Abstract：
:Many proteins possess intrinsic disorder (ID) and lack a rigid three-dimensional structure in at least part of their sequence. ID has been hypothesized to influence protein-protein and protein-ligand interactions. We calculated ID for nearly 400 vertebrate and invertebrate members of the biomedically important nuclear hormone receptor (NHR) superfamily, including all 48 known human NHRs. The predictions correctly identified regions in 20 of the 23 NHRs suggested as disordered based on published X-ray and NMR structures. Of the four major NHR domains (N-terminal domain, DNA-binding domain, D-domain, and ligand-binding domain), we found ID to be highest in the D-domain, a region of NHRs critical in DNA recognition and heterodimerization, coactivator/corepressor interactions and protein-protein interactions. ID in the D-domain and LBD was significantly higher in "hub" human NHRs that have 10 or more downstream proteins in their interaction networks compared to "non-hub" NHRs that interact with fewer than 10 downstream proteins. ID in the D-domain and LBD was also higher in classic, ligand-activated NHRs than in orphan, ligand-independent NHRs in human. The correlation between ID in human and mouse NHRs was high. Less correlation was found for ID between mammalian and non-mammalian vertebrate NHRs. For some invertebrate species, particularly sea squirts ( Ciona), marked differences were observed in ID between invertebrate NHRs and their vertebrate orthologs. Our results indicate that variability of ID within NHRs, particularly in the D-domain and LBD, is likely an important evolutionary force in shaping protein-protein interactions and NHR function. This information enables further understanding of these therapeutic targets.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Krasowski MD,Reschly EJ,Ekins Sdoi
10.1021/pr8003024subject
Has Abstractpub_date
2008-10-01 00:00:00pages
4359-72issue
10eissn
1535-3893issn
1535-3907journal_volume
7pub_type
杂志文章abstract：:Ubiquitin ligases (E3s) serve as key regulators for the ubiquitylation-mediated pathway. The identification of the corresponding relationship between E3 and its substrates is challenging but required for understanding the regulatory network of ubiquitylation. The low abundance of ubiquitinated conjugates and high redu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00673
更新日期：2020-01-03 00:00:00
abstract：:Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells and mediates multiple cellular signaling pathways. In the present study, a 35% decrease of cellular NAD level is achieved by stable expression of the N-terminal truncated CD38, a NAD hydrolase. CD38-expressing (CD38(+)) cells have the lowe...
journal_title：Journal of proteome research
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doi：10.1021/pr4010597
更新日期：2014-02-07 00:00:00
abstract：:Grapes are among the widely cultivated fruit crops in the world. Grape berries like other nonclimacteric fruits undergo a complex set of dynamic, physical, physiological, and biochemical changes during ripening. Muscadine grapes are widely cultivated in the southern United States for fresh fruit and wine. To date, cha...
journal_title：Journal of proteome research
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更新日期：2014-02-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00556
更新日期：2016-10-07 00:00:00
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journal_title：Journal of proteome research
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更新日期：2004-11-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章,评审
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900390t
更新日期：2009-10-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070531n
更新日期：2008-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00249
更新日期：2015-07-02 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060600i
更新日期：2007-07-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049819s
更新日期：2005-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00460
更新日期：2017-10-06 00:00:00
abstract：:A number of aptamers have been selected against cell surface biomarkers or against eukaryotic tissue culture cells themselves. To determine the general utility of aptamers for assessing the cell surface proteome, we developed a standardized flow cytometry assay and carried out a comprehensive study with 7 different ap...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr801048z
更新日期：2009-05-01 00:00:00
abstract：:In this work, we developed a general perturbation theory and machine learning method for data mining of proteomes to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) under a set of experimental query conditions (cqj). The method u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00477
更新日期：2017-11-03 00:00:00
abstract：:In Thailand, diabetes mellitus is the most significant risk factor for melioidosis, a severe disease caused by Burkholderia pseudomallei. In this study, neutrophils isolated from healthy or diabetic subjects were infected with B. thailandensis E555, a variant strain with a B. pseudomallei-like capsular polysaccharide ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00166
更新日期：2019-07-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00406
更新日期：2020-09-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100838x
更新日期：2011-06-03 00:00:00
abstract：:The interaction between the immune system and invading bacteria is sufficient to eradicate microorganisms for the majority of bacterial infections, but suppression of the microbicidal response leads to reactivation or chronic evolution of infections and to bacterial persistence. To identify the cellular pathways affec...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200422f
更新日期：2011-09-02 00:00:00
abstract：:Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an imp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2006704
更新日期：2012-02-03 00:00:00
abstract：:The HIV-1-associated neurocognitive disorder occurs in approximately one-third of infected individuals. It has persisted in the current era of antiretroviral therapy, and its study is complicated by the lack of biomarkers for this condition. Since the cerebrospinal fluid is the most proximal biofluid to the site of pa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800854t
更新日期：2009-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.5b00857
更新日期：2016-01-04 00:00:00
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journal_title：Journal of proteome research
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更新日期：2006-09-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2015-02-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2014-11-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050279o
更新日期：2006-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100593g
更新日期：2010-10-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00764
更新日期：2015-11-06 00:00:00
abstract：:Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0602803
更新日期：2006-10-01 00:00:00
abstract：:The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800641v
更新日期：2009-01-01 00:00:00
abstract：:A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00474
更新日期：2015-09-04 00:00:00
