Document Detail


Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.
MedLine Citation:
PMID:  23341186     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes.
Authors:
W Austin Elam; Travis P Schrank; Andrew J Campagnolo; Vincent J Hilser
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2013-02-21
Journal Detail:
Title:  Protein science : a publication of the Protein Society     Volume:  22     ISSN:  1469-896X     ISO Abbreviation:  Protein Sci.     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-03-20     Completed Date:  2013-08-26     Revised Date:  2014-04-01    
Medline Journal Info:
Nlm Unique ID:  9211750     Medline TA:  Protein Sci     Country:  United States    
Other Details:
Languages:  eng     Pagination:  405-17     Citation Subset:  IM    
Copyright Information:
Copyright © 2013 The Protein Society.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Amino Acids / chemistry,  genetics,  metabolism
Animals
Computer Simulation
Fungal Proteins / chemistry,  genetics,  metabolism
Humans
Mice
Models, Molecular
Molecular Sequence Data
Peptides / chemistry*,  genetics,  metabolism
Phosphoproteins / chemistry*,  genetics,  metabolism
Phosphorylation
Protein Binding
Protein Conformation
Protein Folding
Proteome / chemistry,  genetics,  metabolism
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Fungal Proteins; 0/Peptides; 0/Phosphoproteins; 0/Proteome; 25191-13-3/polyproline
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