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Why do eukaryotic proteins contain more intrinsically disordered regions? [article]

Walter Basile, Arne Elofsson
2018 bioRxiv   pre-print
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?

Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson, Claus O. Wilke
2019 PLoS Computational Biology  
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

Mian Zhou, Tao Wang, Jingjing Fu, Guanghua Xiao, Yi Liu
2015 Molecular Microbiology  
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

Jessica Walton Chen, Pedro Romero, Vladimir N. Uversky, A. Keith Dunker
2006 Journal of Proteome Research  
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

Floriane Montanari, Denis C. Shields, Nora Khaldi, Arthur J. Lustig
2011 PLoS ONE  
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?

Natasha S. Latysheva, Tilman Flock, Robert J. Weatheritt, Sreenivas Chavali, M. Madan Babu
2015 Protein Science  
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]

Gábor Erdõs, Bálint Mészáros, Dana Reichmann, Zsuzsanna Dosztányi
2018 bioRxiv   pre-print
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

Hana Popelka, Vladimir N. Uversky
2022 Membranes  
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

Benjamin J. Reed, Melissa N. Locke, Richard G. Gardner
2015 Journal of Biological Chemistry  
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

Bin Xue, Liwei Li, Samy O. Meroueh, Vladimir N. Uversky, A. Keith Dunker
2009 Molecular Biosystems  
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

Ryotaro Koike, Mutsuki Amano, Kozo Kaibuchi, Motonori Ota
2019 Protein Science  
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

Christopher Warren, David Shechter
2017 Journal of Molecular Biology  
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

Mark A. DePristo, Martine M. Zilversmit, Daniel L. Hartl
2006 Gene  
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

Arita Acharjee
2020 International Research Journal of Multidisciplinary Scope  
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

Tahsin Khan, Gavin M. Douglas, Priyenbhai Patel, Alex N. Nguyen Ba, Alan M. Moses
2015 Genome Biology and Evolution  
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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