scholarly journals The C Terminus of the Ribosomal-Associated Protein LrtA is an Intrinsically Disordered Oligomer

2018 ◽  
Vol 19 (12) ◽  
pp. 3902 ◽  
Author(s):  
José L. Neira ◽  
A. Marcela Giudici ◽  
Felipe Hornos ◽  
Arantxa Arbe ◽  
Bruno Rizzuti
Keyword(s):  
Computational Modelling ◽  
Terminal Region ◽  
Physiological Conditions ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
C Terminus ◽  
Conformational Preferences ◽  
Self Association ◽  
Association Equilibrium ◽  
Post Stress

The 191-residue-long LrtA protein of Synechocystis sp. PCC 6803 is involved in post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family, intervening in protein synthesis. The protein consists of two domains: The N-terminal region (N-LrtA, residues 1101), which is common to all the members of the HPF, and seems to be well-folded; and the C-terminal region (C-LrtA, residues 102-191), which is hypothesized to be disordered. In this work, we studied the conformational preferences of isolated C-LrtA in solution. The protein was disordered, as shown by computational modelling, 1D-1H NMR, steady-state far- UV circular dichroism (CD) and chemical and thermal denaturations followed by fluorescence and far-UV CD. Moreover, at physiological conditions, as indicated by several biochemical and hydrodynamic techniques, isolated C-LrtA intervened in a self-association equilibrium, involving several oligomerization reactions. Thus, C-LrtA was an oligomeric disordered protein.

scholarly journals X-ray structure of the PHF core C-terminus: Insight into the folding of the intrinsically disordered protein tau in Alzheimer's disease

FEBS Letters ◽  
2007 ◽  
Vol 581 (30) ◽  
pp. 5872-5878 ◽  
Author(s):  
Jozef Sevcik ◽  
Rostislav Skrabana ◽  
Radovan Dvorsky ◽  
Natalia Csokova ◽  
Khalid Iqbal ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Intrinsically Disordered Protein ◽  
X Ray ◽  
Protein Tau ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
C Terminus ◽  
Insight Into

scholarly journals Protein-based condensation mechanisms drive the assembly of RNA-rich P granules

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Helen Schmidt ◽  
Andrea Putnam ◽  
Dominique Rasoloson ◽  
Geraldine Seydoux
Keyword(s):  
Intrinsically Disordered Protein ◽  
P Granules ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
The Core ◽  
C Terminus ◽  
Germ Granules

Germ granules are protein-RNA condensates that segregate with the embryonic germline. In C. elegans embryos, germ (P) granule assembly requires MEG-3, an intrinsically-disordered protein that forms RNA-rich condensates on the surface of PGL condensates at the core of P granules. MEG-3 is related to the GCNA family and contains an N-terminal disordered region (IDR) and a predicted ordered C-terminus featuring an HMG-like motif (HMGL). We find that MEG-3 is modular protein that uses its IDR to bind RNA and its C-terminus to drive condensation. The HMGL motif mediates binding to PGL-3 and is required for co-assembly of MEG-3 and PGL-3 condensates in vivo. Mutations in HMGL cause MEG-3 and PGL-3 to form separate condensates that no longer co-segregate to the germline or recruit RNA. Our findings highlight the importance of protein-based condensation mechanisms and condensate-condensate interactions in the assembly of RNA-rich germ granules.

scholarly journals Coordination of RNA and protein condensation by the P granule protein MEG-3

2020 ◽  
Author(s):  
Helen Schmidt ◽  
Andrea Putnam ◽  
Dominique Rasoloson ◽  
Geraldine Seydoux
Keyword(s):  
Protein Interactions ◽  
Intrinsically Disordered Protein ◽  
Protein Protein Interactions ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
C Terminus ◽  
Necessary And Sufficient

ABSTRACTGerm granules are RNA-protein condensates in germ cells. The mechanisms that drive germ granule assembly are not fully understood. MEG-3 is an intrinsically-disordered protein required for germ (P) granule assembly in C. elegans. MEG-3 forms gel-like condensates on liquid condensates assembled by PGL proteins. MEG-3 is related to the GCNA family and contains an N-terminal disordered region (IDR) and a predicted ordered C-terminus featuring an HMG-like motif (HMGL). Using in vitro and in vivo experiments, we find the MEG-3 C-terminus is necessary and sufficient to build MEG-3/PGL co-condensates independent of RNA. The HMGL domain is required for high affinity MEG-3/PGL binding in vitro and for assembly of MEG-3/PGL co-condensates in vivo. The MEG-3 IDR binds RNA in vitro and is required but not sufficient to recruit RNA to P granules. Our findings suggest that P granule assembly depends in part on protein-protein interactions that drive condensation independent of RNA.

The chromatin nuclear protein NUPR1L is intrinsically disordered and binds to the same proteins as its paralogue

2018 ◽  
Vol 475 (14) ◽  
pp. 2271-2291 ◽  
Author(s):  
José L. Neira ◽  
María Belén López ◽  
Paz Sevilla ◽  
Bruno Rizzuti ◽  
Ana Cámara-Artigas ◽  
...  
Keyword(s):  
Hot Spot ◽  
Intrinsically Disordered Protein ◽  
Prothymosin Α ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Conformational Preferences ◽  
Folded Proteins ◽  
Similar Affinity ◽  
Polycomb Complex ◽  
Micromolar Range

NUPR1 is a protumoral multifunctional intrinsically disordered protein (IDP), which is activated during the acute phases of pancreatitis. It interacts with other IDPs such as prothymosin α, as well as with folded proteins such as the C-terminal region of RING1-B (C-RING1B) of the Polycomb complex; in all those interactions, residues around Ala33 and Thr68 (the ‘hot-spot’ region) of NUPR1 intervene. Its paralogue, NUPR1L, is also expressed in response to DNA damage, it is p53-regulated, and its expression down-regulates that of the NUPR1 gene. In this work, we characterized the conformational preferences of isolated NUPR1L and its possible interactions with the same molecular partners of NUPR1. Our results show that NUPR1L was an oligomeric IDP from pH 2.0 to 12.0, as judged by steady-state fluorescence, circular dichroism (CD), dynamic light scattering, 1D 1H-NMR (nuclear magnetic resonance), and as indicated by structural modelling. However, in contrast with NUPR1, there was evidence of local helical- or turn-like structures; these structures were not rigid, as judged by the lack of sigmoidal behaviour in the chemical and thermal denaturation curves obtained by CD and fluorescence. Interestingly enough, NUPR1L interacted with prothymosin α and C-RING1B, and with a similar affinity to that of NUPR1 (in the low micromolar range). Moreover, NUPR1L hetero-associated with NUPR1 with an affinity of 0.4 µM and interacted with the ‘hot-spot’ region of NUPR1. Thus, we suggest that the regulation of NUPR1 gene by NUPR1L does not only happen at the DNA level, but it could also involve direct interactions with NUPR1 natural partners.

scholarly journals Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4930 ◽  
Author(s):  
Leidys French-Pacheco ◽  
Cesar L. Cuevas-Velazquez ◽  
Lina Rivillas-Acevedo ◽  
Alejandra A. Covarrubias ◽  
Carlos Amero
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Intrinsically Disordered Protein ◽  
Late Embryogenesis Abundant ◽  
Terminal Region ◽  
Late Embryogenesis Abundant Protein ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Late Embryogenesis

Late embryogenesis abundant (LEA) proteins accumulate in plants during adverse conditions and their main attributed function is to confer tolerance to stress. One of the deleterious effects of the adverse environment is the accumulation of metal ions to levels that generate reactive oxygen species, compromising the survival of cells. AtLEA4-5, a member of group 4 of LEAs in Arabidopsis, is an intrinsically disordered protein. It has been shown that their N-terminal region is able to undergo transitions to partially folded states and prevent the inactivation of enzymes. We have characterized metal ion binding to AtLEA4-5 by circular dichroism, electronic absorbance spectroscopy (UV–vis), electron paramagnetic resonance, dynamic light scattering, and isothermal titration calorimetry. The data shows that AtLEA4-5 contains a single binding site for Ni(II), while Zn(II) and Cu(II) have multiple binding sites and promote oligomerization. The Cu(II) interacts preferentially with histidine residues mostly located in the C-terminal region with moderate affinity and different coordination modes. These results and the lack of a stable secondary structure formation indicate that an ensemble of conformations remains accessible to the metal for binding, suggesting the formation of a fuzzy complex. Our results support the multifunctionality of LEA proteins and suggest that the C-terminal region of AtLEA4-5 could be responsible for antioxidant activity, scavenging metal ions under stress conditions while the N-terminal could function as a chaperone.

The human disease gene CLEC16A encodes an intrinsically disordered protein region required for mitochondrial quality control

2021 ◽  
Author(s):  
Morgan A. Gingerich ◽  
Xueying Liu ◽  
Biaoxin Chai ◽  
Gemma L. Pearson ◽  
Michael P. Vincent ◽  
...  
Keyword(s):  
Quality Control ◽  
Human Disease ◽  
Intrinsically Disordered Protein ◽  
Mitochondrial Quality Control ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Functional Regions ◽  
C Terminus ◽  
Intrinsically Disordered Protein Region

CLEC16A regulates mitochondrial health through mitophagy and is associated with over 20 human diseases. While CLEC16A has ubiquitin ligase activity, the key structural and functional regions of CLEC16A, and their relevance for human disease, remain unknown. Here, we report that a disease-associated CLEC16A variant lacks a C-terminal intrinsically disordered protein region (IDPR) that is critical for mitochondrial quality control. Using carbon detect NMR, we find that the CLEC16A C terminus lacks secondary structure, validating the presence of an IDPR. Loss of the CLEC16A C-terminal IDPR in vivo impairs pancreatic β-cell mitophagy, mitochondrial function, and glucose-stimulated insulin secretion, ultimately causing glucose intolerance. Deletion of the CLEC16A C-terminal IDPR increases its self-ubiquitination and destabilizes CLEC16A, thus impairing formation of a critical CLEC16A-dependent mitophagy complex. Importantly, CLEC16A stability is dependent on proline bias within the C-terminal IDPR, but not amino acid sequence order or charge. Together, we clarify how an IDPR in CLEC16A prevents diabetes, thus implicating the disruption of IDPRs as novel pathological contributors to diabetes and other CLEC16A-associated diseases.

Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein

2009 ◽  
Vol 422 (2) ◽  
pp. 207-215 ◽  
Author(s):  
Shanhui Liao ◽  
Qiang Shang ◽  
Xuecheng Zhang ◽  
Jiahai Zhang ◽  
Chao Xu ◽  
...  
Keyword(s):  
Nuclear Overhauser Effect ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Intrinsically Disordered Protein ◽  
Spectroscopic Studies ◽  
Chemical Shift Index ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
C Terminus ◽  
Nuclear Overhauser

Pup (prokaryotic ubiquitin-like protein) from Mycobacterium tuberculosis is the first ubiquitin-like protein identified in non-eukaryotic cells. Although different ubiquitin-like proteins from eukaryotes share low sequence similarity, their 3D (three-dimensional) structures exhibit highly conserved typical ubiquitin-like folds. Interestingly, our studies reveal that Pup not only shares low sequence similarity, but also presents a totally distinguished structure compared with other ubiquitin-like superfamily proteins. Diverse structure predictions combined with CD and NMR spectroscopic studies all demonstrate that Pup is an intrinsically disordered protein. Moreover, 1H-15N NOE (nuclear Overhauser effect) data and CSI (chemical shift index) analyses indicate that there is a residual secondary structure at the C-terminus of Pup. In M. tuberculosis, Mpa (mycobacterium proteasomal ATPase) is the regulatory cap ATPase of the proteasome that interacts with Pup and brings the substrates to the proteasome for degradation. In the present paper, SPR (surface plasmon resonance) and NMR perturbation studies imply that the C-terminus of Pup, ranging from residues 30 to 59, binds to Mpa probably through a hydrophobic interface. In addition, phylogenetic analysis clearly shows that the Pup family belongs to a unique and divergent evolutionary branch, suggesting that it is the most ancient and deeply branched family among ubiquitin-like proteins. This might explain the structural distinction between Pup and other ubiquitin-like superfamily proteins.

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