Subclassifying disordered proteins by the CH-CDF plot method

Fei Huang, Christopher Oldfield, Jingwei Meng, Wei Lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, A. Keith Dunker

Research output: Contribution to journalConference article

49 Scopus citations

Abstract

Intrinsically disordered proteins (IDPs) are associated with a wide range of functions. We suggest that sequence-based subtypes, which we call flavors, may provide the basis for different biological functions. The problem is to find a method that separates IDPs into different flavor/function groups. Here we discuss one approach, the (Charge-Hydropathy) versus (Cumulative Distribution Function) plot or CH-CDF plot, which is based the combined use of the CH and CDF disorder predictors. These two predictors are based on significantly different inputs and methods. This CH-CDF plot partitions all proteins into 4 groups: structured, mixed, disordered, and rare. Studies of the Protein Data Bank (PDB) entries and homologous show different structural biases for each group classified by the CH-CDF plot. The mixed class has more order-promoting residues and more ordered regions than the disordered class. To test whether this partition accomplishes any functional separation, we performed gene ontology (GO) term analysis on each class. Some functions are indeed found to be related to subtypes of disorder: the disordered class is highly active in mitosis-related processes among others. Meanwhile, the mixed class is highly associated with signaling pathways, where having both ordered and disordered regions could possibly be important.

Original languageEnglish (US)
Pages (from-to)128-139
Number of pages12
JournalPacific Symposium on Biocomputing
StatePublished - Jan 1 2012
Event17th Pacific Symposium on Biocomputing, PSB 2012 - Kohala Coast, United States
Duration: Jan 3 2012Jan 7 2012

Keywords

  • CDF prediction
  • CH plot
  • Classification
  • Intrinsically disordered protein

ASJC Scopus subject areas

  • Biomedical Engineering
  • Computational Theory and Mathematics

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  • Cite this

    Huang, F., Oldfield, C., Meng, J., Hsu, W. L., Xue, B., Uversky, V. N., Romero, P., & Dunker, A. K. (2012). Subclassifying disordered proteins by the CH-CDF plot method. Pacific Symposium on Biocomputing, 128-139.