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.

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 Identifying molecular features that are associated with biological function of intrinsically disordered protein regions

2020 ◽  
Author(s):  
Taraneh Zarin ◽  
Bob Strome ◽  
Gang Peng ◽  
Iva Pritišanac ◽  
Julie D Forman-Kay ◽  
...  
Keyword(s):  
Isoelectric Point ◽  
Sequence Similarity ◽  
Intrinsically Disordered Protein ◽  
Mitochondrial Targeting ◽  
Mitochondrial Localization ◽  
Multiple Sequence ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Protein ◽  
Molecular Features

AbstractPreviously, we showed that intrinsically disordered regions in proteins (IDRs) contain multiple sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al. 2019). Here, we aim to use these molecular features to make specific functional predictions for individual IDRs and identify the molecular features within them that are responsible for specific functions. We find that the predictable functions are diverse, identifying previously known associated molecular features, as well as features that were previously not known to be associated with these functions. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.

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 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.

Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof

2020 ◽  
Vol 4 (3) ◽  
pp. 307-329 ◽  
Author(s):  
Erik W. Martin ◽  
Alex S. Holehouse
Keyword(s):  
Physical Chemistry ◽  
Phase Separation ◽  
Cell Biology ◽  
Three Dimensional ◽  
Intrinsically Disordered Protein ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Separation Sequence ◽  
Heterogeneous Ensemble

Intrinsically disordered protein regions (IDRs) — regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations — have recently entered mainstream cell biology in the context of liquid–liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than ‘disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.

scholarly journals Identifying molecular features that are associated with biological function of intrinsically disordered protein regions

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Taraneh Zarin ◽  
Bob Strome ◽  
Gang Peng ◽  
Iva Pritišanac ◽  
Julie D Forman-Kay ◽  
...  
Keyword(s):  
Isoelectric Point ◽  
Sequence Similarity ◽  
Intrinsically Disordered Protein ◽  
Biological Functions ◽  
Mitochondrial Targeting ◽  
Mitochondrial Localization ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Protein ◽  
Molecular Features

In previous work, we showed that intrinsically disordered regions (IDRs) of proteins contain sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al., 2019). Here, we aim to use these molecular features to predict specific biological functions for individual IDRs and identify the molecular features within them that are associated with these functions. We find that the predictable functions are diverse. Examining the associated molecular features, we note some that are consistent with previous reports and identify others that were previously unknown. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.

Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain

2018 ◽  
Author(s):  
Sarah Klass ◽  
Matthew J. Smith ◽  
Tahoe Fiala ◽  
Jessica Lee ◽  
Anthony Omole ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Fusion Proteins ◽  
Organic Molecules ◽  
Intrinsically Disordered Protein ◽  
Protein Domain ◽  
Enzymatic Cleavage ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Self Assembling ◽  
Protein Tag

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

Sign in / Sign up

Export Citation Format

Share Document