scholarly journals Regulation of protein phosphatase 1 by intrinsically disordered proteins

2012 ◽  
Vol 40 (5) ◽  
pp. 969-974 ◽  
Author(s):  
Meng S. Choy ◽  
Rebecca Page ◽  
Wolfgang Peti

PP1 (protein phosphatase 1) is an essential serine/threonine phosphatase that plays a critical role in a broad range of biological processes, from muscle contraction to memory formation. PP1 achieves its biological specificity by forming holoenzymes with more than 200 known regulatory proteins. Interestingly, most of these regulatory proteins (≥70%) belong to the class of IDPs (intrinsically disordered proteins). Thus structural studies highlighting the interaction of these IDP regulatory proteins with PP1 are an attractive model system because it allows general parameters for a group of diverse IDPs that interact with the same binding partner to be identified, while also providing fundamental insights into PP1 biology. The present review provides a brief overview of our current understanding of IDP–PP1 interactions, including the importance of pre-formed secondary and tertiary structures for PP1 binding, as well as changes of IDP dynamics upon interacting with PP1.

Author(s):  
Meng S. Choy ◽  
Nicolas Bolik-Coulon ◽  
Tara L. Archuleta ◽  
Wolfgang Peti ◽  
Rebecca Page

Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured. Here, the 2.9 Å resolution crystal structure of human SDS22 in space group P212121 is reported. SDS22 adopts an LRR fold with the horseshoe-like curvature typical for this family of proteins. The structure results in surfaces with distinct chemical characteristics that are likely to be critical for PP1 binding.


2022 ◽  
Vol 119 (3) ◽  
pp. e2117338119
Author(s):  
Rebecca B. Berlow ◽  
H. Jane Dyson ◽  
Peter E. Wright

Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.


2018 ◽  
Vol 115 (40) ◽  
pp. 9929-9934 ◽  
Author(s):  
Gregory L. Dignon ◽  
Wenwei Zheng ◽  
Robert B. Best ◽  
Young C. Kim ◽  
Jeetain Mittal

Proteins that undergo liquid–liquid phase separation (LLPS) have been shown to play a critical role in many physiological functions through formation of condensed liquid-like assemblies that function as membraneless organelles within biological systems. To understand how different proteins may contribute differently to these assemblies and their functions, it is important to understand the molecular driving forces of phase separation and characterize their phase boundaries and material properties. Experimental studies have shown that intrinsically disordered regions of these proteins are a major driving force, as many of them undergo LLPS in isolation. Previous work on polymer solution phase behavior suggests a potential correspondence between intramolecular and intermolecular interactions that can be leveraged to discover relationships between single-molecule properties and phase boundaries. Here, we take advantage of a recently developed coarse-grained framework to calculate the θ temperatureTθ, the Boyle temperatureTB, and the critical temperatureTcfor 20 diverse protein sequences, and we show that these three properties are highly correlated. We also highlight that these correlations are not specific to our model or simulation methodology by comparing between different pairwise potentials and with data from other work. We, therefore, suggest that smaller simulations or experiments to determineTθorTBcan provide useful insights into the corresponding phase behavior.


2020 ◽  
Author(s):  
Irene Ruiz-Ortiz ◽  
David De Sancho

<div>Many intrinsically disordered proteins (IDPs) are involved in complex signalling networks inside the cell. </div><div>Their particular binding modes elicit different types of responses and subtle regulation of biological responses. </div><div>Here we study the binding of two disordered transactivation domains from proteins HIF-1α and CITED2, whose binding to the TAZ1 domain of CBP is critical for the hypoxic response. Experiments have shown that both IDPs compete for their shared partner, and that this competition is mediated by the formation of a ternary intermediate state. Here we use molecular simulations with a coarse-grained model to provide a glimpse of the structure of this intermediate. </div><div>We find that the conserved LP(Q/E)L motif may have a critical role in the displacement of HIF-1α by CITED2 and show a possible mechanism for the transition from the intermediate to the bound state. We also explore the role of TAZ1 dynamics in the binding. The results of our simulations are consistent with many of the experimental observations and provide a detailed molecular description of the emergent properties in the complex binding of these IDPs.</div>


2020 ◽  
Author(s):  
M. F. C. A. Carvajal ◽  
J. M. Preston ◽  
N. M. Jamhawi ◽  
T. M. Sabo ◽  
J. M. Aramini ◽  
...  

ABSTRACTElastin fibers assemble in the extracellular matrix from the precursor protein tropoelastin and provide the flexibility and spontaneous recoil required for arterial function. Unlike many proteins, a structure-function mechanism for elastin has been elusive. We have performed detailed NMR relaxation studies of the dynamics of the minielastin 24x′ in solution and of purified bovine elastin fibers in the presence and absence of mechanical stress. The low sequence complexity of 24x′ enables us to determine dynamical timescales and degrees of local ordering with residue-specific resolution in the cross-link and hydrophobic modules using NMR relaxation. We find an extremely high degree of disorder, with order parameters for the entirety of the hydrophobic domains near zero, resembling that of simple chemical polymers and less than the order parameters that have been observed in other intrinsically disordered proteins. We find that backbone order parameters in natural, purified elastin fibers are comparable to those found in 24x′ in solution. The difference in dynamics, compared to 24x′, is that backbone correlation times are significantly slowed in purified elastin. Moreover, when elastin is mechanically stretched, the high chain disorder in purified elastin is retained - showing that any change in local ordering is below that detectable in our experiment. Combined with our previous finding of a 10-fold increase in the ordering of water when fully hydrated elastin fibers are stretched by 50%, these results support the hypothesis that stretch induced solvent ordering, i.e. the hydrophobic effect, is a key player in the elastic recoil of elastin.SIGNIFICANCEElastin is responsible for the spontaneous recoil of atrial walls that is necessary for cardiovascular function. Despite this critical role, the mechanism driving entropic recoil has remained unclear. Elastin is unusual in that it is intrinsically disordered in both soluble and fibrous forms. Using NMR, we have determined the timescales and amplitudes of dynamics in a soluble elastin mimetic and in cross-linked elastin in both relaxed and stretched states. Although dynamical timescales are different, both the soluble elastin mimetic and fibrillar elastin display an exceptionally high degree of disorder. No detectable increase in protein ordering was observed upon stretching, suggesting that entropic recoil is primarily driven by the hydrophobic effect and not configurational entropy loss.


2020 ◽  
Author(s):  
Irene Ruiz-Ortiz ◽  
David De Sancho

<div>Many intrinsically disordered proteins (IDPs) are involved in complex signalling networks inside the cell. </div><div>Their particular binding modes elicit different types of responses and subtle regulation of biological responses. </div><div>Here we study the binding of two disordered transactivation domains from proteins HIF-1α and CITED2, whose binding to the TAZ1 domain of CBP is critical for the hypoxic response. Experiments have shown that both IDPs compete for their shared partner, and that this competition is mediated by the formation of a ternary intermediate state. Here we use molecular simulations with a coarse-grained model to provide a glimpse of the structure of this intermediate. </div><div>We find that the conserved LP(Q/E)L motif may have a critical role in the displacement of HIF-1α by CITED2 and show a possible mechanism for the transition from the intermediate to the bound state. We also explore the role of TAZ1 dynamics in the binding. The results of our simulations are consistent with many of the experimental observations and provide a detailed molecular description of the emergent properties in the complex binding of these IDPs.</div>


2017 ◽  
Author(s):  
Bálint Mészáros ◽  
László Dobson ◽  
Erzsébet Fichó ◽  
Gábor E. Tusnády ◽  
Zsuzsanna Dosztányi ◽  
...  

SummaryIntrinsically Disordered Proteins (IDPs) fulfill critical biological roles without having the potential to fold on their own. While lacking inherent structure, the majority of IDPs do reach a folded state via interaction with a protein partner, presenting a deep entanglement of the folding and binding process. Protein disorder has been recognized as a major determinant in several properties of proteins; yet the way the binding process is reflected in these features in general lacks this detail of description. Recent advances in database development enabled us to identify three basic scenarios of the interplay between folding and binding in unprecedented detail. These scenarios have fundamentally different properties in terms of protein sequence, structure, function and regulation, depending on the structural properties of the interacting partners. Strikingly, the existence of a binding partner and its structural properties influence all analyzed properties of proteins to the same extent as the divide between inherent order or disorder. The appreciation of this interplay between folding and binding is the basis for the successful charting of unknown territories in the protein interactome, the understanding of how different binding modes assemble regulatory networks, and the development of future pharmaceutical applications.


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