Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and Upon Multisite Phosphorylation

Martin, Erik W.; Holehouse, Alex S.; Pappu, Rohit V.; Mittag, Tanja

doi:10.1016/j.bpj.2016.11.2757

Cited by 6 publications

(6 citation statements)

References 56 publications

(74 reference statements)

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“…Here, the phosphorylation triggers a transient local fold that can result in slowed‐down conformational kinetics . Similar intramolecular charge clamps have already been shown in some cases ; however, the RSK1 CTT phosphoswitch appears to be the first clear case where it acts as a modulator on the assembly of a signaling complex. Since a conserved cluster of basic residues is a hallmark feature of nuclear localization signals or AGC kinase substrate motifs , the functionality of these linear motifs involved in nuclear transport or AGC protein kinase‐mediated phosphorylation, respectively, may also be modulated by adjacent phosphorylation sites.…”

Section: Discussionsupporting

confidence: 58%

Dynamic control of RSK complexes by phosphoswitch‐based regulation

et al. 2017

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Assembly and disassembly of protein-protein complexes needs to be dynamically controlled and phosphoswitches based on linear motifs are crucial in this process. Extracellular signal-regulated kinase 2 (ERK2) recognizes a linearbinding motif at the C-terminal tail (CTT) of ribosomal S6 kinase 1 (RSK1), leading to phosphorylation and subsequent activation of RSK1. The CTT also contains a classical PDZ domain-binding motif which binds RSK substrates (e.g. MAGI-1). We show that autophosphorylation of the disordered CTT promotes the formation of an intramolecular charge clamp, which efficiently masks critical residues and indirectly hinders ERK binding. Thus, RSK1 CTT operates as an autoregulated phosphoswitch: its phosphorylation at specific sites affects its protein-binding capacity and its conformational dynamics. These biochemical feedbacks, which form the structural basis for the rapid dissociation of ERK2-RSK1 and RSK1-PDZ substrate complexes under sustained epidermal growth factor (EGF) stimulation, were structurally characterized and validated in living cells. Overall, conformational changes induced by phosphorylation in disordered regions of protein kinases, coupled to allosteric events occurring in the kinase domain cores, may provide mechanisms that contribute to the emergence of complex signaling activities. In addition, we show that phosphoswitches based on linear motifs can be functionally classified as ON and OFF protein-protein interaction switches or dimmers, depending on the specific positioning of phosphorylation target sites in relation to functional linear-binding motifs. Moreover, interaction of phosphorylated residues with positively charged residues in disordered regions is likely to be a common mechanism of phosphoregulation.

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Section: Discussionsupporting

confidence: 58%

Dynamic control of RSK complexes by phosphoswitch‐based regulation

et al. 2017

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“…Asphericity was also used as another important factor of IDRs . Moreover, phosphorylation sites, polar or hydrophobic residues, even directed‐proline residues could affect the dimension of IDRs . The attracting interaction between domains and linker may stabilize the closed state and increase [B] 0 , while the enhanced excluded‐volume (repulsive) interaction between domains and linker would decrease [B] 0 .…”

Section: Resultsmentioning

confidence: 99%

Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

Cao

Lai

et al. 2018

Protein Science

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There are many multidomain allosteric proteins where an allosteric signal at the allosteric domain modifies the activity of the functional domain. Intrinsically disordered regions (linkers) are widely involved in this kind of regulation process, but the essential role they play therein is not well understood. Here, we investigated the effect of linkers in stabilizing the open or the closed states of multidomain proteins using combined thermodynamic deduction and coarse-grained molecular dynamics simulations. We revealed that the influence of linker can be fully characterized by an effective local concentration [B] . When K is smaller than [B] , the closed state would be favored; while the open state would be preferred when K is larger than [B] . We used four protein systems with markedly different domain-domain binding affinity and structural order/disorder as model systems to understand the relationship between [B] and the linker length as well as its flexibility. The linker length is the main practical determinant of [B] . [B] of a flexible linker with 40-60 residues was determined to be in a narrow range of 0.2-0.6 mM, while a too short or too long length would dramatically decrease [B] . With the revealed [B] range, the introduction of a flexible linker makes the regulation of weakly interacting partners possible.

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“…Furthermore, it does not provide any insight into how protein dimension varies within these classes [33]. When comparing experimental data with predictions inspired to FCR, or more complex composition-based heuristics, collapsed globules turn out to be less frequent than predicted [33][34][35][36]. Possible reasons for these discrepancies could be searched in the weaknesses of either the experimental or the computational approaches: (i) Collapsed globules have higher aggregation propensity compared to expanded coils, hampering structural characterization at the high protein concentrations required for some biophysical techniques (e.g., NMR, small-angle X-ray scattering (SAXS), etc.…”

Section: Compositional Classes Of Idps and Phase Diagrams Of Protein mentioning

confidence: 97%

Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins

Bianchi

Longhi

Grandori

et al. 2020

IJMS

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The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.

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Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and Upon Multisite Phosphorylation

Cited by 6 publications

References 56 publications

Dynamic control of RSK complexes by phosphoswitch‐based regulation

Dynamic control of RSK complexes by phosphoswitch‐based regulation

Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins

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