scholarly journals Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14

2021 ◽  
Vol 22 (12) ◽  
pp. 6190
Author(s):  
Nikoletta Murvai ◽  
Lajos Kalmar ◽  
Beata Szabo ◽  
Eva Schad ◽  
András Micsonai ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Stress Protein ◽  
Early Response ◽  
Disordered Proteins ◽  
Proper Function ◽  
Sequence Motifs ◽  
Protective Function ◽  
Cellular Protection ◽  
Conserved Sequence ◽  
Intrinsically Disordered

Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.

scholarly journals Interplay of Structural Disorder and Short Binding Elements in the Cellular Chaperone Function of Plant Dehydrin ERD14

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1856
Author(s):  
Nikoletta Murvai ◽  
Lajos Kalmar ◽  
Bianka Szalaine Agoston ◽  
Beata Szabo ◽  
Agnes Tantos ◽  
...  
Keyword(s):  
Heat Stress ◽  
Intrinsically Disordered Proteins ◽  
Stress Protein ◽  
Structural Disorder ◽  
Disordered Proteins ◽  
Sequence Motifs ◽  
E Coli ◽  
Intrinsically Disordered

Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed structural analyses based on an in-cell nuclear magnetic resonance experiment. We show that the ID stress protein (IDSP) A. thaliana Early Response to Dehydration (ERD14) is capable of protecting E. coli cells under heat stress. The overexpression of ERD14 increases the viability of E. coli cells from 38.9% to 73.9% following heat stress (50 °C × 15 min). We also provide evidence that the protection is mainly achieved by protecting the proteome of the cells. In-cell NMR experiments performed in E. coli cells show that the protective activity is associated with a largely disordered structural state with conserved, short sequence motifs (K- and H-segments), which transiently sample helical conformations in vitro and engage in partner binding in vivo. Other regions of the protein, such as its S segment and its regions linking and flanking the binding motifs, remain unbound and disordered in the cell. Our data suggest that the cellular function of ERD14 is compatible with its residual structural disorder in vivo.

scholarly journals Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells

2021 ◽  
Author(s):  
Mike T. Veling ◽  
Dan T. Nguyen ◽  
Nicole N. Thadani ◽  
Michela E. Oster ◽  
Nathan J. Rollins ◽  
...  
Keyword(s):  
Phase Separation ◽  
Intrinsically Disordered Proteins ◽  
Human Cells ◽  
Disordered Proteins ◽  
Cellular Protection ◽  
Intrinsically Disordered ◽  
Apoe Protein ◽  
Condensate Formation ◽  
Associated Proteins ◽  
Induced Apoptosis

ABSTRACTMany 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 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 highlight the ability for DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and human cellular protection.

scholarly journals PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability

2018 ◽  
Author(s):  
Ricardo J. Cordeiro Rodrigues ◽  
António Miguel de Jesus Domingues ◽  
Svenja Hellmann ◽  
Sabrina Dietz ◽  
Bruno F. M. de Albuquerque ◽  
...  
Keyword(s):  
Protein Complex ◽  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Disordered Proteins ◽  
Sequence Motif ◽  
C Elegans ◽  
Conserved Sequence ◽  
Intrinsically Disordered ◽  
Rna Biogenesis ◽  
Novel Protein

AbstractPiwi proteins are important for germ cell development in almost all animals studied thus far. These proteins are guided to specific targets, such as transposable elements, by small guide RNAs, often referred to as piRNAs, or 21U RNAs in C. elegans. In this organism, even though genetic screens have uncovered a number of potential 21U RNA biogenesis factors, little is known about how these factors interact or what they do. Based on the previously identified 21U biogenesis factor PID-1, we here define a novel protein complex, PETISCO, that is required for 21U RNA biogenesis. PETISCO contains both potential 5’-cap and 5’-phosphate RNA binding domains, suggesting involvement in 5’ end processing. We define the interaction architecture of PETISCO and reveal a second function for PETISCO in embryonic development. This essential function of PETISCO is not mediated by PID-1, but by TOST-1. Vice versa, TOST-1 is not involved in 21U RNA biogenesis. Both PID-1 and TOST-1 are small, intrinsically disordered proteins that interact directly with the PETISCO protein ERH-2 (enhancer of rudimentary homolog 2) using a conserved sequence motif. Finally, our data suggest an important role for TOST-1:PETISCO in SL1 homeostasis in the early embryo. Our work describes the first molecular platform for 21U RNA production in C. elegans, and strengthens the view that 21U RNA biogenesis is built upon a much more widely used, snRNA-related pathway.

scholarly journals Uncovering non-random sequence patterns within intrinsically disordered proteins

2021 ◽  
Author(s):  
Megan C. Cohan ◽  
Min Kyung Shinn ◽  
Jared M. Lalmansingh ◽  
Rohit V. Pappu
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Random Sequence ◽  
Null Model ◽  
Computational Method ◽  
Disordered Proteins ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Intrinsically Disordered ◽  
Sequence Patterns ◽  
Z Scores

AbstractIntrinsically disordered proteins / regions (IDPs / IDRs) pose unique challenges for deriving sequence-function relationships from multiple sequence alignments. These challenges arise from variations in sequence lengths, similarities, and identities across orthologs. Recent computational efforts have demonstrated the utility of comparing large numbers of distinct sequence features as a strategy to identify conserved sequence-function relationships in IDPs / IDRs. Inspired by these efforts, and by biophysical studies that have established the importance of binary patterning features in IDPs / IDRs, we present here a computational method, NARDINI (Non-random Arrangement of Residues in Disordered Regions Inferred using Numerical Intermixing), to uncover truly non-random binary patterns within disordered proteins / regions. Binary patterns refer to the linear clustering or dispersion of specific residues or residue types with respect to all other residues or specific types of residues. Our approach does not use, nor does it require sequence alignments. Instead for each IDR, we generate an ensemble of scrambled sequences and use this to set up expectations from a composition-specific null model for the patterning parameters of interest. We annotate each IDR in terms of pattern-specific z-score matrices by computing how specific patterns deviate from the null model. The z-scores help in identifying the non-random linear sequence patterns within an IDR. We tested the accuracy of NARDINI derived z-scores by assessing the ability to identify sequence patterns that have been identified as determinants of sequence-function relationships in specific IDPs / IDRs.

scholarly journals Cryoprotective activities of FK20, a human genome-derived intrinsically disordered peptide against cryosensitive enzymes without a stereospecific molecular interaction

2021 ◽  
Vol 3 ◽  
pp. e20
Author(s):  
Naoki Matsuo ◽  
Natsuko Goda ◽  
Takeshi Tenno ◽  
Hidekazu Hiroaki
Keyword(s):  
Amino Acid ◽  
Human Genome ◽  
Intrinsically Disordered Proteins ◽  
Equimolar Mixture ◽  
Disordered Proteins ◽  
Shielding Effect ◽  
Racemic Mixture ◽  
Conserved Sequence ◽  
Intrinsically Disordered ◽  
Amino Acid Length

Background Intrinsically disordered proteins (IDPs) have been shown to exhibit cryoprotective activity toward other cellular enzymes without any obvious conserved sequence motifs. This study investigated relationships between the physical properties of several human genome-derived IDPs and their cryoprotective activities. Methods Cryoprotective activity of three human-genome derived IDPs and their truncated peptides toward lactate dehydrogenase (LDH) and glutathione S-transferase (GST) was examined. After the shortest cryoprotective peptide was defined (named FK20), cryoprotective activity of all-D-enantiomeric isoform of FK20 (FK20-D) as well as a racemic mixture of FK20 and FK20-D was examined. In order to examine the lack of increase of thermal stability of the target enzyme, the CD spectra of GST and LDH in the presence of a racemic mixture of FK20 and FK20-D at varying temperatures were measured and used to estimate Tm. Results Cryoprotective activity of IDPs longer than 20 amino acids was nearly independent of the amino acid length. The shortest IDP-derived 20 amino acid length peptide with sufficient cryoprotective activity was developed from a series of TNFRSF11B fragments (named FK20). FK20, FK20-D, and an equimolar mixture of FK20 and FK20-D also showed similar cryoprotective activity toward LDH and GST. Tm of GST in the presence and absence of an equimolar mixture of FK20 and FK20-D are similar, suggesting that IDPs’ cryoprotection mechanism seems partly from a molecular shielding effect rather than a direct interaction with the target enzymes.

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>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) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>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 local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

Sign in / Sign up

Export Citation Format

Share Document