scholarly journals Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins

2022 ◽  
Vol 119 (3) ◽  
pp. e2117338119
Author(s):  
Rebecca B. Berlow ◽  
H. Jane Dyson ◽  
Peter E. Wright
Keyword(s):  
Transcriptional Control ◽  
Intrinsically Disordered Proteins ◽  
Binding Protein ◽  
Critical Role ◽  
Molecular Switch ◽  
Negative Regulator ◽  
Disordered Proteins ◽  
Creb Binding Protein ◽  
Binding Motifs ◽  
Intrinsically Disordered

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.

scholarly journals Enhancing Binding Affinity of an Intrinsically Disordered Protein by α-Methylation of Key Amino Acid Residues

2019 ◽  
Author(s):  
Valentin Bauer ◽  
Boris Schmidtgall ◽  
Gergő Gógl ◽  
Jozica Dolenc ◽  
Judit Osz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Selective Inhibition ◽  
Disordered Proteins ◽  
Creb Binding Protein ◽  
Alpha Helices ◽  
Intrinsically Disordered ◽  
Order Of Magnitude

Intrinsically disordered proteins (IDPs), which undergo folding upon binding to their targets, are critical players in protein interaction networks. Here we demonstrate that incorporation of non-canonical alpha-methylated amino acids into the unstructured activation domain of the transcriptional coactivator ACTR can stabilize helical conformations and strengthen binding interactions with the nuclear coactivator binding domain (NCBD) of CREB-binding protein (CBP). A combinatorial alpha-methylation scan of the ACTR sequence converged on two substitutions at positions 1055 and 1076 that increase affinity for both NCBD and the full length 270 kDa CBP by one order of magnitude. The first X-ray structure of the modified ACTR domain bound to NCBD revealed that the key alpha-methylated amino acids were localized within alpha-helices. Biophysical studies showed that the observed changes in binding energy are the result of long-range interactions and redistribution of enthalpy and entropy. This proof-of-concept study establishes a potential strategy for selective inhibition of protein-protein interactions involving IDPs in cells.<br>

scholarly journals Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins

2018 ◽  
Vol 19 (11) ◽  
pp. 3614 ◽  
Author(s):  
Do-Hyoung Kim ◽  
Kyou-Hoon Han
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Disordered Proteins ◽  
Ample Evidence ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Long Time ◽  
Science Community ◽  
Target Binding

Intrinsically disordered proteins (IDPs) are unorthodox proteins that do not form three-dimensional structures under non-denaturing conditions, but perform important biological functions. In addition, IDPs are associated with many critical diseases including cancers, neurodegenerative diseases, and viral diseases. Due to the generic name of “unstructured” proteins used for IDPs in the early days, the notion that IDPs would be completely unstructured down to the level of secondary structures has prevailed for a long time. During the last two decades, ample evidence has been accumulated showing that IDPs in their target-free state are pre-populated with transient secondary structures critical for target binding. Nevertheless, such a message did not seem to have reached with sufficient clarity to the IDP or protein science community largely because similar but different expressions were used to denote the fundamentally same phenomenon of presence of such transient secondary structures, which is not surprising for a quickly evolving field. Here, we summarize the critical roles that these transient secondary structures play for diverse functions of IDPs by describing how various expressions referring to transient secondary structures have been used in different contexts.

scholarly journals Role of the CBP catalytic core in intramolecular SUMOylation and control of histone H3 acetylation

2017 ◽  
Vol 114 (27) ◽  
pp. E5335-E5342 ◽  
Author(s):  
Sangho Park ◽  
Robyn L. Stanfield ◽  
Maria A. Martinez-Yamout ◽  
H. Jane Dyson ◽  
Ian A. Wilson ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Critical Role ◽  
Histone H3 ◽  
Negative Regulator ◽  
Creb Binding Protein ◽  
Catalytic Core ◽  
Intrinsically Disordered ◽  
Histone H3 Acetylation ◽  
H3 Acetylation

The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2.4-Å resolution. The BRD, PHD, and HAT domains form an integral structural unit to which the RING and ZZ domains are flexibly attached. The structure of the apo-CBP HAT domain is similar to that of acyl-CoA–bound p300 HAT complexes and shows that the acetyl-CoA binding site is stably formed in the absence of cofactor. The BRD, PHD, and ZZ domains interact with small ubiquitin-like modifier 1 (SUMO-1) and Ubc9, and function as an intramolecular E3 ligase for SUMOylation of the cell cycle regulatory domain 1 (CRD1) of CBP, which is located adjacent to the BRD. In vitro HAT assays suggest that the RING domain, the autoregulatory loop (AL) within the HAT domain, and the ZZ domain do not directly influence catalytic activity, whereas the BRD is essential for histone H3 acetylation in nucleosomal substrates. Several lysine residues in the intrinsically disordered AL are autoacetylated by the HAT domain. Upon autoacetylation, acetyl-K1596 (Ac-K1596) binds intramolecularly to the BRD, competing with histones for binding to the BRD and acting as a negative regulator that inhibits histone H3 acetylation.

scholarly journals Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 168 ◽  
Author(s):  
Carolina Cragnell ◽  
Lasse Staby ◽  
Samuel Lenton ◽  
Birthe Kragelund ◽  
Marie Skepö
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Intrinsically Disordered Proteins ◽  
Divalent Cations ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Binding Motifs ◽  
Histatin 5 ◽  
X Ray ◽  
Intrinsically Disordered ◽  
X Ray Scattering

Intrinsically disordered proteins (IDPs) can form functional oligomers and in some cases, insoluble disease related aggregates. It is therefore vital to understand processes and mechanisms that control pathway distribution. Divalent cations including Zn2+ can initiate IDP oligomerisation through the interaction with histidine residues but the mechanisms of doing so are far from understood. Here we apply a multi-disciplinary approach using small angle X-ray scattering, nuclear magnetic resonance spectroscopy, calorimetry and computations to show that that saliva protein Histatin 5 forms highly dynamic oligomers in the presence of Zn2+. The process is critically dependent upon interaction between Zn2+ ions and distinct histidine rich binding motifs which allows for thermodynamic switching between states. We propose a molecular mechanism of oligomerisation, which may be generally applicable to other histidine rich IDPs. Finally, as Histatin 5 is an important saliva component, we suggest that Zn2+ induced oligomerisation may be crucial for maintaining saliva homeostasis.

scholarly journals The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved

2021 ◽  
Author(s):  
Elin Karlsson ◽  
Frieda A Sorgenfrei ◽  
Eva Andersson ◽  
Jakob Dogan ◽  
Per Jemth ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Dynamic Properties ◽  
Binding Domain ◽  
Disordered Proteins ◽  
Structural Constraints ◽  
Hydrophobic Core ◽  
Creb Binding Protein ◽  
Biophysical Properties ◽  
Interaction Domain ◽  
Intrinsically Disordered

Evolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear co-activator binding domain (NCBD) from CREB-binding protein is a protein-protein interaction domain, which contains a hydrophobic core but is verging on being intrinsically disordered. These highly dynamic 'borderline' properties of NCBD makes it an interesting model system for evolutionary structure-function investigation. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetic methods we show that NCBD has retained its structure and dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD are subject to positive selection and thus important for its function, which includes mediating several distinct protein-protein interactions.

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
Keyword(s):  
Protein Phosphatase ◽  
Intrinsically Disordered Proteins ◽  
Critical Role ◽  
Regulatory Proteins ◽  
Protein Phosphatase 1 ◽  
Disordered Proteins ◽  
Tertiary Structures ◽  
Binding Partner ◽  
Intrinsically Disordered ◽  
Biological Specificity

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.

scholarly journals PGRS Domain of Rv0297 of Mycobacterium tuberculosis Functions in A Calcium Dependent Manner

2021 ◽  
Vol 22 (17) ◽  
pp. 9390
Author(s):  
Tarina Sharma ◽  
Jasdeep Singh ◽  
Sonam Grover ◽  
Manjunath P. ◽  
Firdos Firdos ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Intrinsically Disordered Proteins ◽  
Therapeutic Interventions ◽  
Disordered Proteins ◽  
No Production ◽  
Dependent Manner ◽  
Pathogenic Potential ◽  
Binding Motifs ◽  
Calcium Dependent ◽  
Intrinsically Disordered

Mycobacterium tuberculosis (M.tb), the pathogen causing tuberculosis, is a major threat to human health worldwide. Nearly 10% of M.tb genome encodes for a unique family of PE/PPE/PGRS proteins present exclusively in the genus Mycobacterium. The functions of most of these proteins are yet unexplored. The PGRS domains of these proteins have been hypothesized to consist of Ca2+ binding motifs that help these intrinsically disordered proteins to modulate the host cellular responses. Ca2+ is an important secondary messenger that is involved in the pathogenesis of tuberculosis in diverse ways. This study presents the calcium-dependent function of the PGRS domain of Rv0297 (PE_PGRS5) in M.tb virulence and pathogenesis. Tandem repeat search revealed the presence of repetitive Ca2+ binding motifs in the PGRS domain of the Rv0297 protein (Rv0297PGRS). Molecular Dynamics simulations and fluorescence spectroscopy revealed Ca2+ dependent stabilization of the Rv0297PGRS protein. Calcium stabilized Rv0297PGRS enhances the interaction of Rv0297PGRS with surface localized Toll like receptor 4 (TLR4) of macrophages. The Ca2+ stabilized binding of Rv0297PGRS with the surface receptor of macrophages enhances its downstream consequences in terms of Nitric Oxide (NO) production and cytokine release. Thus, this study points to hitherto unidentified roles of calcium-modulated PE_PGRS proteins in the virulence of M.tb. Understanding the pathogenic potential of Ca2+ dependent PE_PGRS proteins can aid in targeting these proteins for therapeutic interventions.

scholarly journals On the specificity of protein–protein interactions in the context of disorder

2021 ◽  
Vol 478 (11) ◽  
pp. 2035-2050
Author(s):  
Kaare Teilum ◽  
Johan G. Olsen ◽  
Birthe B. Kragelund
Keyword(s):  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Globular Proteins ◽  
Disordered Proteins ◽  
Protein Protein Interactions ◽  
Binding Motifs ◽  
Intrinsically Disordered ◽  
Binding Partners ◽  
Trimer Formation ◽  
Definition Of

With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.

scholarly journals Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

2018 ◽  
Vol 115 (40) ◽  
pp. 9929-9934 ◽  
Author(s):  
Gregory L. Dignon ◽  
Wenwei Zheng ◽  
Robert B. Best ◽  
Young C. Kim ◽  
Jeetain Mittal
Keyword(s):  
Phase Separation ◽  
Phase Behavior ◽  
Single Molecule ◽  
Intrinsically Disordered Proteins ◽  
Critical Role ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Phase Boundaries ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

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.

scholarly journals Adenoviral E1A Exploits Flexibility and Disorder to Target Cellular Proteins

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1541
Author(s):  
Maria Grazia Murrali ◽  
Isabella C. Felli ◽  
Roberta Pierattelli
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Direct Interaction ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Creb Binding Protein ◽  
Adenovirus E1a ◽  
Intrinsically Disordered ◽  
Functional Aspects ◽  
Conformational Freedom

Direct interaction between intrinsically disordered proteins (IDPs) is often difficult to characterize hampering the elucidation of their binding mechanism. Particularly challenging is the study of fuzzy complexes, in which the intrinsically disordered proteins or regions retain conformational freedom within the assembly. To date, nuclear magnetic resonance spectroscopy has proven to be one of the most powerful techniques to characterize at the atomic level intrinsically disordered proteins and their interactions, including those cases where the formed complexes are highly dynamic. Here, we present the characterization of the interaction between a viral protein, the Early region 1A protein from Adenovirus (E1A), and a disordered region of the human CREB-binding protein, namely the fourth intrinsically disordered linker CBP-ID4. E1A was widely studied as a prototypical viral oncogene. Its interaction with two folded domains of CBP was mapped, providing hints for understanding some functional aspects of the interaction with this transcriptional coactivator. However, the role of the flexible linker connecting these two globular domains of CBP in this interaction was never explored before.

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