bims-indpro Biomed News
on Intrinsically disordered proteins
Issue of 2022–02–20
twenty papers selected by
Sara Mingu, Johannes Gutenberg University
  1. Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins.
  2. Modifying Amyloid Motif Aggregation Through Local Structure.
  3. Intrinsically disordered proteins play diverse roles in cell signaling.
  4. Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.
  5. Computational Models for the Study of Protein Aggregation.
  6. Predictive Modeling of Neurotoxic α-Synuclein Polymorphs.
  7. Intrinsically Disordered Proteins: Critical Components of the Wetware.
  8. ATP-responsive biomolecular condensates tune bacterial kinase signaling.
  9. Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.
  10. Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.
  11. The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT.
  12. Tau liquid-liquid phase separation in neurodegenerative diseases.
  13. Challenges in Discovering Drugs That Target the Protein-Protein Interactions of Disordered Proteins.
  14. Discovery of Neuroprotective Agents Based on a 5-(4-Pyridinyl)-1,2,4-triazole Scaffold.
  15. From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases.
  16. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.
  17. Prediction of liquid-liquid phase separating proteins using machine learning.
  18. New Evidence of the Importance of Weak Interactions in the Formation of PML-Bodies.
  19. A Microplate-Based Approach to Map Interactions between TDP-43 and α-Synuclein.
  20. Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.
  1. Methods Mol Biol. 2022 ;2340 105-120
    Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins.
    Marek Cieplak, Łukasz Mioduszewski, Mateusz Chwastyk.
      We review the contact-based description of aggregation of intrinsically disordered proteins in coarse-grained and all-atom models. We consider polyglutamines and polyalanines at various concentrations of the peptides. We also study associations of two chains of α-synuclein and up to 20 chains of a 12-residue-long segment of protein tau. We demonstrate that the total number of two-chain association events (in an aggregate that comprises at least two chains) provides a useful measure of the propensity to aggregate. This measure is consistent, for instance, with the previously reported mass spectroscopy data. The distribution of the number of association events is given essentially by a power law as a function of the duration of these events. The corresponding exponent depends on the protein and the temperature but not on the concentration of the proteins.
    Keywords:  Aggregation of proteins; Coarse-grained models; Contact map; Intrinsically disordered proteins; Molecular dynamics; PolyQ; Protein tau; α-Synuclein
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_6
  2. Methods Mol Biol. 2022 ;2340 343-356
    Modifying Amyloid Motif Aggregation Through Local Structure.
    Sofia Bali, Lukasz A Joachimiak.
      Protein assembly into β-sheet-rich amyloid structures is a general biophysical phenomenon that has significant biological consequences, most notable for their prominent association with neurodegenerative diseases, including Alzheimer's, Huntington's, or Parkinson's diseases. The assembly of amyloid structures is driven by short sequences called amyloid motifs. In many neurodegenerative diseases, intrinsically disordered proteins (IDPs) self-assemble through amyloid motifs, but these motifs are present in all proteins, including folded globular proteins. Importantly, mechanistic knowledge is lacking for how IDPs, which do not adopt a stable tertiary structure, mask these amyloidogenic motifs to mitigate or slow the formation of β-sheet-rich amyloid structures that cause disease. Our recent work has shown that local structural elements can modify the aggregation propensity of amyloid motifs in the intrinsically disordered microtubule-associated protein tau by adopting metastable β-hairpin-like structures that shield the amyloid motif, and disease-causing mutations change the conformation, thus increase aggregation propensity (Chen, Nat Commun 10:2493, 2019). Here we describe a protocol that correlates experimentally determined aggregation propensities for peptides measured by the Thioflavin T (ThT) fluorescence aggregation assay with their conformational ensembles derived from Groningen machine chemical simulations (GROMACS). Integration of experiment and simulation will help uncover structural rules behind changes in conformation that modulate protein aggregation. We anticipate that our general protocol will help identify key interactions in local structures that engage amyloid-forming motifs in IDPs which influence aggregation behavior.
    Keywords:  Amyloid motifs; Beta-turns; IDPs; Intrinsically disordered proteins; Molecular dynamics; Pathogenic mutations; Protein aggregation; Protein folding; Secondary structure
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_15
  3. Cell Commun Signal. 2022 Feb 17. 20(1): 20
    Intrinsically disordered proteins play diverse roles in cell signaling.
    Sarah E Bondos, A Keith Dunker, Vladimir N Uversky.
      Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
    Keywords:  Cell signal amplification; Differentiation; Integration; Propagation; Specificity
    DOI:  https://doi.org/10.1186/s12964-022-00821-7
  4. Chem Rev. 2022 Feb 18.
    Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.
    Anton Abyzov, Martin Blackledge, Markus Zweckstetter.
      Motions in biomolecules are critical for biochemical reactions. In cells, many biochemical reactions are executed inside of biomolecular condensates formed by ultradynamic intrinsically disordered proteins. A deep understanding of the conformational dynamics of intrinsically disordered proteins in biomolecular condensates is therefore of utmost importance but is complicated by diverse obstacles. Here we review emerging data on the motions of intrinsically disordered proteins inside of liquidlike condensates. We discuss how liquid-liquid phase separation modulates internal motions across a wide range of time and length scales. We further highlight the importance of intermolecular interactions that not only drive liquid-liquid phase separation but appear as key determinants for changes in biomolecular motions and the aging of condensates in human diseases. The review provides a framework for future studies to reveal the conformational dynamics of intrinsically disordered proteins in the regulation of biomolecular condensate chemistry.
    DOI:  https://doi.org/10.1021/acs.chemrev.1c00774
  5. Methods Mol Biol. 2022 ;2340 51-78
    Computational Models for the Study of Protein Aggregation.
    Nguyen Truong Co, Mai Suan Li, Pawel Krupa.
      Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
    Keywords:  AMBER; CHARMM; Coarse-grained model; GROMOS; Lattice model; OPLS; Protein aggregation
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_4
  6. Methods Mol Biol. 2022 ;2340 379-399
    Predictive Modeling of Neurotoxic α-Synuclein Polymorphs.
    Liang Xu, Shayon Bhattacharya, Damien Thompson.
      Assembly of monomeric α-synuclein (αS) into aggregation-resistant helically folded tetramers and related multimers is a key target for Parkinson's disease (PD). Protein dynamics hampers experimental characterization of the polymorphism of these structures and so computational modeling and simulation is providing a complementary approach to obtain high-resolution structural information on the assembly of αS and interactions with biological surfaces. These computational techniques are particularly valuable for intrinsically disordered proteins (IDPs) and short-lived peptide and protein assemblies with as yet undetermined 3D structures. Experimental observables such as NMR J-coupling constants and chemical shifts can be predicted directly from simulation data, and compared with available experimental data to generate the most physically realistic atomic-resolution structure. For appropriately validated and benchmarked computational models, macroscopic aggregation properties can be related to the calculated thermodynamic properties at an atomic level. In this chapter, we describe a useful protocol for designing helical αS multimers, especially tetramers, and scanning the peptide-membrane interface for cell-bound αS tetramers. These computationally modeled structures are validated by comparison with the range of available known experimental parameters at time of writing in early 2020, and used to generate predictive design rules to motivate and guide experiments.
    Keywords:  Directed self-assembly; Intrinsically disordered proteins (IDP); Molecular simulation; Neurodegeneration; Peptide –cell interactions
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_17
  7. Chem Rev. 2022 Feb 16.
    Intrinsically Disordered Proteins: Critical Components of the Wetware.
    Prakash Kulkarni, Supriyo Bhattacharya, Srisairam Achuthan, Amita Behal, Mohit Kumar Jolly, Sourabh Kotnala, Atish Mohanty, Govindan Rangarajan, Ravi Salgia, Vladimir Uversky.
      Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
    DOI:  https://doi.org/10.1021/acs.chemrev.1c00848
  8. Sci Adv. 2022 Feb 18. 8(7): eabm6570
    ATP-responsive biomolecular condensates tune bacterial kinase signaling.
    Saumya Saurabh, Trisha N Chong, Camille Bayas, Peter D Dahlberg, Heather N Cartwright, W E Moerner, Lucy Shapiro.
      Biomolecular condensates formed via liquid-liquid phase separation enable spatial and temporal organization of enzyme activity. Phase separation in many eukaryotic condensates has been shown to be responsive to intracellular adenosine triphosphate (ATP) levels, although the consequences of these mechanisms for enzymes sequestered within the condensates are unknown. Here, we show that ATP depletion promotes phase separation in bacterial condensates composed of intrinsically disordered proteins. Enhanced phase separation promotes the sequestration and activity of a client kinase enabling robust signaling and maintenance of viability under the stress posed by nutrient scarcity. We propose that a diverse repertoire of condensates can serve as control knobs to tune enzyme sequestration and reactivity in response to the metabolic state of bacterial cells.
    DOI:  https://doi.org/10.1126/sciadv.abm6570
  9. J Chem Theory Comput. 2022 Feb 17.
    Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.
    Lunna Li, Tommaso Casalini, Paolo Arosio, Matteo Salvalaglio.
      Intrinsically disordered proteins play a key role in many biological processes, including the formation of biomolecular condensates within cells. A detailed characterization of their configurational ensemble and structure-function paradigm is crucial for understanding their biological activity and for exploiting them as building blocks in material sciences. In this work, we incorporate bias-exchange metadynamics and parallel-tempering well-tempered metadynamics with CHARMM36m and CHARMM22* to explore the structural and thermodynamic characteristics of a short archetypal disordered sequence derived from a DEAD-box protein. The conformational landscapes emerging from our simulations are largely congruent across methods and force fields. Nevertheless, differences in fine details emerge from varying combinations of force-fields and sampling methods. For this protein, our analysis identifies features that help to explain the low propensity of this sequence to undergo self-association in vitro, which are common to all force-field/sampling method combinations. Overall, our work demonstrates the importance of using multiple force-field and sampling method combinations for accurate structural and thermodynamic information in the study of disordered proteins.
    DOI:  https://doi.org/10.1021/acs.jctc.1c00889
  10. ACS Synth Biol. 2022 Feb 18.
    Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.
    Mike T Veling, Dan T Nguyen, Nicole N Thadani, Michela E Oster, Nathan J Rollins, Kelly P Brock, Neville P Bethel, Samuel Lim, David Baker, Jeffrey C Way, Debora S Marks, Roger L Chang, Pamela A Silver.
      Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
    Keywords:  apoptosis; intrinsically disordered proteins; phase separation; stress tolerance
    DOI:  https://doi.org/10.1021/acssynbio.1c00572
  11. Int J Mol Sci. 2022 Jan 29. pii: 1589. [Epub ahead of print]23(3):
    The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT.
    Julie Ledoux, Alain Trouvé, Luba Tchertanov.
      RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains-the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events.
    Keywords:  allosteric regulation; conformational transition; free energy landscape; full-length KIT cytoplasmic region; intrinsically disordered regions; modelling; molecular dynamics; phosphotyrosine; receptor tyrosine kinase (RTK)
    DOI:  https://doi.org/10.3390/ijms23031589
  12. Trends Cell Biol. 2022 Feb 15. pii: S0962-8924(22)00026-5. [Epub ahead of print]
    Tau liquid-liquid phase separation in neurodegenerative diseases.
    Solomiia Boyko, Witold K Surewicz.
      Aggregation of the microtubule-associated protein tau plays a major role in Alzheimer's disease and several other neurodegenerative disorders. An exciting recent development is the finding that, akin to some other proteins associated with neurodegenerative disease, tau has a high propensity to condensate via the mechanism of liquid-liquid phase separation (LLPS). Here, we discuss the evidence for tau LLPS in vitro, the molecular mechanisms of this reaction, and the role of post-translational modifications and pathogenic mutations in tau phase separation. We also discuss recent studies on tau LLPS in cells and the insights these studies provide regarding the link between LLPS and neurodegeneration in tauopathies.
    Keywords:  liquid–liquid phase separation; neurodegenerative diseases; protein aggregation; protein condensation; tau
    DOI:  https://doi.org/10.1016/j.tcb.2022.01.011
  13. Int J Mol Sci. 2022 Jan 28. pii: 1550. [Epub ahead of print]23(3):
    Challenges in Discovering Drugs That Target the Protein-Protein Interactions of Disordered Proteins.
    Judit Oláh, Tibor Szénási, Attila Lehotzky, Victor Norris, Judit Ovádi.
      Protein-protein interactions (PPIs) outnumber proteins and are crucial to many fundamental processes; in consequence, PPIs are associated with several pathological conditions including neurodegeneration and modulating them by drugs constitutes a potentially major class of therapy. Classically, however, the discovery of small molecules for use as drugs entails targeting individual proteins rather than targeting PPIs. This is largely because discovering small molecules to modulate PPIs has been seen as extremely challenging. Here, we review the difficulties and limitations of strategies to discover drugs that target PPIs directly or indirectly, taking as examples the disordered proteins involved in neurodegenerative diseases.
    Keywords:  disordered proteins; drug target; neurodegeneration; protein–protein interaction
    DOI:  https://doi.org/10.3390/ijms23031550
  14. ACS Chem Neurosci. 2022 Feb 18.
    Discovery of Neuroprotective Agents Based on a 5-(4-Pyridinyl)-1,2,4-triazole Scaffold.
    Rosaria Gitto, Serena Vittorio, Federica Bucolo, Samuel Peña-Díaz, Rosalba Siracusa, Salvatore Cuzzocrea, Salvador Ventura, Rosanna Di Paola, Laura De Luca.
      Parkinson's disease (PD) is characterized by the death of dopaminergic neurons. The common histopathological hallmark in PD patients is the formation of intracellular proteinaceous accumulations. The main constituent of these inclusions is alpha-synuclein (α-syn), an intrinsically disordered protein that in pathological conditions creates amyloid aggregates that lead to neurotoxicity and neurodegeneration. The main goal of our study was to optimize our previously identified α-syn aggregation inhibitors of 5-(4-pyridinyl)-1,2,4-triazole chemotype in terms of in vivo efficacy. Our efforts resulted in the identification of ethyl 2-((4-amino-5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl)thio)acetate (15), which displayed the ability to prevent 1-methyl-4-phenyl-1,2,3,6-tetrahydropiridine-induced bradykinesia as well as to affect the levels of PD markers after the administration of the same neurotoxin. In addition to the in vivo evaluation, for the 5-(4-pyridinyl)-1,2,4-triazole-based compounds, we measured the prevention of the fibrillization process using light scattering and a ThT binding assay; these compounds have been shown to slightly reduce the α-syn aggregation.
    Keywords:  5-(4-pyridinyl)-1,2,4-triazoles; MPTP; Parkinson’s disease; alpha synuclein; synthesis
    DOI:  https://doi.org/10.1021/acschemneuro.1c00849
  15. Methods Mol Biol. 2022 ;2340 139-173
    From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases.
    Orkid Coskuner-Weber, M Gokhan Habiboglu, David Teplow, Vladimir N Uversky.
      The amyloid β-protein is an intrinsically disordered protein that has the potential to assemble into myriad structures, including oligomers and fibrils. These structures are neurotoxic and are thought to initiate a cascade of events leading to Alzheimer's disease. Understanding this pathogenetic process and elucidating targets for drug therapy depends on elucidation of the structural dynamics of Aβ assembly. In this chapter, we describe work packages required to determine the three-dimensional structures of Aβ and of smaller bioactive fragments thereof, which may be important in AD pathogenesis. These packages include density functional theory, Car-Parrinello molecular dynamics simulations, temperature-dependent replica exchange molecular dynamics simulations, disorder predictors based on bioinformatics, and neural network deep learning.
    Keywords:  CPMD simulations; DFT; Deep learning; Disorder predictors; T-REMD simulations
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_8
  16. Methods Mol Biol. 2022 ;2340 401-448
    Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.
    Shayon Bhattacharya, Liang Xu, Damien Thompson.
      Prototypical amyloidogenic peptides amyloid-β (Aβ) and α-synuclein (αS) can undergo helix-helix associations via partially folded helical conformers, which may influence pathological progression to Alzheimer's (AD) and Parkinson's disease (PD), respectively. At the other extreme, stable folded helical conformers have been reported to resist self-assembly and amyloid formation. Experimental characterisation of such disparities in aggregation profiles due to subtle differences in peptide stabilities is precluded by the conformational heterogeneity of helical subspace. The diverse physical models used in molecular simulations allow sampling distinct regions of the phase space and are extensive in capturing the ensemble of rich helical subspace. Robust and powerful computational predictive methods utilizing network theory and free energy mapping can model the origin of helical population shifts in amyloidogenic peptides, which highlight their inherent aggregability. In this chapter, we discuss computational models, methods, design rules, and strategies to identify the driving force behind helical self-assembly and the molecular origin of aggregation resistance in helical intermediates of Aβ42 and αS. By extensive multiscale mapping of intrapeptide interactions, we show that the computational models can capture features that are otherwise imperceptible to experiments. Our models predict that targeting terminal residues may allow modulation and control of initial pathogenic aggregability of amyloidogenic peptides.
    Keywords:  Central hydrophobic domain; Charged terminal groups; Cross-correlation network analyses; Helical intermediates; Intrinsically disordered proteins; Molecular dynamics simulations; Neurodegenerative disease; Peptide self-assembly; Predictive molecular design
    DOI:  https://doi.org/10.1007/978-1-0716-1546-1_18
  17. BMC Bioinformatics. 2022 Feb 15. 23(1): 72
    Prediction of liquid-liquid phase separating proteins using machine learning.
    Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei.
       BACKGROUND: The liquid-liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular function. Dysregulation of LLPS is implicated in a number of diseases. Although the LLPS of biomolecules has been investigated intensively in recent years, the knowledge of the prevalence and distribution of phase separation proteins (PSPs) is still lag behind. Development of computational methods to predict PSPs is therefore of great importance for comprehensive understanding of the biological function of LLPS.
    RESULTS: Based on the PSPs collected in LLPSDB, we developed a sequence-based prediction tool for LLPS proteins (PSPredictor), which is an attempt at general purpose of PSP prediction that does not depend on specific protein types. Our method combines the componential and sequential information during the protein embedding stage, and, adopts the machine learning algorithm for final predicting. The proposed method achieves a tenfold cross-validation accuracy of 94.71%, and outperforms previously reported PSPs prediction tools. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which is accessible for prediction of potential PSPs.
    CONCLUSIONS: PSPredictor could identifie novel scaffold proteins for stress granules and predict PSPs candidates in the human genome for further study. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which provides valuable information for potential PSPs recognition.
    Keywords:  Liquid–liquid phase separation (LLPS); Machine learning; Phase separation proteins (PSPs); Predictor
    DOI:  https://doi.org/10.1186/s12859-022-04599-w
  18. Int J Mol Sci. 2022 Jan 30. pii: 1613. [Epub ahead of print]23(3):
    New Evidence of the Importance of Weak Interactions in the Formation of PML-Bodies.
    Alexander V Fonin, Sergey A Silonov, Anna S Fefilova, Olesya V Stepanenko, Anastasia A Gavrilova, Alexey V Petukhov, Anna E Romanovich, Anna L Modina, Tatiana S Zueva, Evgeniy M Nedelyaev, Nadejda M Pleskach, Mirya L Kuranova, Irina M Kuznetsova, Vladimir N Uversky, Konstantin K Turoverov.
      In this work, we performed a comparative study of the formation of PML bodies by full-length PML isoforms and their C-terminal domains in the presence and absence of endogenous PML. Based on the analysis of the distribution of intrinsic disorder predisposition in the amino acid sequences of PML isoforms, regions starting from the amino acid residue 395 (i.e., sequences encoded by exons 4-6) were assigned as the C-terminal domains of these proteins. We demonstrate that each of the full-sized nuclear isoforms of PML is capable of forming nuclear liquid-droplet compartments in the absence of other PML isoforms. These droplets possess dynamic characteristics of the exchange with the nucleoplasm close to those observed in the wild-type cells. Only the C-terminal domains of the PML-II and PML-V isoforms are able to be included in the composition of the endogenous PML bodies, while being partially distributed in the nucleoplasm. The bodies formed by the C-terminal domain of the PML-II isoform are dynamic liquid droplet compartments, regardless of the presence or absence of endogenous PML. The C-terminal domain of PML-V forms dynamic liquid droplet compartments in the knockout cells (PML-/-), but when the C-terminus of the PML-V isoform is inserted into the existing endogenous PML bodies, the molecules of this protein cease to exchange with the nucleoplasm. It was demonstrated that the K490R substitution, which disrupts the PML sumoylation, promotes diffuse distribution of the C-terminal domains of PML-II and PML-V isoforms in endogenous PML knockout HeLa cells, but not in the wild-type cells. These data indicate the ability of the C-terminal domains of the PML-II and PML-V isoforms to form dynamic liquid droplet-like compartments, regardless of the ordered N-terminal RBCC motifs of the PML. This indicates a significant role of the non-specific interactions between the mostly disordered C-terminal domains of PML isoforms for the initiation of liquid-liquid phase separation (LLPS) leading to the formation of PML bodies.
    Keywords:  PML-bodies; acute hydrogen peroxide-induced oxidative stress; fluorescence recovery after photobleaching (FRAP); liquid–liquid phase separation (LLPS); membrane-less organelles (MLOs); promyelocytic leukemia protein (PML) isoforms
    DOI:  https://doi.org/10.3390/ijms23031613
  19. J Clin Med. 2022 Jan 24. pii: 573. [Epub ahead of print]11(3):
    A Microplate-Based Approach to Map Interactions between TDP-43 and α-Synuclein.
    Angelo M Jamerlan, Seong Soo A An.
      Trans-active response DNA-binding protein (TDP-43) is a multifunctional regulatory protein, whose abnormal deposition in neurons was linked to debilitating neurodegenerative diseases, such as amyotrophic lateral sclerosis, frontotemporal lobar degeneration, Limbic-predominant age-related TDP-43 encephalopathy, and Alzheimer's disease with a secondary pathology. Several reports showed that TDP-43 proteinopathy as a comorbidity can form aggregates with other pathological proteins. The co-deposition of alpha synuclein and TDP-43 inclusions was previously reported in glial cells and by observing TDP-43 proteinopathy in Lewy body disease. In this study, it was hypothesized that alpha synuclein and TDP-43 may co-aggregate, resulting in comorbid synucleinopathy and TDP-43 proteinopathy. A solid-phase microplate-based immunoassay was used to map out the epitopes of anti-TDP-43 antibodies and locate the interaction of TDP-43 with α-synuclein. A region of the low complexity domain of TDP-43 (aa 311-314) was shown to interact with full-length α-synuclein. Conversely, full-length TDP-43 was shown to bind to the non-amyloid beta component of α-synuclein. Using in silico sequence-based prediction, the affinity and dissociation constant of full-length TDP-43 and α-synuclein were calculated to be -10.83 kcal/mol and 1.13 × 10-8, respectively. Taken together, this microplate-based method is convenient, economical, and rapid in locating antibody epitopes as well as interaction sites of two proteins.
    Keywords:  ELISA; TDP-43; aggregation; alpha synuclein; comorbidity; epitope mapping; proteinopathy
    DOI:  https://doi.org/10.3390/jcm11030573
  20. Nat Struct Mol Biol. 2022 Feb;29(2): 130-142
    Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.
    Veselin I Andreev, Changwei Yu, Juncheng Wang, Jakob Schnabl, Laszlo Tirian, Maja Gehre, Dominik Handler, Peter Duchek, Maria Novatchkova, Lisa Baumgartner, Katharina Meixner, Grzegorz Sienski, Dinshaw J Patel, Julius Brennecke.
      Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors on binding to nascent target RNAs are poorly understood. Here, we explain the mechanism by which the PIWI-interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. We find that Panoramix, a corepressor required for piRNA-guided heterochromatin formation, is SUMOylated on chromatin in a Piwi-dependent manner. SUMOylation, together with an amphipathic LxxLL motif in Panoramix's intrinsically disordered repressor domain, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc-finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that eliminate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, Piwi engages the heterochromatin machinery specifically at transposon loci by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation.
    DOI:  https://doi.org/10.1038/s41594-022-00721-x
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:17.