scholarly journals Biological Functions of the Intrinsically Disordered N-Terminal Domain of the Prion Protein: A Possible Role of Liquid–Liquid Phase Separation

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1201
Author(s):  
Stella A. Polido ◽  
Janine Kamps ◽  
Jörg Tatzelt
Keyword(s):  
Prion Protein ◽  
Tertiary Structure ◽  
Polypeptide Chain ◽  
Protein A ◽  
Interacting Proteins ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Protein Classes ◽  
Liquid Liquid Phase Separation

The mammalian prion protein (PrPC) is composed of a large intrinsically disordered N-terminal and a structured C-terminal domain, containing three alpha-helical regions and a short, two-stranded beta-sheet. Traditionally, the activity of a protein was linked to the ability of the polypeptide chain to adopt a stable secondary/tertiary structure. This concept has been extended when it became evident that intrinsically disordered domains (IDDs) can participate in a broad range of defined physiological activities and play a major functional role in several protein classes including transcription factors, scaffold proteins, and signaling molecules. This ability of IDDs to engage in a variety of supramolecular complexes may explain the large number of PrPC-interacting proteins described. Here, we summarize diverse physiological and pathophysiological activities that have been described for the unstructured N-terminal domain of PrPC. In particular, we focus on subdomains that have been conserved in evolution.

Role of Prion Disease-Linked Mutations in the Intrinsically Disordered N-Terminal Domain of the Prion Protein

2013 ◽  
Vol 9 (11) ◽  
pp. 5158-5167 ◽  
Author(s):  
Xiaojing Cong ◽  
Nicola Casiraghi ◽  
Giulia Rossetti ◽  
Sandipan Mohanty ◽  
Gabriele Giachin ◽  
...  
Keyword(s):  
Prion Protein ◽  
Prion Disease ◽  
Intrinsically Disordered ◽  
Terminal Domain

scholarly journals The Mutation of Conservative Asp268 Residue in the Peptidoglycan-Associated Domain of the OmpA Protein Affects Multiple Acinetobacter baumannii Virulence Characteristics

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1972 ◽  
Author(s):  
Jūratė Skerniškytė ◽  
Emilija Karazijaitė ◽  
Julien Deschamps ◽  
Renatas Krasauskas ◽  
Romain Briandet ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Protein A ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Clinical Strain ◽  
Infection Model ◽  
Terminal Domain ◽  
Ompa Protein

Acinetobacter baumannii is a nosocomial human pathogen of increasing concern due to its multidrug resistance profile. The outer membrane protein A (OmpA) is an abundant bacterial cell surface component involved in A. baumannii pathogenesis. It has been shown that the C-terminal domain of OmpA is located in the periplasm and non-covalently associates with the peptidoglycan layer via two conserved amino acids, thereby anchoring OmpA to the cell wall. Here, we investigated the role of one of the respective residues, D268 in OmpA of A. baumannii clinical strain Ab169, on its virulence characteristics by complementing the ΔompA mutant with the plasmid-borne ompAD268A allele. We show that while restoring the impaired biofilm formation of the ΔompA strain, the Ab169ompAD268A mutant tended to form bacterial filaments, indicating the abnormalities in cell division. Moreover, the Ab169 OmpA D268-mediated association to peptidoglycan was required for the manifestation of twitching motility, desiccation resistance, serum-induced killing, adhesion to epithelial cells and virulence in a nematode infection model, although it was dispensable for the uptake of β-lactam antibiotics by outer membrane vesicles. Overall, the results of this study demonstrate that the OmpA C-terminal domain-mediated association to peptidoglycan is critical for a number of virulent properties displayed by A. baumannii outside and within the host.

scholarly journals Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Tertiary Structure ◽  
Protein A ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Non Local

<p>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies “blobs” of 5-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between Val66 and Val94 (on either side of the linker) with specific side-chain interactions between Met66 and Met95.The protein backbone in the vicinity of Met95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.</p>

Quadruplex Folding of DNA Promotes the Condensation of Linker Histones via Liquid-Liquid Phase Separation

2020 ◽  
Author(s):  
Masahiro Mimura ◽  
Shunsuke Tomita ◽  
Yoichi Shinkai ◽  
Kentaro Shiraki ◽  
Ryoji Kurita
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Electrostatic Interactions ◽  
Droplet Formation ◽  
Liquid Phase Separation ◽  
Intrinsically Disordered ◽  
G Quadruplex ◽  
Dna Quadruplex ◽  
Liquid Liquid Phase Separation

<p>Liquid-liquid phase separation (LLPS) of proteins and DNA has recently emerged as a possible mechanism underlying the dynamic organization of chromatin. We herein report the role of DNA quadruplex folding in liquid droplet formation via LLPS induced by interactions between DNA and linker histone H1 (H1), a key regulator of chromatin organization. Fluidity measurements inside the droplets and binding assays using G-quadruplex-selective probes demonstrated that quadruplex DNA structures, such as the G-quadruplex and i-motif, promote droplet formation with H1 and decrease molecular motility within droplets. The dissolution of the droplets in the presence of additives indicated that in addition to electrostatic interactions between the DNA and the intrinsically disordered region of H1, π-π stacking between quadruplex DNAs could potentially drive droplet formation. Given that DNA quadruplex structures are well documented in heterochromatin regions, it is imperative to understand the role of DNA quadruplex folding in the context of intranuclear LLPS.<b></b></p>

scholarly journals Quadruplex Folding of DNA Promotes the Condensation of Linker Histones via Liquid-Liquid Phase Separation

2020 ◽  
Author(s):  
Masahiro Mimura ◽  
Shunsuke Tomita ◽  
Yoichi Shinkai ◽  
Kentaro Shiraki ◽  
Ryoji Kurita
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Electrostatic Interactions ◽  
Droplet Formation ◽  
Liquid Phase Separation ◽  
Intrinsically Disordered ◽  
G Quadruplex ◽  
Dna Quadruplex ◽  
Liquid Liquid Phase Separation

<p>Liquid-liquid phase separation (LLPS) of proteins and DNA has recently emerged as a possible mechanism underlying the dynamic organization of chromatin. We herein report the role of DNA quadruplex folding in liquid droplet formation via LLPS induced by interactions between DNA and linker histone H1 (H1), a key regulator of chromatin organization. Fluidity measurements inside the droplets and binding assays using G-quadruplex-selective probes demonstrated that quadruplex DNA structures, such as the G-quadruplex and i-motif, promote droplet formation with H1 and decrease molecular motility within droplets. The dissolution of the droplets in the presence of additives indicated that in addition to electrostatic interactions between the DNA and the intrinsically disordered region of H1, π-π stacking between quadruplex DNAs could potentially drive droplet formation. Given that DNA quadruplex structures are well documented in heterochromatin regions, it is imperative to understand the role of DNA quadruplex folding in the context of intranuclear LLPS.<b></b></p>

scholarly journals ATP regulates TDP-43 pathogenesis by specifically binding to an inhibitory component of a delicate network controlling LLPS

2020 ◽  
Author(s):  
Dang Mei ◽  
Liangzhong Lim ◽  
Jian Kang ◽  
Jianxing Song
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Neuron Death ◽  
Physiological Conditions ◽  
Intrinsically Disordered ◽  
Physicochemical Features ◽  
First Time ◽  
Inhibitory Interactions ◽  
Liquid Liquid Phase Separation

ABSTRACTVery recently, liquid-liquid phase separation (LLPS) of cytoplasmic TDP-43 independent of forming stress granule (SG) has been decoded to initiate the neuron death for ALS. Mysteriously neurons maintain ATP concentrations of ∼3 mM, but whether ATP modulates TDP-43 LLPS remains completely unknown. Here we characterized the effects of ATP on LLPS of TDP-43 PLD and its six mutants by DIC and NMR. For the first time, the results revealed: 1) ATP does induce and subsequently dissolve LLPS of TDP-43 PLD. 2) ATP achieves the modulation all by specifically binding Arg mostly saturated at 1:100. 3) LLPS of TDP-43 PLD and its exaggeration into aggregation are controlled by a delicate network composed of both attractive and inhibitory interactions, thus rationalizing the susceptibility of TDP-43 PLD to various ALS-causing mutations. Our studies together establish that ATP specifically binds Arg in intrinsically-disordered domains even not RGG-/R-rich, implying that ATP might be a universal regulator for most, if not all, R-containing intrinsically-disordered domains by altering their physicochemical features, conformations, dynamics, LLPS and assembly. Under physiological conditions, TDP-43 even in neuronal cytoplasm is highly bound with ATP and thus inhibited for its toxic LLPS, highlighting a central role of ATP in TDP-43 pathogenesis and aging.

scholarly journals Liquid-liquid phase separation and aggregation of the prion protein globular domain modulated by a high-affinity DNA aptamer

2019 ◽  
Author(s):  
Carolina O. Matos ◽  
Yulli M. Passos ◽  
Mariana J. do Amaral ◽  
Bruno Macedo ◽  
Matheus Tempone ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Prion Protein ◽  
Liquid Phase Separation ◽  
Cellular Prion Protein ◽  
Globular Domain ◽  
Structural Conversion ◽  
High Affinity ◽  
Liquid Liquid Phase Separation

ABSTRACTStructural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events for the onset of Transmissible Spongiform Encephalopathies (TSEs). Experimental evidences support the role of nucleic acids (NAs) in assisting the protein conversion process. Here, we used the SELEX methodology to identify two 25-mer DNA aptamers against the globular domain of recombinant murine PrP (rPrP90-231), namely A1 and A2. High-affinity binding of A1 and A2 to rPrP was verified by ITC. Aptamers structure was characterized by theoretical predictions, CD, NMR and SAXS, revealing that A1 adopts a hairpin conformation. Aptamer binding caused dynamic aggregation of rPrP90-231, resulting from the ability of rPrP90-231to undergo liquid-liquid phase separation (LLPS). While free rPrP90-231phase separated into large droplets, aptamer binding increased the amount but reduced the size of the condensates. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced transition to an ordered state, suggestive of amyloid formation on the surface of the droplets. Our results describe for the first time PrP:NA interaction leading to LLPS and modulation of this effect depending on NA structure and binding stoichiometry, shedding light on the role of NAs in PrP misfolding and TSEs.

scholarly journals Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Tertiary Structure ◽  
Protein A ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Non Local

<p>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies “blobs” of 5-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between Val66 and Val94 (on either side of the linker) with specific side-chain interactions between Met66 and Met95.The protein backbone in the vicinity of Met95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.</p>

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