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MINIREVIEW PROLOGUE THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 291, NO. 13, pp. 6679 –6680, March 25, 2016 © 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.
Introduction to the Thematic Minireview Series on Intrinsically Disordered Proteins* Published, JBC Papers in Press, February 5, 2016, DOI 10.1074/jbc.R116.719930
Ruma Banerjee1 From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
In this thematic minireview series, the JBC presents six exciting articles on low complexity or intrinsically disordered proteins (IDPs). The dynamical and fluctuating structures of IDPs or of disordered regions within proteins result in virtually all of their primary sequence being exposed, at least at some time, to potential interacting partners. Their structural versatility underlies their often wide functional repertoires, which is further expanded by post-translational modifications. Given these characteristics, it is not surprising that IDPs serve as important hubs in signaling networks, scaffolding multivalent interactions. They are also important for organizing membrane-less protein organelles. This collection of reviews discusses biophysical approaches for studying IDPs and illuminates their importance to critical functions such as cell cycle control, transcription, and translation, as well as their regulation via cellular input signals.
How are IDPs2 or protein regions scripted in primary sequence space? In the first article in this series, Uversky notes that the sequence space of IDPs is typified by a low content of hydrophobic amino acid residues and high content of uncompensated charges (1). Missing an innate folding code, IDPs rely on binding partners to confer structural order, which, depending on the ligand, can lead to differently folded structures. Posttranslational modifications (PTMs) represent yet another strategy for modulating IDPs. Moreover, functionally significant structural transitions can involve differently disordered forms. Hence, the potential multiplicity of form and function in IDPs defies the conventional one structure-one function notion. In fact, many hub proteins that link protein-protein interaction networks and integrate signals are IDPs exemplifying the importance of dynamic structural remodeling for supporting a range of functions. The review ends with provocative ideas about the evolution of IDPs, which are more prevalent in com-
* This work was supported by National Institutes of Health Grants DK45776, HL58984, and GM112455 (to R. B.). The author declares that she has no conflicts of interest with the contents of this article. The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health. 1 To whom correspondence should be addressed: 4220C MSRB III, 1150 W. Medical Center Dr., University of Michigan, Ann Arbor, MI 48109-0600. Tel.: 734-615-5238; E-mail: [email protected]. 2 The abbreviations used are: IDP, intrinsically disordered protein; PTM, posttranslational modification; CBP, CREB-binding protein; CREB, cAMP-response element-binding protein.
MARCH 25, 2016 • VOLUME 291 • NUMBER 13
plex organisms and are often encoded by regions of mRNA affected by alternative splicing. The utility of kinetic approaches for illuminating the mechanism of coupled folding and binding of IDPs is the subject of the second article in the series by Clarke and co-workers (2). Charged residues are overrepresented in IDPs, which can be exacerbated by their propensity for PTMs such as phosphorylation. Hence, electrostatic steering is considered to be important for enhancing coupled folding and binding of IDPs. Kinetic studies are also important for addressing the chicken and egg question of whether binding (in which folding is induced upon binding) or folding (in which only a select conformer from the ensemble can bind) comes first. Finally, the authors discuss how the combination of mutagenesis and kinetic studies can allow the molecular interactions in the transition state between IDPs and their partners to be mapped. In the third article in the series, Bah and Forman-Kay discuss modulation of IDP function by PTMs (3). The structural and therefore functional versatility of IDPs is further expanded by PTMs, which can occur singly or in combination, and can trigger marked state changes, e.g. between disordered and folded or between dispersed monomeric and phase-separated. The authors illustrate the functional consequences of PTMs on IDPs by using several examples including multisite phosphorylation of the transcription factor, Ets-1, and the translation initiation factor, 4E-BP2. Exciting new insights into the organization of membrane-less protein organelles are discussed where intrinsically disordered regions play an important role in scaffolding multivalent interactions. Here too, PTMs are important, e.g. by affecting the phase transition temperature and thereby regulating assembly/disassembly of protein organelles in response to signal inputs. Finally, the authors discuss some solutions to the bottlenecks for producing large quantities of homogenous and site-specifically modified IDPs for biophysical studies. In the next article, Stultz and co-workers introduce the concept of quantifiable metrics of disorder to describe protein structure within the order-disorder continuum (4). For ordered proteins, the average structure is representative of the structure of all thermally accessible sub-states within the conformational ensemble. For IDPs, the conformational ensemble is vast and heterogeneous and the structure of a single sub-state is not representative of the entire population. Specific examples are introduced to illustrate the functional importance of proteins that lie at the unstructured end of the order-disorder continuum. Take the bacterial toxin colicin E9, for example, which is deployed by some Escherichia coli to reduce competition from other bacteria. A disordered segment within colicin is critical for allowing it to fish for and recruit the translocation machinery needed for its passage through the bacterial membrane, following which it promotes cell death. Other examples that are discussed reveal the importance of disordered domains for regulating fundamentally important cellular processes such as translation and transcription. JOURNAL OF BIOLOGICAL CHEMISTRY
6679
MINIREVIEW: Minireview Series on IDPs The transcriptional co-activators, CREB-binding protein (CBP) and p300, richly exemplify the power of disorder-order transitions for expressing functional complexity, as discussed by Dyson and Wright in the next review (5). CBP and p300 interact with ⬎400 partner proteins and represent important fulcra in eukaryotic transcriptional networks. These megalithic proteins contain ⬎1400 intrinsically disordered residues interspersed between seven folded domains. Subsets of the folded domains interact with intrinsically disordered domains of cellular transcription factors, regulatory proteins, and viral oncoproteins in a combinatorial fashion leading to the regulation of a vast array of target genes. The review provides structural insights into promiscuity, which underlies the interaction between the folded domains of CBP/p300 and intrinsically disordered regions in target proteins and facilitates cross-talk between signaling pathways. The importance of protein disorder for selecting substrates for ubiquitination and targeting them to the proteasome is the subject of the next article by Tompa and co-workers (6). PTMs in disordered regions of E3 ligases are critical for steering their subcellular localization and for regulating their activity. For example, the E3 ligase BRCA1 has an ⬃1500-residue-long disordered region that functions as a scaffold for bringing together interacting partners. It is estimated that ⬃80% of degrons or primary sequence motifs on protein targets that are recognized
6680 JOURNAL OF BIOLOGICAL CHEMISTRY
by E3 ligases are present in disordered regions. Synergistic folding has been seen in some cases where a disordered segment in an E3 ligase binds an unstructured region in a target protein. Degrons themselves are targets of PTMs, which regulate their recognition by E3 ligases. Finally, long disordered regions in the vicinity of degrons are important for proteasome-dependent degradation. References 1. Uversky, V. N. (2016) Dancing protein clouds: the strange biology and chaotic physics of intrinsically disordered proteins. J. Biol. Chem. 291, 6681– 6688 2. Shammas, S. L., Crabtree, M. D., Dahal, L., Wicky, B. I. M., and Clarke, J. (2016) Insights into coupled folding and binding mechanisms from kinetic studies. J. Biol. Chem. 291, 6689 – 6695 3. Bah, A., and Forman-Kay, J. D. (2016) Modulation of intrinsically disordered protein function by post-translational modifications. J. Biol. Chem. 291, 6696 – 6705 4. Burger, V. M., Nolasco, D. O., and Stultz, C. M. (2016) Expanding the range of protein function at the far end of the order-structure continuum. J. Biol. Chem. 291, 6706 – 6713 5. Dyson, H. J., and Wright, P. E. (2016) Role of intrinsic protein disorder in the function and interactions of the transcriptional coactivators CREBbinding protein (CBP) and p300. J. Biol. Chem. 291, 6714 – 6722 6. Guharoy, M., Bhowmick, P., and Tompa, P. (2016) Design principles involving protein disorder facilitate specific substrate selection and degradation by the ubiquitin-proteasome system. J. Biol. Chem. 291, 6723– 6731
VOLUME 291 • NUMBER 13 • MARCH 25, 2016
MINIREVIEW PROLOGUE THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 291, NO. 13, pp. 6679 –6680, March 25, 2016 © 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.
Introduction to the Thematic Minireview Series on Intrinsically Disordered Proteins* Published, JBC Papers in Press, February 5, 2016, DOI 10.1074/jbc.R116.719930
Ruma Banerjee1 From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
In this thematic minireview series, the JBC presents six exciting articles on low complexity or intrinsically disordered proteins (IDPs). The dynamical and fluctuating structures of IDPs or of disordered regions within proteins result in virtually all of their primary sequence being exposed, at least at some time, to potential interacting partners. Their structural versatility underlies their often wide functional repertoires, which is further expanded by post-translational modifications. Given these characteristics, it is not surprising that IDPs serve as important hubs in signaling networks, scaffolding multivalent interactions. They are also important for organizing membrane-less protein organelles. This collection of reviews discusses biophysical approaches for studying IDPs and illuminates their importance to critical functions such as cell cycle control, transcription, and translation, as well as their regulation via cellular input signals.
How are IDPs2 or protein regions scripted in primary sequence space? In the first article in this series, Uversky notes that the sequence space of IDPs is typified by a low content of hydrophobic amino acid residues and high content of uncompensated charges (1). Missing an innate folding code, IDPs rely on binding partners to confer structural order, which, depending on the ligand, can lead to differently folded structures. Posttranslational modifications (PTMs) represent yet another strategy for modulating IDPs. Moreover, functionally significant structural transitions can involve differently disordered forms. Hence, the potential multiplicity of form and function in IDPs defies the conventional one structure-one function notion. In fact, many hub proteins that link protein-protein interaction networks and integrate signals are IDPs exemplifying the importance of dynamic structural remodeling for supporting a range of functions. The review ends with provocative ideas about the evolution of IDPs, which are more prevalent in com-
* This work was supported by National Institutes of Health Grants DK45776, HL58984, and GM112455 (to R. B.). The author declares that she has no conflicts of interest with the contents of this article. The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health. 1 To whom correspondence should be addressed: 4220C MSRB III, 1150 W. Medical Center Dr., University of Michigan, Ann Arbor, MI 48109-0600. Tel.: 734-615-5238; E-mail: [email protected]. 2 The abbreviations used are: IDP, intrinsically disordered protein; PTM, posttranslational modification; CBP, CREB-binding protein; CREB, cAMP-response element-binding protein.
MARCH 25, 2016 • VOLUME 291 • NUMBER 13
plex organisms and are often encoded by regions of mRNA affected by alternative splicing. The utility of kinetic approaches for illuminating the mechanism of coupled folding and binding of IDPs is the subject of the second article in the series by Clarke and co-workers (2). Charged residues are overrepresented in IDPs, which can be exacerbated by their propensity for PTMs such as phosphorylation. Hence, electrostatic steering is considered to be important for enhancing coupled folding and binding of IDPs. Kinetic studies are also important for addressing the chicken and egg question of whether binding (in which folding is induced upon binding) or folding (in which only a select conformer from the ensemble can bind) comes first. Finally, the authors discuss how the combination of mutagenesis and kinetic studies can allow the molecular interactions in the transition state between IDPs and their partners to be mapped. In the third article in the series, Bah and Forman-Kay discuss modulation of IDP function by PTMs (3). The structural and therefore functional versatility of IDPs is further expanded by PTMs, which can occur singly or in combination, and can trigger marked state changes, e.g. between disordered and folded or between dispersed monomeric and phase-separated. The authors illustrate the functional consequences of PTMs on IDPs by using several examples including multisite phosphorylation of the transcription factor, Ets-1, and the translation initiation factor, 4E-BP2. Exciting new insights into the organization of membrane-less protein organelles are discussed where intrinsically disordered regions play an important role in scaffolding multivalent interactions. Here too, PTMs are important, e.g. by affecting the phase transition temperature and thereby regulating assembly/disassembly of protein organelles in response to signal inputs. Finally, the authors discuss some solutions to the bottlenecks for producing large quantities of homogenous and site-specifically modified IDPs for biophysical studies. In the next article, Stultz and co-workers introduce the concept of quantifiable metrics of disorder to describe protein structure within the order-disorder continuum (4). For ordered proteins, the average structure is representative of the structure of all thermally accessible sub-states within the conformational ensemble. For IDPs, the conformational ensemble is vast and heterogeneous and the structure of a single sub-state is not representative of the entire population. Specific examples are introduced to illustrate the functional importance of proteins that lie at the unstructured end of the order-disorder continuum. Take the bacterial toxin colicin E9, for example, which is deployed by some Escherichia coli to reduce competition from other bacteria. A disordered segment within colicin is critical for allowing it to fish for and recruit the translocation machinery needed for its passage through the bacterial membrane, following which it promotes cell death. Other examples that are discussed reveal the importance of disordered domains for regulating fundamentally important cellular processes such as translation and transcription. JOURNAL OF BIOLOGICAL CHEMISTRY
6679
MINIREVIEW: Minireview Series on IDPs The transcriptional co-activators, CREB-binding protein (CBP) and p300, richly exemplify the power of disorder-order transitions for expressing functional complexity, as discussed by Dyson and Wright in the next review (5). CBP and p300 interact with ⬎400 partner proteins and represent important fulcra in eukaryotic transcriptional networks. These megalithic proteins contain ⬎1400 intrinsically disordered residues interspersed between seven folded domains. Subsets of the folded domains interact with intrinsically disordered domains of cellular transcription factors, regulatory proteins, and viral oncoproteins in a combinatorial fashion leading to the regulation of a vast array of target genes. The review provides structural insights into promiscuity, which underlies the interaction between the folded domains of CBP/p300 and intrinsically disordered regions in target proteins and facilitates cross-talk between signaling pathways. The importance of protein disorder for selecting substrates for ubiquitination and targeting them to the proteasome is the subject of the next article by Tompa and co-workers (6). PTMs in disordered regions of E3 ligases are critical for steering their subcellular localization and for regulating their activity. For example, the E3 ligase BRCA1 has an ⬃1500-residue-long disordered region that functions as a scaffold for bringing together interacting partners. It is estimated that ⬃80% of degrons or primary sequence motifs on protein targets that are recognized
6680 JOURNAL OF BIOLOGICAL CHEMISTRY
by E3 ligases are present in disordered regions. Synergistic folding has been seen in some cases where a disordered segment in an E3 ligase binds an unstructured region in a target protein. Degrons themselves are targets of PTMs, which regulate their recognition by E3 ligases. Finally, long disordered regions in the vicinity of degrons are important for proteasome-dependent degradation. References 1. Uversky, V. N. (2016) Dancing protein clouds: the strange biology and chaotic physics of intrinsically disordered proteins. J. Biol. Chem. 291, 6681– 6688 2. Shammas, S. L., Crabtree, M. D., Dahal, L., Wicky, B. I. M., and Clarke, J. (2016) Insights into coupled folding and binding mechanisms from kinetic studies. J. Biol. Chem. 291, 6689 – 6695 3. Bah, A., and Forman-Kay, J. D. (2016) Modulation of intrinsically disordered protein function by post-translational modifications. J. Biol. Chem. 291, 6696 – 6705 4. Burger, V. M., Nolasco, D. O., and Stultz, C. M. (2016) Expanding the range of protein function at the far end of the order-structure continuum. J. Biol. Chem. 291, 6706 – 6713 5. Dyson, H. J., and Wright, P. E. (2016) Role of intrinsic protein disorder in the function and interactions of the transcriptional coactivators CREBbinding protein (CBP) and p300. J. Biol. Chem. 291, 6714 – 6722 6. Guharoy, M., Bhowmick, P., and Tompa, P. (2016) Design principles involving protein disorder facilitate specific substrate selection and degradation by the ubiquitin-proteasome system. J. Biol. Chem. 291, 6723– 6731
VOLUME 291 • NUMBER 13 • MARCH 25, 2016
