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. Dunker

Research output: Contribution to journalArticle

42 Citations (Scopus)

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. Pacific Symposium on Biocomputing
StatePublished - 2012

Fingerprint

Intrinsically Disordered Proteins
Gene Ontology
Mitosis
Proteins
Databases

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Subclassifying disordered proteins by the CH-CDF plot method. / Huang, Fei; Oldfield, Christopher; Meng, Jingwei; Hsu, Wei Lun; Xue, Bin; Uversky, Vladimir N.; Romero, Pedro; Dunker, A.

In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2012, p. 128-139.

Research output: Contribution to journalArticle

Huang, F, Oldfield, C, Meng, J, Hsu, WL, Xue, B, Uversky, VN, Romero, P & Dunker, A 2012, 'Subclassifying disordered proteins by the CH-CDF plot method.', Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 128-139.
Huang, Fei ; Oldfield, Christopher ; Meng, Jingwei ; Hsu, Wei Lun ; Xue, Bin ; Uversky, Vladimir N. ; Romero, Pedro ; Dunker, A. / Subclassifying disordered proteins by the CH-CDF plot method. In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2012 ; pp. 128-139.
@article{b2f55049a207416492e83728c315962d,
title = "Subclassifying disordered proteins by the CH-CDF plot method.",
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.",
author = "Fei Huang and Christopher Oldfield and Jingwei Meng and Hsu, {Wei Lun} and Bin Xue and Uversky, {Vladimir N.} and Pedro Romero and A. Dunker",
year = "2012",
language = "English (US)",
pages = "128--139",
journal = "Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing",
issn = "2335-6936",

}

TY - JOUR

T1 - Subclassifying disordered proteins by the CH-CDF plot method.

AU - Huang, Fei

AU - Oldfield, Christopher

AU - Meng, Jingwei

AU - Hsu, Wei Lun

AU - Xue, Bin

AU - Uversky, Vladimir N.

AU - Romero, Pedro

AU - Dunker, A.

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84891464898&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84891464898&partnerID=8YFLogxK

M3 - Article

SP - 128

EP - 139

JO - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

JF - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

SN - 2335-6936

ER -