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3 pages, 189 KiB

Open AccessEditorial

The Amazing World of IDPs in Human Diseases II

by Simona Maria Monti, Giuseppina De Simone and Emma Langella

Biomolecules 2022, 12(3), 369; https://doi.org/10.3390/biom12030369 - 25 Feb 2022

Cited by 4 | Viewed by 1576

Abstract

Intrinsically Disordered Proteins (IDPs) lack stable tertiary and secondary structures and are extensively distributed across eukaryotic cells, playing critical roles in cell signaling and regulation [...] Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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16 pages, 4104 KiB

Open AccessEditor’s ChoiceArticle

DJ-1 Acts as a Scavenger of α-Synuclein Oligomers and Restores Monomeric Glycated α-Synuclein

by Tamr B. Atieh, Jonathan Roth, Xue Yang, Cody L. Hoop and Jean Baum

Biomolecules 2021, 11(10), 1466; https://doi.org/10.3390/biom11101466 - 6 Oct 2021

Cited by 7 | Viewed by 3927

Abstract

Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson’s disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that [...] Read more.

Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson’s disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that plays a critical role in PD pathology, has been proposed to repair glycation in proteins, yet a mechanism has not been elucidated. In this study, we integrate solution nuclear magnetic resonance (NMR) spectroscopy and liquid atomic force microscopy (AFM) techniques to characterize glycated N-terminally acetylated-αSyn (glyc-ac-αSyn) and its interaction with DJ-1. Glycation of ac-αSyn by methylglyoxal increases oligomer formation, as visualized by AFM in solution, resulting in decreased dynamics of the monomer amide backbone around the Lys residues, as measured using NMR. Upon addition of DJ-1, this NMR signature of glyc-ac-αSyn monomers reverts to a native ac-αSyn-like character. This phenomenon is reversible upon removal of DJ-1 from the solution. Using relaxation-based NMR, we have identified the binding site on DJ-1 for glycated and native ac-αSyn as the catalytic pocket and established that the oxidation state of the catalytic cysteine is imperative for binding. Based on our results, we propose a novel mechanism by which DJ-1 scavenges glyc-ac-αSyn oligomers without chemical deglycation, suppresses glyc-ac-αSyn monomer–oligomer interactions, and releases free glyc-ac-αSyn monomers in solution. The interference of DJ-1 with ac-αSyn oligomers may promote free ac-αSyn monomer in solution and suppress the propagation of toxic oligomer and fibril species. These results expand the understanding of the role of DJ-1 in PD pathology by acting as a scavenger for aggregated αSyn. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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19 pages, 1710 KiB

Open AccessArticle

Design of Inhibitors of the Intrinsically Disordered Protein NUPR1: Balance between Drug Affinity and Target Function

by Bruno Rizzuti, Wenjun Lan, Patricia Santofimia-Castaño, Zhengwei Zhou, Adrián Velázquez-Campoy, Olga Abián, Ling Peng, José L. Neira, Yi Xia and Juan L. Iovanna

Biomolecules 2021, 11(10), 1453; https://doi.org/10.3390/biom11101453 - 3 Oct 2021

Cited by 15 | Viewed by 3271

Abstract

Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of [...] Read more.

Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of several tumors. We have previously repurposed trifluoperazine (TFP) as a drug targeting NUPR1 and, by using a ligand-based approach, designed the drug ZZW-115 starting from the TFP scaffold. Such derivative compound hinders the development of pancreatic ductal adenocarcinoma (PDAC) in mice, by hampering nuclear translocation of NUPR1. Aiming to further improve the activity of ZZW-115, here we have used an indirect drug design approach to modify its chemical features, by changing the substituent attached to the piperazine ring. As a result, we have synthesized a series of compounds based on the same chemical scaffold. Isothermal titration calorimetry (ITC) showed that, with the exception of the compound preserving the same chemical moiety at the end of the alkyl chain as ZZW-115, an increase of the length by a single methylene group (i.e., ethyl to propyl) significantly decreased the affinity towards NUPR1 measured in vitro, whereas maintaining the same length of the alkyl chain and adding heterocycles favored the binding affinity. However, small improvements of the compound affinity towards NUPR1, as measured by ITC, did not result in a corresponding improvement in their inhibitory properties and in cellulo functions, as proved by measuring three different biological effects: hindrance of the nuclear translocation of the protein, sensitization of cells against DNA damage mediated by NUPR1, and prevention of cancer cell growth. Our findings suggest that a delicate compromise between favoring ligand affinity and controlling protein function may be required to successfully design drugs against NUPR1, and likely other IDPs. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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21 pages, 3798 KiB

Open AccessArticle

A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein

by Christophe Cardone, Claire-Marie Caseau, Benjamin Bardiaux, Aurélien Thureaux, Marie Galloux, Monika Bajorek, Jean-François Eléouët, Marc Litaudon, François Bontems and Christina Sizun

Biomolecules 2021, 11(8), 1225; https://doi.org/10.3390/biom11081225 - 17 Aug 2021

Cited by 6 | Viewed by 2432

Abstract

The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a [...] Read more.

The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (P_OD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV P_OD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of P_Cα, a domain that is C-terminal to P_OD and constitutes the RSV L-binding region together with P_OD. By using small phosphoprotein fragments centered on or adjacent to P_OD, we obtained a structural picture of the P_OD–P_Cα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed P_OD–P_Cα inter-domain contacts and showed that small molecules were able to modify the dynamics of P_Cα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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18 pages, 2653 KiB

Open AccessFeature PaperArticle

Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2

by David Ortega-Alarcon, Rafael Claveria-Gimeno, Sonia Vega, Olga C. Jorge-Torres, Manel Esteller, Olga Abian and Adrian Velazquez-Campoy

Biomolecules 2021, 11(8), 1216; https://doi.org/10.3390/biom11081216 - 16 Aug 2021

Cited by 10 | Viewed by 2662

Abstract

Intrinsic disorder plays an important functional role in proteins. Disordered regions are linked to posttranslational modifications, conformational switching, extra/intracellular trafficking, and allosteric control, among other phenomena. Disorder provides proteins with enhanced plasticity, resulting in a dynamic protein conformational/functional landscape, with well-structured and disordered [...] Read more.

Intrinsic disorder plays an important functional role in proteins. Disordered regions are linked to posttranslational modifications, conformational switching, extra/intracellular trafficking, and allosteric control, among other phenomena. Disorder provides proteins with enhanced plasticity, resulting in a dynamic protein conformational/functional landscape, with well-structured and disordered regions displaying reciprocal, interdependent features. Although lacking well-defined conformation, disordered regions may affect the intrinsic stability and functional properties of ordered regions. MeCP2, methyl-CpG binding protein 2, is a multifunctional transcriptional regulator associated with neuronal development and maturation. MeCP2 multidomain structure makes it a prototype for multidomain, multifunctional, intrinsically disordered proteins (IDP). The methyl-binding domain (MBD) is one of the key domains in MeCP2, responsible for DNA recognition. It has been reported previously that the two disordered domains flanking MBD, the N-terminal domain (NTD) and the intervening domain (ID), increase the intrinsic stability of MBD against thermal denaturation. In order to prove unequivocally this stabilization effect, ruling out any artifactual result from monitoring the unfolding MBD with a local fluorescence probe (the single tryptophan in MBD) or from driving the protein unfolding by temperature, we have studied the MBD stability by differential scanning calorimetry (reporting on the global unfolding process) and chemical denaturation (altering intramolecular interactions by a different mechanism compared to thermal denaturation). Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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16 pages, 6401 KiB

Open AccessArticle

Molecular Dynamics Simulations of Human FOXO3 Reveal Intrinsically Disordered Regions Spread Spatially by Intramolecular Electrostatic Repulsion

by Robert O.J. Weinzierl

Biomolecules 2021, 11(6), 856; https://doi.org/10.3390/biom11060856 - 8 Jun 2021

Cited by 11 | Viewed by 3467

Abstract

The human transcription factor FOXO3 (a member of the ‘forkhead’ family of transcription factors) controls a variety of cellular functions that make it a highly relevant target for intervention in anti-cancer and anti-aging therapies. FOXO3 is a mostly intrinsically disordered protein (IDP). Absence [...] Read more.

The human transcription factor FOXO3 (a member of the ‘forkhead’ family of transcription factors) controls a variety of cellular functions that make it a highly relevant target for intervention in anti-cancer and anti-aging therapies. FOXO3 is a mostly intrinsically disordered protein (IDP). Absence of knowledge of its structural properties outside the DNA-binding domain constitutes a considerable obstacle to a better understanding of structure/function relationships. Here, I present extensive molecular dynamics (MD) simulation data based on implicit solvation models of the entire FOXO3/DNA complex, and accelerated MD simulations under explicit solvent conditions of a central region of particular structural interest (FOXO3^120–530). A new graphical tool for studying and visualizing the structural diversity of IDPs, the Local Compaction Plot (LCP), is introduced. The simulations confirm the highly disordered nature of FOXO3 and distinguish various degrees of folding propensity. Unexpectedly, two ‘linker’ regions immediately adjacent to the DNA-binding domain are present in a highly extended conformation. This extended conformation is not due to their amino acid composition, but rather is caused by electrostatic repulsion of the domains connected by the linkers. FOXO3 is thus an IDP present in an unusually extended conformation to facilitate interaction with molecular interaction partners. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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10 pages, 919 KiB

Open AccessArticle

Protein–Protein Connections—Oligomer, Amyloid and Protein Complex—By Wide Line ¹H NMR

by Mónika Bokor and Ágnes Tantos

Biomolecules 2021, 11(5), 757; https://doi.org/10.3390/biom11050757 - 18 May 2021

Cited by 2 | Viewed by 2455

Abstract

The amount of bonds between constituting parts of a protein aggregate were determined in wild type (WT) and A53T α-synuclein (αS) oligomers, amyloids and in the complex of thymosin-β₄–cytoplasmic domain of stabilin-2 (Tβ₄-stabilin CTD). A53T αS aggregates have more [...] Read more.

The amount of bonds between constituting parts of a protein aggregate were determined in wild type (WT) and A53T α-synuclein (αS) oligomers, amyloids and in the complex of thymosin-β₄–cytoplasmic domain of stabilin-2 (Tβ₄-stabilin CTD). A53T αS aggregates have more extensive βsheet contents reflected by constant regions at low potential barriers in difference (to monomers) melting diagrams (MDs). Energies of the intermolecular interactions and of secondary structures bonds, formed during polymerization, fall into the 5.41 kJ mol⁻¹ ≤ E_a ≤ 5.77 kJ mol⁻¹ range for αS aggregates. Monomers lose more mobile hydration water while forming amyloids than oligomers. Part of the strong mobile hydration water–protein bonds break off and these bonding sites of the protein form intermolecular bonds in the aggregates. The new bonds connect the constituting proteins into aggregates. Amyloid–oligomer difference MD showed an overall more homogeneous solvent accessible surface of A53T αS amyloids. From the comparison of the nominal sum of the MDs of the constituting proteins to the measured MD of the Tβ₄-stabilin CTD complex, the number of intermolecular bonds connecting constituent proteins into complex is 20(1) H₂O/complex. The energies of these bonds are in the 5.40(3) kJ mol⁻¹ ≤ E_a ≤ 5.70(5) kJ mol⁻¹ range. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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13 pages, 2498 KiB

Open AccessArticle

Structural Analysis of the cl-Par-4 Tumor Suppressor as a Function of Ionic Environment

by Krishna K. Raut, Komala Ponniah and Steven M. Pascal

Biomolecules 2021, 11(3), 386; https://doi.org/10.3390/biom11030386 - 5 Mar 2021

Cited by 4 | Viewed by 2352

Abstract

Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at [...] Read more.

Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate the 25 kDa functionally active cleaved Par-4 protein (cl-Par-4) that inhibits NF-κB-mediated cell survival pathways and causes selective apoptosis in tumor cells. Here, we have employed circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) to assess the effects of various monovalent and divalent salts upon the conformation of cl-Par-4 in vitro. We have previously shown that high levels of sodium can induce the cl-Par-4 fragment to form highly compact, highly helical tetramers in vitro. Spectral characteristics suggest that most or at least much of the helical content in these tetramers are non-coiled coils. Here, we have shown that potassium produces a similar effect as was previously reported for sodium and that magnesium salts also produce a similar conformation effect, but at an approximately five times lower ionic concentration. We have also shown that anion identity has far less influence than does cation identity. The degree of helicity induced by each of these salts suggests that the “Selective for Apoptosis in Cancer cells” (SAC) domain—the region of Par-4 that is most indispensable for its apoptotic function—is likely to be helical in cl-Par-4 under the studied high salt conditions. Furthermore, we have shown that under medium-strength ionic conditions, a combination of high molecular weight aggregates and smaller particles form and that the smaller particles are also highly helical, resembling at least in secondary structure, the tetramers found at high salt. Full article

(This article belongs to the Special Issue The Amazing World of IDPs in Human Diseases II)

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