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Why do eukaryotic proteins contain more intrinsically disordered regions?
[article]
2018
bioRxiv
pre-print
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Intrinsic disorder is an important aspect in eukaryotic proteins. However, it is not clear why intrinsic disorder is significantly more frequent in eukaryotic proteins than in prokaryotic proteins. ...
Eukaryotic proteins contain about 8% serine, while prokaryotic proteins have roughly 6%. ...
Why do eukaryotic proteins contain more intrinsically disordered regions? ...
doi:10.1101/270694
fatcat:ws4fc7kwobeznlpkr6uhihgq6i
Why do eukaryotic proteins contain more intrinsically disordered regions?
2019
PLoS Computational Biology
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Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. ...
Eukaryotic proteins have more extended linker regions, and in addition, the eukaryotic linkers are significantly more disordered, 38% vs. 12-16% disordered residues. ...
Increase of disorder in eukaryotic proteins ...
doi:10.1371/journal.pcbi.1007186
pmid:31329574
pmcid:PMC6675126
fatcat:wfsk53nxv5dvxaifez7bgojcf4
Nonoptimal codon usage influences protein structure in intrinsically disordered regions
2015
Molecular Microbiology
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Importantly, we found genome-wide correlations between codon choices and predicted protein secondary structures: Non-optimal codons are preferentially used in intrinsically disordered regions, and more ...
Furthermore, the correlations between codon usage and protein disorder tendency are conserved in other eukaryotes. ...
more intrinsically disordered structures. ...
doi:10.1111/mmi.13079
pmid:26032251
pmcid:PMC4636118
fatcat:gnmexhmehfb37lsvkaav7lxiou
Conservation of Intrinsic Disorder in Protein Domains and Families: I. A Database of Conserved Predicted Disordered Regions
2006
Journal of Proteome Research
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Many protein regions have been shown to be intrinsically disordered, lacking unique structure under physiological conditions. ...
These intrinsically disordered regions are not only very common in proteomes, they are also crucial to the function of many proteins, especially those involved in signaling, recognition, and regulation ...
In both this work and previous work, eukaryotes had on the order of ten times more proteins containing long disordered regions than did archaea and bacteria. ...
doi:10.1021/pr060048x
pmid:16602695
pmcid:PMC2543136
fatcat:r3mbtar72zdsdns2xhefrapfgi
Differences in the Number of Intrinsically Disordered Regions between Yeast Duplicated Proteins, and Their Relationship with Functional Divergence
2011
PLoS ONE
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for retaining intrinsically disordered proteins in duplicate. ...
In this work we examined the dynamics of gain and loss of intrinsically disordered regions in duplicated proteins to inspect if changes after genome duplication can create functional divergence. ...
This result is also seen when we alternatively define proteins as intrinsically disordered when they contain one or more intrinsically disordered region: 793 of the total 1100 ohnologs (550 pairs) contain ...
doi:10.1371/journal.pone.0024989
pmid:21949823
pmcid:PMC3174238
fatcat:36oj4yxndbafxlvxv6hnqave7q
How do disordered regions achieve comparable functions to structured domains?
2015
Protein Science
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In recent years, it has been established that unstructured, intrinsically disordered regions (IDRs) in proteins are equally crucial elements for protein function, regulation and homeostasis. ...
We also discuss studies that provide insights into how mutations within functional regions of IDRs can lead to human diseases. ...
Acknowledgments Since this is a review based on the Protein Science's Protein Society Young Investigator award lecture, the authors have in some instances emphasized the work done by their group, while ...
doi:10.1002/pro.2674
pmid:25752799
pmcid:PMC4456105
fatcat:h7eian643fdtbnotoxdmji5dn4
Large-scale analysis of redox-sensitive conditionally disordered protein regions reveal their widespread nature and key roles in high-level eukaryotic processes
[article]
2018
bioRxiv
pre-print
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Here, we use a recently developed sequence-based prediction tool incorporated into the IUPred2A web server to estimate redox-sensitive conditionally disordered regions on a large scale. ...
proteins. ...
Our analysis suggests that these pathogens contain significantly large fractions of proteins with redox-sensitive intrinsically disordered regions ( Figure 3A ). ...
doi:10.1101/412692
fatcat:5wdvhil3pbcexpwytk57chjd2q
Theater in the Self-Cleaning Cell: Intrinsically Disordered Proteins or Protein Regions Acting with Membranes in Autophagy
2022
Membranes
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Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally ...
Here, we discuss molecular mechanisms related to the protein disorder-based interactions of the autophagy machinery with membranes. ...
These polypeptides are referred to as intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) [1] [2] [3] [4] . ...
doi:10.3390/membranes12050457
pmid:35629783
fatcat:25sie4fjcjcjhgxky4476kgyey
A Conserved Deubiquitinating Enzyme Uses Intrinsically Disordered Regions to Scaffold Multiple Protein Interaction Sites
2015
Journal of Biological Chemistry
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However, the past decade has seen a dramatic growth in the identification of proteins with extensive intrinsically disordered regions (IDRs), which are conformationally plastic and do not appear to adopt ...
Many proteins that regulate ubiquitination possess intrinsically disordered regions (IDRs), but little is known about how IDRs function. ...
disorder. ...
doi:10.1074/jbc.m115.650952
pmid:26149687
pmcid:PMC4536463
fatcat:2i2tnnzi35hhfpythlc56r3cn4
Analysis of structured and intrinsically disordered regions of transmembrane proteins
2009
Molecular Biosystems
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We found 120 disorder-containing integral membrane proteins having a total of 33,675 residues, with 3209 of the residues distributed among 240 different disordered regions. ...
For cytosolic, water-soluble proteins, signaling and regulatory functions are often carried out by intrinsically disordered regions. ...
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDRs) do not have rigid three dimensional or stable secondary structures under physiological conditions [10] [11] ...
doi:10.1039/b905913j
pmid:19585006
pmcid:PMC2887740
fatcat:e6iikako7nhlzhilmngshsl56a
Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins
2019
Protein Science
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disordered proteins. ...
In this report, data of kinase-substrate pairs identified by the Kinase-Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically ...
This approach revealed that phosphosites tend to be located in intrinsically disordered regions (IDRs) of intrinsically disordered proteins (IDPs), 23 and this tendency has been already taken into account ...
doi:10.1002/pro.3789
pmid:31724233
pmcid:PMC6954741
fatcat:q7p2zdpcgnfytij7a3t6pfnfp4
Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches
2017
Journal of Molecular Biology
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Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. ...
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. ...
Intrinsically disordered regions (IDRs) are also highly prevalent on histone chaperones. ...
doi:10.1016/j.jmb.2017.06.005
pmid:28610839
pmcid:PMC5544577
fatcat:5ug4nfduurdldkum7yxbj5un74
On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins
2006
Gene
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Protein sequences frequently contain regions composed of a reduced number of amino acids. ...
Despite their presence in about half of all proteins and their unusual prevalence in the malaria parasite Plasmodium falciparum, the function and evolution of such low-complexity regions (LCRs) remain ...
LCRs are closely related to two other types of degenerate sequences, namely microsatellites and intrinsically unstructured regions (IURs) in proteins. ...
doi:10.1016/j.gene.2006.03.023
pmid:16806741
fatcat:xestgrwdbjeizjycuebxfl36wa
Structural Bioinformatics Predicts Large Intrinsically Disordered Regions of Erythrocyte Binding-Like Proteins of Plasmodium sp.: Functional Implications
2020
International Research Journal of Multidisciplinary Scope
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Our study reveals that its major parts of the unstructured portions consist of Intrinsically Disordered Regions (IDR). ...
In this study, it is reported that EBL protein consists of massive unstructured regions in between two compact structured portions, viz., the DBD and a C-terminus trans-membrane domain as predicted from ...
Near about 44% of human protein-coding genes contain disordered regions having >30 amino acids in length (29) and 6.4% of all protein coding genes do not even have any functional annotation. ...
doi:10.47857/irjms.2020.v01i02.008
fatcat:mi2ckamcajcb7l2o6zhgqla4ru
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions
2015
Genome Biology and Evolution
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Intrinsically disordered protein regions are abundant in eukaryotic proteins and lack stable tertiary structures and enzymatic functions. ...
First, we show that single nucleotide polymorphisms in disordered regions are under weaker negative selection compared with more structured protein regions and have a higher proportion of neutral non-synonymous ...
Therefore, it remains unclear how these disordered regions have been maintained through evolutionary time and why they are so predominant in eukaryotic proteins. ...
doi:10.1093/gbe/evv105
pmid:26047845
pmcid:PMC4494057
fatcat:vbxa3bylkbgmvphsncjckbfsgi
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