Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

: Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations – including our own – revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

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Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies

International Journal of Molecular Sciences ◽

10.3390/ijms20061322 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1322 ◽

Cited By ~ 12

Author(s):

Anne Martinelli ◽

Fernanda Lopes ◽

Elisa John ◽

Célia Carlini ◽

Rodrigo Ligabue-Braun

Keyword(s):

Neurodegenerative Diseases ◽

Structural Changes ◽

Intrinsically Disordered Proteins ◽

Alpha Synuclein ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Future Developments ◽

Regulatory Metabolism ◽

Eukaryotic Genomes ◽

New Strategies

Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.

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Multisite Phosphorylation and Binding Alter Conformational Dynamics of the 4E-BP2 Protein

10.1101/2022.01.14.476386 ◽

2022 ◽

Author(s):

Spencer Smyth ◽

Zhenfu Zhang ◽

Alaji Bah ◽

Thomas Tsangaris ◽

Jennifer Dawson ◽

...

Keyword(s):

Conformational Changes ◽

Intrinsically Disordered Proteins ◽

Regulatory Protein ◽

Conformational Dynamics ◽

Correlation Spectroscopy ◽

Terminal Region ◽

Disordered Proteins ◽

Initiation Factor ◽

Dependent Manner ◽

Intrinsically Disordered

Intrinsically disordered proteins (IDPs) play critical roles in regulatory protein interactions, but detailed structural/dynamics characterization of their ensembles remain challenging, both in isolation and they form dynamic fuzzy complexes. Such is the case for mRNA cap-dependent translation initiation, which is regulated by the interaction of the predominantly folded eukaryotic initiation factor 4E (eIF4E) with the intrinsically disordered eIF4E binding proteins (4E-BPs) in a phosphorylation-dependent manner. Single-molecule Forster resonance energy transfer showed that the conformational changes of 4E-BP2 induced by binding to eIF4E are non-uniform along the sequence; while a central region containing both motifs that bind to eIF4E expands and becomes stiffer, the C-terminal region is less affected. Fluorescence anisotropy decay revealed a nonuniform segmental flexibility around six different labelling sites along the chain. Dynamic quenching of these fluorescent probes by intrinsic aromatic residues measured via fluorescence correlation spectroscopy report on transient intra- and inter-molecular contacts on nanosecond-microsecond timescales. Upon hyperphosphorylation, which induces folding of ~40 residues in 4E-BP2, the quenching rates decreased at labelling sites closest to the phosphorylation sites and within the folded domain, and increased at the other sites. The chain dynamics around sites in the C-terminal region far away from the two binding motifs were significantly reduced upon binding to eIF4E, suggesting that this region is also involved in the highly dynamic 4E-BP2:eIF4E complex. Our time-resolved fluorescence data paint a sequence-level rigidity map of three states of 4E-BP2 differing in phosphorylation or binding status and distinguish regions that form contacts with eIF4E. This study adds complementary structural and dynamics information to recent studies of 4E-BP2, and it constitutes an important step towards a mechanistic understanding of this important IDP via integrative modelling.

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Ensemble allosteric model: energetic frustration within the intrinsically disordered glucocorticoid receptor

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0175 ◽

2018 ◽

Vol 373 (1749) ◽

pp. 20170175 ◽

Cited By ~ 10

Author(s):

Jordan T. White ◽

Jing Li ◽

Emily Grasso ◽

James O. Wrabl ◽

Vincent J. Hilser

Keyword(s):

Glucocorticoid Receptor ◽

Conformational Changes ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Coupling Energy ◽

Precise Control ◽

Intrinsically Disordered ◽

Protein Allostery ◽

Multiple Interfaces ◽

Allosteric Model

Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins. One central finding from this model is that energetic coupling, the transmission of a signal between separate regions (or domains) of a protein, is maximized when one or more domains are disordered. This is due to a disorder–order transition that contributes additional coupling energy to the allosteric system through formation of a molecular interaction surface or interface. A second key finding is that multiple interfaces may constructively or destructively interfere with each other, resulting in a new form of allosteric regulation called ‘energetic frustration’. Articulating protein allostery in terms of the thermodynamic ensemble permits formulation of experimentally testable hypotheses which can increase fundamental understanding and direct drug-design efforts. These ideas are illustrated here with the specific case of human glucocorticoid receptor, a medically important multi-domain allosteric protein that contains both structured and disordered regions and exemplifies ‘energetic frustration’. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.

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Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics ◽

10.1016/j.bbapap.2019.07.013 ◽

2019 ◽

Vol 1867 (11) ◽

pp. 140260 ◽

Cited By ~ 5

Author(s):

Gopa Mitra

Keyword(s):

Mass Spectrometry ◽

Neurodegenerative Diseases ◽

Intrinsically Disordered Proteins ◽

Native Mass Spectrometry ◽

Disordered Proteins ◽

Special Focus ◽

Intrinsically Disordered

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Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1914349117 ◽

2020 ◽

Vol 117 (33) ◽

pp. 19953-19962

Author(s):

Takuya Mizukami ◽

Shunta Furuzawa ◽

Satoru G. Itoh ◽

Saho Segawa ◽

Teikichi Ikura ◽

...

Keyword(s):

Conformational Changes ◽

Intrinsically Disordered Proteins ◽

Flux Ratio ◽

Staphylococcal Nuclease ◽

Binding Energies ◽

Disordered Proteins ◽

Flux Analysis ◽

Intrinsically Disordered ◽

Substrate Analog ◽

Statistical Mechanical

Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled intra- and intermolecular events. Such reactions are often discussed in terms of two limiting kinetic mechanisms, conformational selection (CS), where folding precedes binding, and induced fit (IF), where binding precedes folding. It has been shown that coupled folding/binding reactions can proceed along both CS and IF pathways with the flux ratio depending on conditions such as ligand concentration. However, the structural and energetic basis of such complex reactions remains poorly understood. Therefore, we used experimental, theoretical, and computational approaches to explore structural and energetic aspects of the coupled-folding/binding reaction of staphylococcal nuclease in the presence of the substrate analog adenosine-3′,5′-diphosphate. Optically monitored equilibrium and kinetic data, combined with a statistical mechanical model, gave deeper insight into the relative importance of specific and Coulombic protein–ligand interactions in governing the reaction mechanism. We also investigated structural aspects of the reaction at the residue level using NMR and all-atom replica-permutation molecular dynamics simulations. Both approaches yielded clear evidence for accumulation of a transient protein–ligand encounter complex early in the reaction under IF-dominant conditions. Quantitative analysis of the equilibrium/kinetic folding revealed that the ligand-dependent CS-to-IF shift resulted from stabilization of the compact transition state primarily by weakly ligand-dependent Coulombic interactions with smaller contributions from specific binding energies. At a more macroscopic level, the CS-to-IF shift was represented as a displacement of the reaction “route” on the free energy surface, which was consistent with a flux analysis.

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Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy

International Journal of Molecular Sciences ◽

10.3390/ijms20205181 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5181 ◽

Cited By ~ 2

Author(s):

Roberta Corti ◽

Claudia A. Marrano ◽

Domenico Salerno ◽

Stefania Brocca ◽

Antonino Natalello ◽

...

Keyword(s):

Mass Spectrometry ◽

Single Molecule ◽

Conformational Changes ◽

Intrinsically Disordered Proteins ◽

Force Spectroscopy ◽

Native Mass Spectrometry ◽

Disordered Proteins ◽

Unique Contribution ◽

Single Molecule Force Spectroscopy ◽

Intrinsically Disordered

Description of heterogeneous molecular ensembles, such as intrinsically disordered proteins, represents a challenge in structural biology and an urgent question posed by biochemistry to interpret many physiologically important, regulatory mechanisms. Single-molecule techniques can provide a unique contribution to this field. This work applies single molecule force spectroscopy to probe conformational properties of α-synuclein in solution and its conformational changes induced by ligand binding. The goal is to compare data from such an approach with those obtained by native mass spectrometry. These two orthogonal, biophysical methods are found to deliver a complex picture, in which monomeric α-synuclein in solution spontaneously populates compact and partially compacted states, which are differently stabilized by binding to aggregation inhibitors, such as dopamine and epigallocatechin-3-gallate. Analyses by circular dichroism and Fourier-transform infrared spectroscopy show that these transitions do not involve formation of secondary structure. This comparative analysis provides support to structural interpretation of charge-state distributions obtained by native mass spectrometry and helps, in turn, defining the conformational components detected by single molecule force spectroscopy.

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Protein conformation as a regulator of cell–matrix adhesion

Physical Chemistry Chemical Physics ◽

10.1039/c3cp54884h ◽

2014 ◽

Vol 16 (14) ◽

pp. 6342-6357 ◽

Cited By ~ 27

Author(s):

Vesa P. Hytönen ◽

Bernhard Wehrle-Haller

Keyword(s):

Conformational Changes ◽

Posttranslational Modifications ◽

Protein Conformation ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Matrix Adhesion ◽

Cell Matrix ◽

Conformational Regulation ◽

Cell Matrix Adhesion

Conformational changes within proteins play key roles in the regulation of cell–matrix adhesion. We discuss the mechanisms involved in conformational regulation, including mechanical signals, posttranslational modifications and intrinsically disordered proteins.

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