bims-indpro Biomed News
on Intrinsically disordered proteins
Issue of 2022–04–24
thirteen papers selected by
Sara Mingu, Johannes Gutenberg University
  1. idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R.
  2. Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions.
  3. Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.).
  4. Backbone NMR assignments of the extensive human and chicken TRPV4 N-terminal intrinsically disordered regions as important players in ion channel regulation.
  5. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.
  6. IGF-dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2.
  7. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins.
  8. α-Synuclein Fibrils as Penrose Machines: A Chameleon in the Gear.
  9. Generating Ensembles of Dynamic Misfolding Proteins.
  10. The intrinsically disordered CARDs-Helicase linker in RIG-I is a molecular gate for RNA proofreading.
  11. Development of Low-Molecular-Weight Compounds Targeting the Cancer-Associated KLF5 Transcription Factor.
  12. Insights Into the Role of Heat Shock Protein 27 in the Development of Neurodegeneration.
  13. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept.
  1. PLoS One. 2022 ;17(4): e0266929
    idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R.
    William M McFadden, Judith L Yanowitz.
      Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are proteins or protein-domains that do not have a single native structure, rather, they are a class of flexible peptides that can rapidly adopt multiple conformations. IDPs are quite abundant, and their dynamic characteristics provide unique advantages for various biological processes. The field of "unstructured biology" has emerged, in part, because of numerous computational studies that had identified the unique characteristics of IDPs and IDRs. The package 'idpr', short for Intrinsically Disordered Proteins in R, implements several R functions that match the established characteristics of IDPs to protein sequences of interest. This includes calculations of residue composition, charge-hydropathy relationships, and predictions of intrinsic disorder. Additionally, idpr integrates several amino acid substitution matrices and calculators to supplement IDP-based workflows. Overall, idpr aims to integrate tools for the computational analysis of IDPs within R, facilitating the analysis of these important, yet under-characterized, proteins. The idpr package can be downloaded from Bioconductor (https://bioconductor.org/packages/idpr/).
    DOI:  https://doi.org/10.1371/journal.pone.0266929
  2. J Membr Biol. 2022 Apr 22.
    Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions.
    Chandra Has, P Sivadas, Sovan Lal Das.
      Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein's ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure-function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
    Keywords:  Disordered proteins; Entropic effect; Membrane curvature; Protein–membrane interactions
    DOI:  https://doi.org/10.1007/s00232-022-00237-x
  3. Biomolecules. 2022 Apr 18. pii: 592. [Epub ahead of print]12(4):
    Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.).
    Miloš Avramov, Éva Schád, Ágnes Révész, Lilla Turiák, Iva Uzelac, Ágnes Tantos, László Drahos, Željko D Popović.
      Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that combines wet lab methods with bioinformatics tools to identify and analyze intrinsically disordered proteins in a non-model insect species that is cold-hardy. Due to their known resilience to the effects of extreme temperatures, these proteins likely play important roles in this insect's adaptive mechanisms to sub-zero temperatures. The approach involves IDP enrichment by sample heating and double-digestion of proteins, followed by peptide and protein identification. Next, proteins are bioinformatically analyzed for disorder content, presence of long disordered regions, amino acid composition, and processes they are involved in. Finally, IDP detection is validated with an in-house 2D PAGE. In total, 608 unique proteins were identified, with 39 being mostly disordered, 100 partially disordered, 95 nearly ordered, and 374 ordered. One-third contain at least one long disordered segment. Functional information was available for only 90 proteins with intrinsic disorders out of 312 characterized proteins. Around half of the 90 proteins are cytoskeletal elements or involved in translational processes.
    Keywords:  IUPred analysis; LC–MS/MS; Ostrinia nubilalis; cold hardiness; intrinsically disordered protein regions (IDRs); intrinsically disordered proteins (IDPs)
    DOI:  https://doi.org/10.3390/biom12040592
  4. Biomol NMR Assign. 2022 Apr 22.
    Backbone NMR assignments of the extensive human and chicken TRPV4 N-terminal intrinsically disordered regions as important players in ion channel regulation.
    Benedikt Goretzki, Frederike Tebbe, Sarah-Ana Mitrovic, Ute A Hellmich.
      Transient receptor potential (TRP) channels are important pharmacological targets due to their ability to act as sensory transducers on the organismic and cellular level, as polymodal signal integrators and because of their role in numerous diseases. However, a detailed molecular understanding of the structural dynamics of TRP channels and their integration into larger cellular signalling networks remains challenging, in part due to the systematic absence of highly dynamic regions pivotal for channel regulation from available structures. In human TRP vanilloid 4 (TRPV4), a ubiquitously expressed homotetrameric cation channel involved in temperature, osmo- and mechano-sensation and in a multitude of (patho)physiological processes, the intrinsically disordered N-terminus encompasses 150 amino acids and thus represents > 17% of the entire channel sequence. Its deletion renders the channel significantly less excitable to agonists supporting a crucial role in TRPV4 activation and regulation. For a structural understanding and a comparison of its properties across species, we determined the NMR backbone assignments of the human and chicken TRPV4 N-terminal IDRs.
    Keywords:  Intrinsically disordered protein; Ion channel; Regulatory domain; Structural dynamics; TRP vanilloid; Transient receptor potential
    DOI:  https://doi.org/10.1007/s12104-022-10080-9
  5. Chem Rev. 2022 Apr 21.
    NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.
    Aldo R Camacho-Zarco, Vincent Schnapka, Serafima Guseva, Anton Abyzov, Wiktor Adamski, Sigrid Milles, Malene Ringkjøbing Jensen, Lukas Zidek, Nicola Salvi, Martin Blackledge.
      Intrinsically disordered proteins are ubiquitous throughout all known proteomes, playing essential roles in all aspects of cellular and extracellular biochemistry. To understand their function, it is necessary to determine their structural and dynamic behavior and to describe the physical chemistry of their interaction trajectories. Nuclear magnetic resonance is perfectly adapted to this task, providing ensemble averaged structural and dynamic parameters that report on each assigned resonance in the molecule, unveiling otherwise inaccessible insight into the reaction kinetics and thermodynamics that are essential for function. In this review, we describe recent applications of NMR-based approaches to understanding the conformational energy landscape, the nature and time scales of local and long-range dynamics and how they depend on the environment, even in the cell. Finally, we illustrate the ability of NMR to uncover the mechanistic basis of functional disordered molecular assemblies that are important for human health.
    DOI:  https://doi.org/10.1021/acs.chemrev.1c01023
  6. Proteins. 2022 Apr 20.
    IGF-dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2.
    Garima Jaipuria, Divya Shet, Shahid Malik, Monalisa Swain, Hanudatta S Atreya, Charles A Galea, Mark G Slomiany, Steven A Rosenzweig, Briony E Forbes, Raymond S Norton, Somnath Mondal.
      Functional regulation via conformational dynamics is well known in structured proteins, but less well characterized in intrinsically disordered proteins and their complexes. Using NMR spectroscopy we have identified a dynamic regulatory mechanism in the human insulin-like growth factor (IGF) system involving the central, intrinsically disordered linker domain of human IGF-binding protein-2 (hIGFBP2). The bioavailability of IGFs is regulated by the proteolysis of IGF-binding proteins. In the case of hIGFBP2, the linker domain (L-hIGFBP2) retains its intrinsic disorder upon binding IGF-1 but its dynamics are significantly altered, both in the IGF binding region and distantly located protease cleavage sites. The increase in flexibility of the linker domain upon IGF-1 binding may explain the IGF-dependent modulation of proteolysis of IGFBP2 in this domain. As IGF homeostasis is important for cell growth and function, and its dysregulation is a key contributor to several cancers, our findings open up new avenues for the design of IGFBP analogs inhibiting IGF-dependent tumors.
    DOI:  https://doi.org/10.1002/prot.26350
  7. Biomolecules. 2022 Apr 09. pii: 561. [Epub ahead of print]12(4):
    Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins.
    Greta Bianchi, Marco Mangiagalli, Alberto Barbiroli, Sonia Longhi, Rita Grandori, Carlo Santambrogio, Stefania Brocca.
      Intrinsically disordered proteins (IDPs) are ensembles of interconverting conformers whose conformational properties are governed by several physico-chemical factors, including their amino acid composition and the arrangement of oppositely charged residues within the primary structure. In this work, we investigate the effects of charge patterning on the average compactness and shape of three model IDPs with different proline content. We model IDP ensemble conformations as ellipsoids, whose size and shape are calculated by combining data from size-exclusion chromatography and native mass spectrometry. For each model IDP, we analyzed the wild-type protein and two synthetic variants with permuted positions of charged residues, where positive and negative amino acids are either evenly distributed or segregated. We found that charge clustering induces remodeling of the conformational ensemble, promoting compaction and/or increasing spherical shape. Our data illustrate that the average shape and volume of the ensembles depend on the charge distribution. The potential effect of other factors, such as chain length, number of proline residues, and secondary structure content, is also discussed. This methodological approach is a straightforward way to model IDP average conformation and decipher the salient sequence attributes influencing IDP structural properties.
    Keywords:  average shape of conformational ensembles; charge clustering; charged-residue patterning; conformational compactness; ellipsoid model; hydrodynamic radius; polyelectrolytes; proline content; solvent-accessible surface area
    DOI:  https://doi.org/10.3390/biom12040561
  8. Biomolecules. 2022 Mar 24. pii: 494. [Epub ahead of print]12(4):
    α-Synuclein Fibrils as Penrose Machines: A Chameleon in the Gear.
    Francesca De Giorgi, Vladimir N Uversky, François Ichas.
      In 1957, Lionel Penrose built the first man-made self-replicating mechanical device and illustrated its function in a series of machine prototypes, prefiguring our current view of the genesis and the proliferation of amyloid fibrils. He invented and demonstrated, with the help of his son Roger, the concepts that decades later, would become the fundamentals of prion and prion-like neurobiology: nucleation, seeding and conformational templating of monomers, linear polymer elongation, fragmentation, and spread. He published his premonitory discovery in a movie he publicly presented at only two conferences in 1958, a movie we thus reproduce here. By making a 30-year-jump in the early 90's, we evoke the studies performed by Peter Lansbury and his group in which α-Synuclein (α-Syn) was for the first time (i) compared to a prion; (ii) shown to contain a fibrillization-prone domain capable of seeding its own assembly into fibrils; (iii) identified as an intrinsically disordered protein (IDP), and which, in the early 2000s, (iv) was described by one of us as a protein chameleon. We use these temporally distant breakthroughs to propose that the combination of the chameleon nature of α-Syn with the rigid gear of the Penrose machine is sufficient to account for a phenomenon that is of current interest: the emergence and the spread of a variety of α-Syn fibril strains in α-Synucleinopathies.
    Keywords:  Parkinson’s disease; PrP; amyloid; fibril; intrinsically disordered protein; prion; seeding; self-replication; strain; sup35; templating; α-Synuclein
    DOI:  https://doi.org/10.3390/biom12040494
  9. Front Neurosci. 2022 ;16 881534
    Generating Ensembles of Dynamic Misfolding Proteins.
    Theodoros K Karamanos, Arnout P Kalverda, Sheena E Radford.
      The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
    Keywords:  NMR spectroscopy; ensemble calculations; intrinsic disorder; machine learning; oligomerization; protein misfolding
    DOI:  https://doi.org/10.3389/fnins.2022.881534
  10. EMBO J. 2022 Apr 19. e109782
    The intrinsically disordered CARDs-Helicase linker in RIG-I is a molecular gate for RNA proofreading.
    Brandon D Schweibenz, Swapnil C Devarkar, Mihai Solotchi, Candice Craig, Jie Zheng, Bruce D Pascal, Samantha Gokhale, Ping Xie, Patrick R Griffin, Smita S Patel.
      The innate immune receptor RIG-I provides a first line of defense against viral infections. Viral RNAs are recognized by RIG-I's C-terminal domain (CTD), but the RNA must engage the helicase domain to release the signaling CARD (Caspase Activation and Recruitment Domain) domains from their autoinhibitory CARD2:Hel2i interactions. Because the helicase itself lacks RNA specificity, mechanisms to proofread RNAs entering the helicase domain must exist. Although such mechanisms would be crucial in preventing aberrant immune responses by non-specific RNAs, they remain largely uncharacterized to date. This study reveals a previously unknown proofreading mechanism through which RIG-I ensures that the helicase engages RNAs explicitly recognized by the CTD. A crucial part of this mechanism involves the intrinsically disordered CARDs-Helicase Linker (CHL), which connects the CARDs to the helicase subdomain Hel1. CHL uses its negatively charged regions to antagonize incoming RNAs electrostatically. In addition to this RNA gating function, CHL is essential for stabilization of the CARD2:Hel2i interface. Overall, we uncover that the CHL and CARD2:Hel2i interface work together to establish a tunable gating mechanism that allows CTD-chosen RNAs to bind the helicase domain, while at the same time blocking non-specific RNAs. These findings also indicate that CHL could represent a novel target for RIG-I-based therapeutics.
    Keywords:  RIG-I; RNA discrimination; intrinsically disordered linker; regulatory region; self-vs-non-self
    DOI:  https://doi.org/10.15252/embj.2021109782
  11. ACS Med Chem Lett. 2022 Apr 14. 13(4): 687-694
    Development of Low-Molecular-Weight Compounds Targeting the Cancer-Associated KLF5 Transcription Factor.
    Takeo Nakaya, Kenichi Aizawa, Yuki Taguchi, Kentaro Tsuji, Sachi Sekine, Kazuhiro Murakami, Masaji Kasai, Hirofumi Nakano, Yasumitsu Kondoh, Shingo Dan, Atsushi Yoshimori, Hiroyuki Kouji, Dai Takehara, Toru Suzuki, Hiroyuki Osada, Masayuki Murata, Akira Tanaka, Ryozo Nagai.
      Krüppel-like factor 5 (KLF5) is a potential target for anticancer drugs. However, as an intrinsically disordered protein (IDP) whose tertiary structure cannot be solved, innovative strategies are needed. We focused on its hydrophobic α-helix structure, defined as an induced helical motif (IHM), which is a possible interface for protein-protein interaction. Using mathematical analyses predicting the α-helix's structure and hydrophobicity, a 4-amino-acid site (V-A-I-F) was identified as an IHM. Low-molecular-weight compounds that mimic the main chain conformation of the α-helix with the four side chains of V-A-I-F were synthesized using bicyclic pyrazinooxadiazine-4,7-dione. These compounds selectively suppressed the proliferation and survival of cancer cells but not noncancer cells and decreased the protein but not mRNA levels of KLF5 in addition to reducing proteins of Wnt signaling. The compounds further suppressed transplanted colorectal cancer cells in vivo without side effects. Our approach appears promising for developing drugs against key IDPs.
    DOI:  https://doi.org/10.1021/acsmedchemlett.1c00721
  12. Front Mol Neurosci. 2022 ;15 868089
    Insights Into the Role of Heat Shock Protein 27 in the Development of Neurodegeneration.
    Bianka A Holguin, Zacariah L Hildenbrand, Ricardo A Bernal.
      Small heat shock protein 27 is a critically important chaperone, that plays a key role in several essential and varied physiological processes. These include thermotolerance, apoptosis, cytoskeletal dynamics, cell differentiation, protein folding, among others. Despite its relatively small size and intrinsically disordered termini, it forms large and polydisperse oligomers that are in equilibrium with dimers. This equilibrium is driven by transient interactions between the N-terminal region, the α-crystallin domain, and the C-terminal region. The continuous redistribution of binding partners results in a conformationally dynamic protein that allows it to adapt to different functions where substrate capture is required. However, the intrinsic disorder of the amino and carboxy terminal regions and subsequent conformational variability has made structural investigations challenging. Because heat shock protein 27 is critical for so many key cellular functions, it is not surprising that it also has been linked to human disease. Charcot-Marie-Tooth and distal hereditary motor neuropathy are examples of neurodegenerative disorders that arise from single point mutations in heat shock protein 27. The development of possible treatments, however, depends on our understanding of its normal function at the molecular level so we might be able to understand how mutations manifest as disease. This review will summarize recent reports describing investigations into the structurally elusive regions of Hsp27. Recent insights begin to provide the required context to explain the relationship between a mutation and the resulting loss or gain of function that leads to Charcot-Marie Tooth disease and distal hereditary motor neuropathy.
    Keywords:  Charcot-Marie-Tooth disease (CMT); distal hereditary motor neuropathy (dHMN); heat shock protein; small heat shock protein 27 (Hsp27); α-crystallin domain (ACD)
    DOI:  https://doi.org/10.3389/fnmol.2022.868089
  13. Cell Mol Life Sci. 2022 Apr 20. 79(5): 251
    Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept.
    Iuliia A Antifeeva, Alexander V Fonin, Anna S Fefilova, Olesya V Stepanenko, Olga I Povarova, Sergey A Silonov, Irina M Kuznetsova, Vladimir N Uversky, Konstantin K Turoverov.
      At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
    Keywords:  Intrinsically disordered proteins; Liquid-liquid phase separation; Membrane-less organelles
    DOI:  https://doi.org/10.1007/s00018-022-04276-4
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