Obradovic, Z. & Dunker, A. K. (2002). Intrinsic disorder in cell-signaling and cancer-associated proteins. Journal of Molecular Biology 323, 573–584.CrossRefGoogle ScholarPubMed
Iakoucheva, L. M. & Dunker, A. K. (2003). Order, disorder, and flexibility: prediction from protein sequence. Structure 11, 1316–1317.CrossRefGoogle ScholarPubMed
Iakoucheva, L. M., Radivojac, P., Brown, C. J., O'Connor, T. R., Sikes, J. G., Obradovic, Z. & Dunker, A. K. (2004). The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Research 32, 1037–1049.CrossRefGoogle ScholarPubMed
Iwahara, J. & Clore, G. M. (2010). Structure-independent analysis of the breadth of the positional distribution of disordered groups in macromolecules from order parameters for long, variable-length vectors using NMR paramagnetic relaxation enhancement. Journal of the American Chemical Society 132, 13346–13356.CrossRefGoogle ScholarPubMed
Jaakola, V. P., Prilusky, J., Sussman, J. L. & Goldman, A. (2005). G protein-coupled receptors show unusual patterns of intrinsic unfolding. Protein Engineering, Design and Selection 18, 103–110.CrossRefGoogle ScholarPubMed
James, L. C., Roversi, P. & Tawfik, D. S. (2003). Antibody multispecificity mediated by conformational diversity. Science 299, 1362–1367.CrossRefGoogle ScholarPubMed
James, L. C. & Tawfik, D. S. (2003). The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness. Protein Science 12, 2183–2193.CrossRefGoogle ScholarPubMed
James, L. C. & Tawfik, D. S. (2005). Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proceedings of the National Academy of Sciences of the United States of America 102, 12730–12735.CrossRefGoogle ScholarPubMed
Jariel-Encontre, I., Bossis, G. & Piechaczyk, M. (2008). Ubiquitin-independent degradation of proteins by the proteasome. Biochimica et Biophysica Acta 1786, 153–177.Google ScholarPubMed
Jowitt, T. A., Murdoch, A. D., Baldock, C., Berry, R., Day, J. M. & Hardingham, T. E. (2010). Order within disorder: Aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered. Proteins 78, 3317–3327.CrossRefGoogle ScholarPubMed
Kanelis, V., Hudson, R. P., Thibodeau, P. H., Thomas, P. J. & Forman-Kay, J. D. (2010). NMR evidence for differential phosphorylation-dependent interactions in WT and ΔF508 CFTR. EMBO Journal 29, 263–277.CrossRefGoogle ScholarPubMed
Kast, D., Espinoza-Fonseca, L. M., Yi, C. & Thomas, D. D. (2010). Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain. Proceedings of the National Academy of Sciences of the United States of America 107, 8207–8212.CrossRefGoogle ScholarPubMed
Kavalenka, A., Urbancic, I., Belle, V., Rouger, S., Costanzo, S., Kure, S., Fournel, A., Longhi, S., Guigliarelli, B. & Strancar, J. (2010). Conformational analysis of the partially disordered measles virus N(TAIL)-XD complex by SDSL EPR spectroscopy. Biophysical Journal 98, 1055–1064.CrossRefGoogle ScholarPubMed
Kim, D. H., Lee, S. H., Nam, K. H., Chi, S. W., Chang, I. & Han, K. H. (2009). Multiple hTAF(II)31-binding motifs in the intrinsically unfolded transcriptional activation domain of VP16. BMB Reports 42, 411–417.CrossRefGoogle ScholarPubMed
Kim, P. M., Sboner, A., Xia, Y. & Gerstein, M. (2008). The role of disorder in interaction networks: a structural analysis. Molecular Systems Biology 4, 179.CrossRefGoogle ScholarPubMed
Kjaergaard, M., Teilum, K. & Poulsen, F. M. (2010). Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP. Proceedings of the National Academy of Sciences of the United States of America 107, 12535–12540.CrossRefGoogle ScholarPubMed
Kovacs, E., Tompa, P., Liliom, K. & Kalmar, L. (2010). Dual coding in alternative reading frames correlates with intrinsic protein disorder. Proceedings of the National Academy of Sciences of the United States of America 107, 5429–5434.CrossRefGoogle ScholarPubMed
Kriwacki, R. W., Hengst, L., Tennant, L., Reed, S. I. & Wright, P. E. (1996). Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proceedings of the National Academy of Sciences of the United States of America 93, 11504–11509.CrossRefGoogle ScholarPubMed
Kucera, N. J., Hodsdon, M. E. & Wolin, S. L. (2011). An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors. Proceedings of the National Academy of Sciences of the United States of America 108, 1308–1313.CrossRefGoogle Scholar
Kumar, R. & Thompson, E. B. (2010). Influence of flanking sequences on signaling between the activation function AF1 and DNA-binding domain of the glucocorticoid receptor. Archives of Biochemistry and Biophysics 496, 140–145.CrossRefGoogle ScholarPubMed
Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J. & Pavletich, N. P. (1996). Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274, 948–953.CrossRefGoogle Scholar
Lah, J., Simic, M., Vesnaver, G., Marianovsky, I., Glaser, G., Engelberg-Kulka, H. & Loris, R. (2005). Energetics of structural transitions of the addiction antitoxin MazE: is a programmed bacterial cell death dependent on the intrinsically flexible nature of the antitoxins? Journal of Biological Chemistry 280, 17397–17407.CrossRefGoogle Scholar
Laity, J. H., Dyson, H. J. & Wright, P. E. (2000). DNA-induced α-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2–His2 zinc fingers. Journal of Molecular Biology 295, 719–727.CrossRefGoogle Scholar
Lando, D., Peet, D. J., Whelan, D. A., Gorman, J. J. & Whitelaw, M. L. (2002). Asparagine hydroxylation of the HIF transactivation domain: a hypoxic switch. Science 295, 858–861.CrossRefGoogle Scholar
Lee, C., Kim, S. J., Jeong, D. G., Lee, S. M. & Ryu, S. E. (2003). Structure of human FIH-1 reveals a unique active site pocket and interaction sites for HIF-1 and von Hippel-Lindau. Journal of Biological Chemistry 278, 7558–7563.CrossRefGoogle ScholarPubMed
Lee, C. W., Arai, M., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2009). Mapping the interactions of the p53 transactivation domain with the KIX domain of CBP. Biochemistry 48, 2115–2124.CrossRefGoogle ScholarPubMed
Lee, C. W., Ferreon, J. C., Ferreon, A. C., Arai, M. & Wright, P. E. (2010a). Graded enhancement of p53 binding to CREB-binding protein (CBP) by multisite phosphorylation. Proceedings of the National Academy of Sciences of the United States of America 107, 19290–19295.CrossRefGoogle ScholarPubMed
Lee, C. W., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2010b). Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein. Biochemistry 49, 9964–9971.CrossRefGoogle ScholarPubMed
Lee, H., Mok, K. H., Muhandiram, R., Park, K. H., Suk, J. E., Kim, D. H., Chang, J., Sung, Y. C., Choi, K. Y. & Han, K. H. (2000). Local structural elements in the mostly unstructured transcriptional activation domain of human p53. Journal of Biological Chemistry 275, 29426–29432.CrossRefGoogle ScholarPubMed
Lee, J. O., Russo, A. A. & Pavletich, N. P. (1998). Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7. Nature 391, 859–865.CrossRefGoogle ScholarPubMed
Lee, M. S., Gippert, G., Soman, K. Y., Case, D. A. & Wright, P. E. (1989). Three-dimensional solution structure of a single zinc finger binding domain. Science 245, 635–637.CrossRefGoogle ScholarPubMed
Leroy, A., Landrieu, I., Huvent, I., Legrand, D., Codeville, B., Wieruszeski, J. M. & Lippens, G. (2010). Spectroscopic studies of GSK3{beta} phosphorylation of the neuronal tau protein and its interaction with the N-terminal domain of apolipoprotein E. Journal of Biological Chemistry 285, 33435–33444.CrossRefGoogle ScholarPubMed
Lewis, H. A., Wang, C., Zhao, X., Hamuro, Y., Conners, K., Kearins, M. C., Lu, F., Sauder, J. M., Molnar, K. S., Coales, S. J., Maloney, P. C., Guggino, W. B., Wetmore, D. R., Weber, P. C. & Hunt, J. F. (2010). Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry. Journal of Molecular Biology 396, 406–430.CrossRefGoogle ScholarPubMed
Li, S., Iakoucheva, L. M., Mooney, S. D. & Radivojac, P. (2010). Loss of post-translational modification sites in disease. Pacific Symposium on Biocomputing 15, 337–347.Google Scholar
Li, Y. & Palmer, A. G. (2010). Narrowing of protein NMR spectral lines broadened by chemical exchange. Journal of the American Chemical Society 132, 8856–8857.CrossRefGoogle ScholarPubMed
Lieutaud, P., Canard, B. & Longhi, S. (2008). MeDor: a metaserver for predicting protein disorder. BMC Genomics 9 (Suppl. 2), S25.CrossRefGoogle ScholarPubMed
Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J. & Russell, R. B. (2003a). Protein disorder prediction: implications for structural proteomics. Structure 11, 1453–1459.CrossRefGoogle ScholarPubMed
Linding, R., Russell, R. B., Neduva, V. & Gibson, T. J. (2003b). GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Research 31, 3701–3708.CrossRefGoogle ScholarPubMed
Lipari, G. & Szabo, A. (1982). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. Journal of the American Chemical Society 104, 4546–4559.CrossRefGoogle Scholar
Liu, J., Faeder, J. R. & Camacho, C. J. (2009). Toward a quantitative theory of intrinsically disordered proteins and their function. Proceedings of the National Academy of Sciences of the United States of America 106, 19819–19823.CrossRefGoogle Scholar
Liu, J. & Nussinov, R. (2009). The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation. PLoS Computational Biology 5, e1000527.CrossRefGoogle ScholarPubMed
Liu, J. & Nussinov, R. (2010a). Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. Journal of Molecular Biology 396, 1508–1523.CrossRefGoogle ScholarPubMed
Liu, J. & Nussinov, R. (2010b). Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation. Biophysical Journal 99, 736–744.CrossRefGoogle ScholarPubMed
Liu, X. & Marmorstein, R. (2007). Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a tumor suppressor. Genes and Development 21, 2711–2716.CrossRefGoogle ScholarPubMed
Lobanov, M. Y., Furletova, E. I., Bogatyreva, N. S., Roytberg, M. A. & Galzitskaya, O. V. (2010a). Library of disordered patterns in 3D protein structures. PLoS Computational Biology 6, e1000958.CrossRefGoogle ScholarPubMed
Lobanov, M. Y., Shoemaker, B. A., Garbuzynskiy, S. O., Fong, J. H., Panchenko, A. R. & Galzitskaya, O. V. (2010b). ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Research 38, D283–D287.CrossRefGoogle ScholarPubMed
Lobley, A., Swindells, M. B., Orengo, C. A. & Jones, D. T. (2007). Inferring function using patterns of native disorder in proteins. PLoS Computational Biology 3, 1567–1579.CrossRefGoogle ScholarPubMed
London, N., Movshovitz-Attias, D. & Schueler-Furman, O. (2010). The structural basis of peptide-protein binding strategies. Structure 18, 188–199.CrossRefGoogle ScholarPubMed
Love, J. J., Li, X., Chung, J., Dyson, H. J. & Wright, P. E. (2004). The LEF-1 high-mobility group domain undergoes a disorder-to-order transition upon formation of a complex with cognate DNA. Biochemistry 43, 8725–8734.CrossRefGoogle ScholarPubMed
Love, J. J., Li, X. A., Case, D. A., Giese, K., Grosschedl, R. & Wright, P. E. (1995). Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376, 791–795.CrossRefGoogle ScholarPubMed
Löw, C., Homeyer, N., Weininger, U., Sticht, H. & Balbach, J. (2009). Conformational switch upon phosphorylation: human CDK inhibitor p19INK4d between the native and partially folded state. Acs Chemical Biology 4, 53–63.CrossRefGoogle ScholarPubMed
Lowry, D. F., Hausrath, A. C. & Daughdrill, G. W. (2008a). A robust approach for analyzing a heterogeneous structural ensemble. Proteins 73, 918–928.CrossRefGoogle ScholarPubMed
Lowry, D. F., Stancik, A., Shrestha, R. M. & Daughdrill, G. W. (2008b). Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53. Proteins 71, 587–598.CrossRefGoogle ScholarPubMed
Lu, H. P. (2005). Probing single-molecule protein conformational dynamics. Accounts of Chemical Research 38, 557–565.CrossRefGoogle ScholarPubMed
Ma, B. & Nussinov, R. (2009). Regulating highly dynamic unstructured proteins and their coding mRNAs. Genome Biology 10, 204.CrossRefGoogle ScholarPubMed
Mackay, J. P., Sunde, M., Lowry, J. A., Crossley, M. & Matthews, J. M. (2007). Protein interactions: is seeing believing? Trends in Biochemical Sciences 32, 530–531.CrossRefGoogle ScholarPubMed
Mao, A. H., Crick, S. L., Vitalis, A., Chicoine, C. L. & Pappu, R. V. (2010). Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America 107, 8183–8188.CrossRefGoogle ScholarPubMed
Marsh, J. A., Dancheck, B., Ragusa, M. J., Allaire, M., Forman-Kay, J. D. & Peti, W. (2010). Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. Structure 18, 1094–1103.CrossRefGoogle ScholarPubMed
Marsh, J. A. & Forman-Kay, J. D. (2010). Sequence determinants of compaction in intrinsically disordered proteins. Biophysical Journal 98, 2383–2390.CrossRefGoogle ScholarPubMed
Mathes, E., Wang, L., Komives, E. & Ghosh, G. (2010). Flexible regions within IκBα create the ubiquitin-independent degradation signal. Journal of Biological Chemistry 285, 32927–32936.CrossRefGoogle ScholarPubMed
Matsushima, N., Yoshida, H., Kumaki, Y., Kamiya, M., Tanaka, T., Izumi, Y. & Kretsinger, R. H. (2008). Flexible structures and ligand interactions of tandem repeats consisting of proline, glycine, asparagine, serine, and/or threonine rich oligopeptides in proteins. Current Protein and Peptide Science 9, 591–610.CrossRefGoogle ScholarPubMed
Mayer, B. J., Hamaguchi, M. & Hanafusa, H. (1988). A novel viral oncogene with structural similarity to phospholipase C. Nature 332, 272–275.CrossRefGoogle ScholarPubMed
Meier, S., Blackledge, M. & Grzesiek, S. (2008). Conformational distributions of unfolded polypeptides from novel NMR techniques. Journal of Chemical Physics 128, 052204.CrossRefGoogle ScholarPubMed
Merlini, G. & Bellotti, V. (2003). Molecular mechanisms of amyloidosis. New England Journal of Medicine 349, 583–596.CrossRefGoogle ScholarPubMed
Midic, U., Oldfield, C. J., Dunker, A. K., Obradovic, Z. & Uversky, V. N. (2009). Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasome. Protein and Peptide Letters 16, 1533–1547.CrossRefGoogle ScholarPubMed
Miller, M. (2009). The importance of being flexible: the case of basic region leucine zipper transcriptional regulators. Current Protein and Peptide Science 10, 244–269.CrossRefGoogle ScholarPubMed
Mittag, T., Marsh, J., Grishaev, A., Orlicky, S., Lin, H., Sicheri, F., Tyers, M. & Forman-Kay, J. D. (2010). Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18, 494–506.CrossRefGoogle Scholar
Mittermaier, A. K. & Kay, L. E. (2009). Observing biological dynamics at atomic resolution using NMR. Trends in Biochemical Sciences 34, 601–611.CrossRefGoogle ScholarPubMed
Mobley, D. L. & Dill, K. A. (2009). Binding of small-molecule ligands to proteins: “what you see” is not always “what you get”. Structure 17, 489–498.CrossRefGoogle Scholar
Mohan, A., Oldfield, C. J., Radivojac, P., Vacic, V., Cortese, M. S., Dunker, A. K. & Uversky, V. N. (2006). Analysis of molecular recognition features (MoRFs). Journal of Molecular Biology 362, 1043–1059.CrossRefGoogle ScholarPubMed
Mohan, A., Sullivan, W. J. Jr., Radivojac, P., Dunker, A. K. & Uversky, V. N. (2008). Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes. Molecular Biosystems 4, 328–340.CrossRefGoogle ScholarPubMed
Morin, B., Bourhis, J. M., Belle, V., Woudstra, M., Carriere, F., Guigliarelli, B., Fournel, A. & Longhi, S. (2006). Assessing induced folding of an intrinsically disordered protein by site-directed spin-labeling electron paramagnetic resonance spectroscopy. Journal of Physical Chemistry B 110, 20596–20608.CrossRefGoogle ScholarPubMed
Motácková, V., Novácek, J., Zawadzka-Kazimierczuk, A., Kazimierczuk, K., Zídek, L., Sanderová, H., KrásnÝ, L., Kozminski, W. & Sklenár, V. (2010). Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. Journal of Biomolecular NMR 48, 169–177.CrossRefGoogle ScholarPubMed
Mukrasch, M. D., Bibow, S., Korukottu, J., Jeganathan, S., Biernat, J., Griesinger, C., Mandelkow, E. & Zweckstetter, M. (2009). Structural polymorphism of 441-residue tau at single residue resolution. PLoS Biology 7, e34.CrossRefGoogle ScholarPubMed
Müller-Späth, S., Soranno, A., Hirschfeld, V., Hofmann, H., Rüegger, S., Reymond, L., Nettels, D. & Schuler, B. (2010). Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America 107, 14609–14614.CrossRefGoogle ScholarPubMed
Narayanan, A. & Jacobson, M. P. (2009). Computational studies of protein regulation by post-translational phosphorylation. Current Opinion in Structural Biology 19, 156–163.CrossRefGoogle ScholarPubMed
Nguyen, D. X., Baglia, L. A., Huang, S. M., Baker, C. M. & Mccance, D. J. (2004). Acetylation regulates the differentiation-specific functions of the retinoblastoma protein. EMBO Journal 23, 1609–1618.CrossRefGoogle ScholarPubMed
Niu, X., Bruschweiler-Li, L., Davulcu, O., Skalicky, J. J., Bruschweiler, R. & Chapman, M. S. (2011). Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. Journal of Molecular Biology 405, 479–496.CrossRefGoogle ScholarPubMed
Nocula-Lugowska, M., Rymarczyk, G., Lisowski, M. & Ozyhar, A. (2009). Isoform-specific variation in the intrinsic disorder of the ecdysteroid receptor N-terminal domain. Proteins 76, 291–308.CrossRefGoogle ScholarPubMed
Noutsou, M., Duarte, A. M., Anvarian, Z., Didenko, T., Minde, D. P., Kuper, I., De, R. I., Oikonomou, C., Friedler, A., Boelens, R., Rudiger, S. G. & Maurice, M. M. (2011). Critical scaffolding regions of the tumor suppressor axin1 are natively unfolded. Journal of Molecular Biology 405, 773–786.CrossRefGoogle ScholarPubMed
O'Dea, E. L., Barken, D., Peralta, R. Q., Tran, K. T., Werner, S. L., Kearns, J. D., Levchenko, A. & Hoffmann, A. (2007). A homeostatic model of IκB metabolism to control constitutive NF-κB activity. Molecular Systems Biology 3, 111.CrossRefGoogle ScholarPubMed
Ohgushi, M. & Wada, A. (1983). ‘Molten-globule state’: a compact form of globular proteins with mobile side chains. FEBS Letters 164, 21–24.CrossRefGoogle Scholar
Oldfield, C. J., Cheng, Y., Cortese, M. S., Romero, P., Uversky, V. N. & Dunker, A. K. (2005). Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44, 12454–12470.CrossRefGoogle ScholarPubMed
Oldfield, C. J., Meng, J., Yang, J. Y., Yang, M. Q., Uversky, V. N. & Dunker, A. K. (2008). Flexible nets: disorder and induced fit in the associations of p53 and 14–3-3 with their partners. BMC Genomics 9 (Suppl. 1), S1.CrossRefGoogle ScholarPubMed
Olson, K. E., Narayanaswami, P., Vise, P. D., Lowry, D. F., Wold, M. S. & Daughdrill, G. W. (2005). Secondary structure and dynamics of an intrinsically unstructured linker domain. Journal of Biomolecular Structure and Dynamics 23, 113–124.CrossRefGoogle ScholarPubMed
Olzscha, H., Schermann, S. M., Woerner, A. C., Pinkert, S., Hecht, M. H., Tartaglia, G. G., Vendruscolo, M., Hayer-Hartl, M., Hartl, F. U. & Vabulas, R. M. (2011). Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions. Cell 144, 67–78.CrossRefGoogle ScholarPubMed
Onitsuka, M., Kamikubo, H., Yamazaki, Y. & Kataoka, M. (2008). Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants. Proteins 72, 837–847.CrossRefGoogle ScholarPubMed
Paliy, O., Gargac, S. M., Cheng, Y., Uversky, V. N. & Dunker, A. K. (2008). Protein disorder is positively correlated with gene expression in Escherichia coli. Journal of Proteome Research 7, 2234–2245.CrossRefGoogle ScholarPubMed
Palmer, A. G. (2004). NMR characterization of the dynamics of biomacromolecules. Chemical Reviews 104, 3623–3640.CrossRefGoogle ScholarPubMed
Park, S. J., Borin, B. N., Martinez-Yamout, M. A. & Dyson, H. J. (2011). The client protein p53 forms a molten globule-like state in the presence of Hsp90. Nature Structural and Molecular Biology 18, 537–541.CrossRefGoogle Scholar
Parker, D., Rivera, M., Zor, T., Henrion-Caude, A., Radhakrishnan, I., Kumar, A., Shapiro, L. H., Wright, P. E., Montminy, M. & Brindle, P. K. (1999). Role of secondary structure in discrimination between constitutive and inducible activators. Molecular and Cellular Biology 19, 5601–5607.CrossRefGoogle ScholarPubMed
Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L., Young, E. T. & Klevit, R. E. (1988). Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241, 1489–1492.CrossRefGoogle ScholarPubMed
Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K. & Obradovic, Z. (2006). Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7, 208CrossRefGoogle ScholarPubMed
Pentony, M. M. & Jones, D. T. (2010). Modularity of intrinsic disorder in the human proteome. Proteins 78, 212–221.CrossRefGoogle ScholarPubMed
Perez, Y., Gairi, M., Pons, M. & Bernado, P. (2009). Structural characterization of the natively unfolded N-terminal domain of human c-Src kinase: insights into the role of phosphorylation of the unique domain. Journal of Molecular Biology 391, 136–148.CrossRefGoogle ScholarPubMed
Petsko, G. A. (2001). Structural basis of thermostability in hyperthermophilic proteins, or “there's more than one way to skin a cat”. Methods in Enzymology 334, 469–478.CrossRefGoogle ScholarPubMed
Pratt, W. B. & Toft, D. O. (1997). Steroid receptor interactions with heat shock protein and immunophilin chaperones. Endocrine Reviews 18, 306–360.Google ScholarPubMed
Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man, O., Beckmann, J. S., Silman, I. & Sussman, J. L. (2005). FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, 3435–3438.CrossRefGoogle ScholarPubMed
Privalov, P. L., Dragan, A. I., Crane-Robinson, C., Breslauer, K. J., Remeta, D. P. & Minetti, C. A. S. A. (2007). What drives proteins into the major or minor grooves of DNA? Journal of Molecular Biology 365, 1–9.CrossRefGoogle ScholarPubMed
Ptitsyn, O. B. (1973). Stages in the mechanism of self-organization of protein molecules. Doklady Akademii nauk SSSR 210, 1213–1215.Google ScholarPubMed
Qin, B. Y., Liu, C., Srinath, H., Lam, S. S., Correia, J. J., Derynck, R. & Lin, K. (2005). Crystal structure of IRF-3 in complex with CBP. Structure 13, 1269–1277.CrossRefGoogle ScholarPubMed
Radhakrishnan, I., Perez-Alvarado, G. C., Dyson, H. J. & Wright, P. E. (1998). Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB. FEBS Letters 430, 317–322.CrossRefGoogle ScholarPubMed
Radhakrishnan, I., Perez-Alvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R. & Wright, P. E. (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.CrossRefGoogle Scholar
Radivojac, P., Vacic, V., Haynes, C., Cocklin, R. R., Mohan, A., Heyen, J. W., Goebl, M. G. & Iakoucheva, L. M. (2010). Identification, analysis, and prediction of protein ubiquitination sites. Proteins 78, 365–380.CrossRefGoogle ScholarPubMed
Radivojac, P., Vucetic, S., O'Connor, T. R., Uversky, V. N., Obradovic, Z. & Dunker, A. K. (2006). Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition. Proteins 63, 398–410.CrossRefGoogle ScholarPubMed
Rancurel, C., Khosravi, M., Dunker, A. K., Romero, P. R. & Karlin, D. (2009). Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. Journal of Virology 83, 10719–10736.CrossRefGoogle ScholarPubMed
Ravindranathan, S., Oberstrass, F. C. & Allain, F. H. (2010). Increase in backbone mobility of the VTS1p-SAM domain on binding to SRE-RNA. Journal of Molecular Biology 396, 732–746.CrossRefGoogle ScholarPubMed
Reingewertz, T. H., Benyamini, H., Lebendiker, M., Shalev, D. E. & Friedler, A. (2009). The C-terminal domain of the HIV-1 Vif protein is natively unfolded in its unbound state. Protein Engineering Design and Selection 22, 281–287.CrossRefGoogle ScholarPubMed
Ren, S., Uversky, V. N., Chen, Z., Dunker, A. K. & Obradovic, Z. (2008). Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions. BMC Genomics 9(Suppl. 2), S26.CrossRefGoogle ScholarPubMed
Romero, P., Obradovic, Z. & Dunker, A. K. (1999). Folding minimal sequences: the lower bound for sequence complexity of globular proteins. FEBS Letters 462, 363–367.CrossRefGoogle ScholarPubMed
Romero, P., Obradovic, Z. & Dunker, A. K. (2004). Natively disordered proteins: functions and predictions. Applied Bioinformatics 3, 105–113.CrossRefGoogle ScholarPubMed
Romero, P., Obradovic, Z., Kissinger, C. R., Villafranca, J. E. & Dunker, A. K. (1997). Identifying disordered regions in proteins from amino acid sequences. Proceedings of the IEEE International Conference on Neural Networks 1, 90–95.Google Scholar
Romero, P., Obradovic, Z., Kissinger, C. R., Villafranca, J. E., Garner, E., Guilliot, S. & Dunker, A. K. (1998). Thousands of proteins likely to have long disordered regions. Pacific Symposium on Biocomputing 3, 435–446.Google Scholar
Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J. & Dunker, A. K. (2001). Sequence complexity of disordered protein. Proteins 42, 38–48.3.0.CO;2-3>CrossRefGoogle ScholarPubMed
Romero, P. R., Zaidi, S., Fang, Y. Y., Uversky, V. N., Radivojac, P., Oldfield, C. J., Cortese, M. S., Sickmeier, M., Legall, T., Obradovic, Z. & Dunker, A. K. (2006). Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proceedings of the National Academy of Sciences of the United States of America 103, 8390–8395.CrossRefGoogle ScholarPubMed
Rospigliosi, C. C., Mcclendon, S., Schmid, A. W., Ramlall, T. F., Barre, P., Lashuel, H. A. & Eliezer, D. (2009). E46K Parkinson's-linked mutation enhances C-terminal-to-N-terminal contacts in alpha-synuclein. J. Mol. Biol. 388, 1022–1032.CrossRefGoogle ScholarPubMed
Salmon, L., Nodet, G., Ozenne, V., Yin, G., Jensen, M. R., Zweckstetter, M. & Blackledge, M. (2010). NMR characterization of long-range order in intrinsically disordered proteins. Journal of the American Chemical Society 132, 8407–8418.CrossRefGoogle ScholarPubMed
Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Roder, L., Euzenat, J., Rechenmann, F. & Jacq, B. (1999). Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Research 27, 89–94.CrossRefGoogle ScholarPubMed
Sandhu, K. S. (2009). Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins. Journal of Molecular Recognition 22, 1–8.CrossRefGoogle ScholarPubMed
Schlessinger, A., Punta, M. & Rost, B. (2007). Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23, 2376–2384.CrossRefGoogle ScholarPubMed
Sgourakis, N. G., Patel, M. M., Garcia, A. E., Makhatadze, G. I. & Mccallum, S. A. (2010). Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. Journal of Molecular Biology 396, 1128–1144.CrossRefGoogle ScholarPubMed
Shoemaker, B. A., Portman, J. J. & Wolynes, P. G. (2000). Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proceedings of the National Academy of Sciences of the United States of America 97, 8868–8873.CrossRefGoogle ScholarPubMed
Sickmeier, M., Hamilton, J. A., Legall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z. & Dunker, A. K. (2007). DisProt: the database of disordered proteins. Nucleic Acids Research 35, D786–D793.CrossRefGoogle ScholarPubMed
Sigalov, A. B. (2010). Protein intrinsic disorder and oligomericity in cell signaling. Molecular Biosystems 6, 451–461.CrossRefGoogle ScholarPubMed
Sigalov, A. B., Kim, W. M., Saline, M. & Stern, L. J. (2008). The intrinsically disordered cytoplasmic domain of the T cell receptor zeta chain binds to the nef protein of simian immunodeficiency virus without a disorder-to-order transition. Biochemistry 47, 12942–12944.CrossRefGoogle Scholar
Singh, G. P. & Dash, D. (2007). Intrinsic disorder in yeast transcriptional regulatory network. Proteins 68, 602–605.CrossRefGoogle ScholarPubMed
Singh, G. P., Ganapathi, M. & Dash, D. (2007). Role of intrinsic disorder in transient interactions of hub proteins. Proteins 66, 761–765.CrossRefGoogle ScholarPubMed
Sivakolundu, S. G., Nourse, A., Moshiach, S., Bothner, B., Ashley, C., Satumba, J., Lahti, J. & Kriwacki, R. W. (2008). Intrinsically unstructured domains of Arf and Hdm2 form bimolecular oligomeric structures in vitro and in vivo. Journal of Molecular Biology 384, 240–254.CrossRefGoogle ScholarPubMed
Smock, R. G. & Gierasch, L. M. (2009). Sending signals dynamically. Science 324, 198–203.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Sotomayor Perez, A. C., Karst, J. C., Davi, M., Guijarro, J. I., Ladant, D. & Chenal, A. (2010). Characterization of the regions involved in the calcium-induced folding of the intrinsically disordered RTX motifs from the bordetella pertussis adenylate cyclase toxin. Journal of Molecular Biology 397, 534–549.CrossRefGoogle ScholarPubMed
Srere, P. A. (2000). Macromolecular interactions: tracing the roots. Trends in Biochemical Sciences 25, 150–153.CrossRefGoogle ScholarPubMed
Stahl, M. L., Ferenz, C. R., Kelleher, K. L., Kriz, R. W. & Knopf, J. L. (1988). Sequence similarity of phospholipase C with the non-catalytic region of src. Nature 332, 269–272.CrossRefGoogle ScholarPubMed
Staneva, I. & Wallin, S. (2009). All-atom Monte Carlo approach to protein-peptide binding. Journal of Molecular Biology 393, 1118–1128.CrossRefGoogle ScholarPubMed
Stein, A., Pache, R. A., Bernado, P., Pons, M. & Aloy, P. (2009). Dynamic interactions of proteins in complex networks: a more structured view. The FEBS Journal 276, 5390–5405.CrossRefGoogle ScholarPubMed
Sue, S. C., Cervantes, C., Komives, E. A. & Dyson, H. J. (2008). Transfer of flexibility between ankyrin repeats in IκBα upon formation of the NF-κB complex. Journal of Molecular Biology 380, 917–931.CrossRefGoogle ScholarPubMed
Sue, S.-C., Alverdi, V., Komives, E. A. & Dyson, H. J. (2011). Detection of a ternary complex of NF-κB and IκBa with DNA provides insights into how IκBα removes NF-κB from transcription sites. Proceedings of the National Academy of Sciences of the United States of America 108, 1367–1372.CrossRefGoogle Scholar
Sugase, K., Dyson, H. J. & Wright, P. E. (2007a). Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447, 1021–1025.CrossRefGoogle ScholarPubMed
Sugase, K., Lansing, J. C., Dyson, H. J. & Wright, P. E. (2007b). Tailoring relaxation dispersion experiments for fast-associating protein complexes. Journal of the American Chemical Society 129, 13406–13407.CrossRefGoogle ScholarPubMed
Sung, Y. & Eliezer, D. (2007). Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family. Journal of Molecular Biology 372, 689–707.CrossRefGoogle ScholarPubMed
Tainer, J. A., Getzoff, E. D., Alexander, H., Houghten, R. A., Olson, A. J., Lerner, R. A. & Hendrickson, W. A. (1984). The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature 312, 127–133.CrossRefGoogle ScholarPubMed
Takenaga, K. (2011). Angiogenic signaling aberrantly induced by tumor hypoxia. Frontiers in Bioscience 16, 31–48.CrossRefGoogle ScholarPubMed
Thakur, A. K., Jayaraman, M., Mishra, R., Thakur, M., Chellgren, V. M., Byeon, I. J. L., Anjum, D. H., Kodali, R., Creamer, T. P., Conway, J. F., Gronenborn, A. M. & Wetzel, R. (2009). Polyglutamine disruption of the huntingtin exon 1 N terminus triggers a complex aggregation mechanism. Nature Structural and Molecular Biology 16, 380–389.CrossRefGoogle ScholarPubMed
Tokuriki, N. & Tawfik, D. S. (2009). Protein dynamism and evolvability. Science 324, 203–207.CrossRefGoogle ScholarPubMed
Tompa, P. & Csermely, P. (2004). The role of structural disorder in the function of RNA and protein chaperones. FASEB Journal 18, 1169–1175.CrossRefGoogle ScholarPubMed
Tompa, P., Dosztanyi, Z. & Simon, I. (2006). Prevalent structural disorder in E. coli and S. cerevisiae proteomes. Journal of Proteome Research 5, 1996–2000.CrossRefGoogle Scholar
Tompa, P. & Fuxreiter, M. (2008). Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends in Biochemical Sciences 33, 2–8.CrossRefGoogle ScholarPubMed
Tompa, P. & Kalmar, L. (2010). Power law distribution defines structural disorder as a structural element directly linked with function. Journal of Molecular Biology 403, 346–350.CrossRefGoogle ScholarPubMed
Tran, H. T., Mao, A. & Pappu, R. V. (2008). Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. Journal of the American Chemical Society 130, 7380–7392.CrossRefGoogle ScholarPubMed
Tran, H. T., Wang, X. & Pappu, R. V. (2005). Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins. Biochemistry 44, 11369–11380.CrossRefGoogle ScholarPubMed
Truhlar, S. M., Torpey, J. W. & Komives, E. A. (2006). Regions of IκBα that are critical for its inhibition of NF-κB.DNA interaction fold upon binding to NF-κB. Proceedings of the National Academy of Science of the United States of America 103, 18951–18956.CrossRefGoogle ScholarPubMed
Tsai, C. J., Del, S. A. & Nussinov, R. (2009a). Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Molecular Biosystems 5, 207–216.CrossRefGoogle ScholarPubMed
Tsai, C. J., Ma, B. & Nussinov, R. (2009b). Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends in Biochemical Sciences 34, 594–600.CrossRefGoogle ScholarPubMed
Tsunaka, Y., Toga, J., Yamaguchi, H., Tate, S., Hirose, S. & Morikawa, K. (2009). Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements. Journal of Biological Chemistry 284, 24610–24621.CrossRefGoogle ScholarPubMed
Tsvetkov, P., Reuven, N., Prives, C. & Shaul, Y. (2009a). Susceptibility of p53 unstructured N terminus to 20 S proteasomal degradation programs the stress response. Journal of Biological Chemistry 284, 26234–26242.CrossRefGoogle ScholarPubMed
Tsvetkov, P., Reuven, N. & Shaul, Y. (2009b). The nanny model for IDPs. Nature Chemical Biology 5, 778–781.CrossRefGoogle ScholarPubMed
Turjanski, A. G., Gutkind, J. S., Best, R. B. & Hummer, G. (2008). Binding-induced folding of a natively unstructured transcription factor. PLoS Computational Biology 4, e1000060.CrossRefGoogle ScholarPubMed
Tyagi, M., Shoemaker, B. A., Bryant, S. H. & Panchenko, A. R. (2009). Exploring functional roles of multibinding protein interfaces. Protein Science 18, 1674–1683.CrossRefGoogle ScholarPubMed
Tyka, M. D., Keedy, D. A., Andre, I., Dimaio, F., Song, Y., Richardson, D. C., Richardson, J. S. & Baker, D. (2010). Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology 405, 607–618.CrossRefGoogle ScholarPubMed
Uversky, V. N. (2002). Natively unfolded proteins: a point where biology waits for physics. Protein Science 11, 739–756.CrossRefGoogle ScholarPubMed
Uversky, V. N. (2009a). Intrinsic disorder in proteins associated with neurodegenerative diseases. Frontiers in Bioscience 14, 5188–5238.CrossRefGoogle ScholarPubMed
Uversky, V. N. (2009b). Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein Journal 28, 305–325.CrossRefGoogle ScholarPubMed
Uversky, V. N. (2010). Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. Chemical Society Reviews 40, 1623–1634.CrossRefGoogle ScholarPubMed
Uversky, V. N. & Eliezer, D. (2009). Biophysics of Parkinson's disease: structure and aggregation of α-synuclein. Current Protein and Peptide Science 10, 483–499.CrossRefGoogle ScholarPubMed
Uversky, V. N., Gillespie, J. R. & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41, 415–427.3.0.CO;2-7>CrossRefGoogle ScholarPubMed
Uversky, V. N., Oldfield, C. J. & Dunker, A. K. (2008). Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annual Review of Biophysics 37, 215–246.CrossRefGoogle ScholarPubMed
Uversky, V. N. & Ptitsyn, O. B. (1994). “Partly folded” state, a new equilibrium state of protein molecules: Four-state guanidinium chloride-induced unfolding of β-lactamase at low temperature. Biochemistry 33, 2782–2791.CrossRefGoogle Scholar
Uversky, V. N. & Ptitsyn, O. B. (1996). Further evidence on the equilibrium “pre-molten globule state”: Four-state guanidinium chloride-induced unfolding of carbonic anhydrase B at low temperature. Journal of Molecular Biology 255, 215–228.CrossRefGoogle ScholarPubMed
Uversky, V. N., Roman, A., Oldfield, C. J. & Dunker, A. K. (2006). Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. Journal of Proteome Research 5, 1829–1842.CrossRefGoogle ScholarPubMed
Vacic, V., Oldfield, C. J., Mohan, A., Radivojac, P., Cortese, M. S., Uversky, V. N. & Dunker, A. K. (2007). Characterization of molecular recognition features, MoRFs, and their binding partners. Journal of Proteome Research 6, 2351–2366.CrossRefGoogle ScholarPubMed
Vallee-Belisle, A., Ricci, F. & Plaxco, K. W. (2009). Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors. Proceedings of the National Academy of Sciences of the United States of America 106, 13802–13807.CrossRefGoogle ScholarPubMed
Viles, J. H., Donne, D. G., Kroon, G. J. A., Prusiner, S. B., Cohen, F. E., Dyson, H. J. & Wright, P. E. (2001). Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry 40, 2743–2753.Google ScholarPubMed
Vuzman, D., Azia, A. & Levy, Y. (2010a). Searching DNA via a “Monkey Bar” mechanism: the significance of disordered tails. Journal of Molecular Biology 396, 674–684.CrossRefGoogle Scholar
Vuzman, D., Polonsky, M. & Levy, Y. (2010b). Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker. Biophysical Journal 99, 1202–1211.CrossRefGoogle Scholar
Wang, F., Marshall, C. B., Li, G. Y., Yamamoto, K., Mak, T. W. & Ikura, M. (2009). Synergistic interplay between promoter recognition and CBP/p300 coactivator recruitment by FOXO3a. Acs Chemical Biology 4, 1017–1027.CrossRefGoogle ScholarPubMed
Wang, X., Koulov, A. V., Kellner, W. A., Riordan, J. R. & Balch, W. E. (2008). Chemical and biological folding contribute to temperature-sensitive ΔF508 CFTR trafficking. Traffic 9, 1878–1893.CrossRefGoogle ScholarPubMed
Wang, X., Zhang, S., Zhang, J., Huang, X., Xu, C., Wang, W., Liu, Z., Wu, J. & Shi, Y. (2010). A large intrinsically disordered region in SKIP and its disorder–order transition induced by PPIL1 binding revealed by NMR. Journal of Biological Chemistry 285, 4951–4963.CrossRefGoogle ScholarPubMed
Wang, Y., Filippov, I., Richter, C., Luo, R. & Kriwacki, R. W. (2005). Solution NMR studies of an intrinsically unstructured protein within a dilute 75 kDa eukaryotic protein assembly; probing the practical limits for efficiently assigning polypeptide backbone resonances. ChemBiochem: A European Journal of Chemical Biology 6, 2242–2246.CrossRefGoogle ScholarPubMed
Ward, J. J., Sodhi, J. S., Mcguffin, L. J., Buxton, B. F. & Jones, D. T. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. Journal of Molecular Biology 337, 635–645.CrossRefGoogle ScholarPubMed
Waters, L., Yue, B., Veverka, V., Renshaw, P., Bramham, J., Matsuda, S., Frenkiel, T., Kelly, G., Muskett, F., Carr, M. & Heery, D. M. (2006). Structural diversity in p160/CREB-binding protein coactivator complexes. Journal of Biological Chemistry 281, 14787–14795.CrossRefGoogle ScholarPubMed
Weathers, E. A., Paulaitis, M. E., Woolf, T. B. & Hoh, J. H. (2004). Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein. FEBS Letters 576, 348–352.CrossRefGoogle ScholarPubMed
Weinreb, P. H., Zhen, W., Poon, A. W., Conway, K. A. & Lansbury, P. T. (1996). NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded. Biochemistry 35, 13709–13715.CrossRefGoogle ScholarPubMed
Welch, G. R. (2009). The “fuzzy” interactome. Trends in Biochemical Sciences 34, 1–2.CrossRefGoogle Scholar
Wilkins, M. R. & Kummerfeld, S. K. (2008). Sticking together? Falling apart? Exploring the dynamics of the interactome. Trends in Biochemical Sciences 33, 195–200.CrossRefGoogle ScholarPubMed
Williams, R. M., Obradovic, Z., Mathura, V., Braun, W., Garner, E. C., Young, J., Takayama, S., Brown, C. J. & Dunker, A. K. (2001). The protein non-folding problem: amino acid determinants of intrinsic order and disorder. Pacific Symposium on Biocomputing 6, 89–100.Google Scholar
Wilson, I. A., Haft, D. H., Getzoff, E. D., Tainer, J. A., Lerner, R. A. & Brenner, S. (1985). Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition. Proceedings of the National Academy of Sciences of the United States of America 82, 5255–5259.CrossRefGoogle ScholarPubMed
Winkler, G. R., Harkins, S. B., Lee, J. C. & Gray, H. B. (2006). α-synuclein structures probed by 5-fluorotryptophan fluorescence and 19F NMR spectroscopy. Journal of Physical Chemistry B 110, 7058–7061.CrossRefGoogle ScholarPubMed
Wojciak, J. M., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2009). Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains. EMBO Journal 28, 948–958.CrossRefGoogle ScholarPubMed
Won, H. S., Low, L. Y., Guzman, R. D., Martinez-Yamout, M., Jakob, U. & Dyson, H. J. (2004). The zinc-dependent redox switch domain of the chaperone Hsp33 has a novel fold. Journal of Molecular Biology 341, 893–899.CrossRefGoogle Scholar
Wright, P. E. & Dyson, H. J. (1999). Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293, 321–331.CrossRefGoogle ScholarPubMed
Wright, P. E. & Dyson, H. J. (2009). Linking folding and binding. Current Opinion in Structural Biology 19, 31–38.CrossRefGoogle ScholarPubMed
Wu, K. P. & Baum, J. (2010). Detection of transient interchain interactions in the intrinsically disordered protein α-synuclein by NMR paramagnetic relaxation enhancement. Journal of the American Chemical Society 132, 5546–5547.CrossRefGoogle ScholarPubMed
Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M. & Wright, P. E. (1997). Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. Journal of Molecular Biology 273, 183–206.CrossRefGoogle Scholar
Xu, J. & Xia, J. (2006). Structure and function of PICK1. Neurosignals 15, 190–201.CrossRefGoogle ScholarPubMed
Xue, B., Li, L., Meroueh, S. O., Uversky, V. N. & Dunker, A. K. (2009a). Analysis of structured and intrinsically disordered regions of transmembrane proteins. Molecular Biosystems 5, 1688–1702.CrossRefGoogle ScholarPubMed
Xue, B., Oldfield, C. J., Dunker, A. K. & Uversky, V. N. (2009b). CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions. FEBS Letters 583, 1469–1474.CrossRefGoogle ScholarPubMed
Xue, B., Williams, R. W., Oldfield, C. J., Dunker, A. K. & Uversky, V. N. (2010a). Archaic chaos: intrinsically disordered proteins in Archaea. BMC Systems Biology 4(Suppl 1), S1.CrossRefGoogle ScholarPubMed
Xue, B., Williams, R. W., Oldfield, C. J., Goh, G. K., Dunker, A. K. & Uversky, V. N. (2010b). Viral disorder or disordered viruses: do viral proteins possess unique features? Protein and Peptide Letters 17, 932–951.CrossRefGoogle ScholarPubMed
Xue, Y., Podkorytov, I. S., Rao, D. K., Benjamin, N., Sun, H. & Skrynnikov, N. R. (2009c). Paramagnetic relaxation enhancements in unfolded proteins: theory and application to drkN SH3 domain. Protein Science 18, 1401–1424.CrossRefGoogle ScholarPubMed
Zhu, F., Kapitan, J., Tranter, G. E., Pudney, P. D. A., Isaacs, N. W., Hecht, L. & Barron, L. D. (2008). Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data. Proteins 70, 823–833.CrossRefGoogle ScholarPubMed
Zor, T., Mayr, B. M., Dyson, H. J., Montminy, M. R. & Wright, P. E. (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. Journal of Biological Chemistry 277, 42241–42248.CrossRefGoogle ScholarPubMed
Zwier, M. C. & Chong, L. T. (2010). Reaching biological timescales with all-atom molecular dynamics simulations. Current Opinion in Pharmacology 10, 745–752.CrossRefGoogle ScholarPubMed