TOP-IDP-scale: A new amino acid scale measuring propensity for intrinsic disorder

Andrew Campen, Ryan M. Williams, Celeste J. Brown, Jingwei Meng, Vladimir N. Uversky, A. Dunker

Research output: Contribution to journalArticle

213 Citations (Scopus)

Abstract

Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(so | χ) and P(sd | χ) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(so | χ) and P(sd | χ) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute's power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10%. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/ disindex.php).

Original languageEnglish
Pages (from-to)956-963
Number of pages8
JournalProtein and Peptide Letters
Volume15
Issue number9
DOIs
StatePublished - Sep 2008

Fingerprint

Inosine Diphosphate
Intrinsically Disordered Proteins
Amino Acids
Simulated annealing
Servers

Keywords

  • Amino acid scale
  • Conditional probability
  • Intrinsic disorder

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology

Cite this

TOP-IDP-scale : A new amino acid scale measuring propensity for intrinsic disorder. / Campen, Andrew; Williams, Ryan M.; Brown, Celeste J.; Meng, Jingwei; Uversky, Vladimir N.; Dunker, A.

In: Protein and Peptide Letters, Vol. 15, No. 9, 09.2008, p. 956-963.

Research output: Contribution to journalArticle

Campen, Andrew ; Williams, Ryan M. ; Brown, Celeste J. ; Meng, Jingwei ; Uversky, Vladimir N. ; Dunker, A. / TOP-IDP-scale : A new amino acid scale measuring propensity for intrinsic disorder. In: Protein and Peptide Letters. 2008 ; Vol. 15, No. 9. pp. 956-963.
@article{957e867728294efbbc0d3a9017a79713,
title = "TOP-IDP-scale: A new amino acid scale measuring propensity for intrinsic disorder",
abstract = "Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(so | χ) and P(sd | χ) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(so | χ) and P(sd | χ) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute's power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10{\%}. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/ disindex.php).",
keywords = "Amino acid scale, Conditional probability, Intrinsic disorder",
author = "Andrew Campen and Williams, {Ryan M.} and Brown, {Celeste J.} and Jingwei Meng and Uversky, {Vladimir N.} and A. Dunker",
year = "2008",
month = "9",
doi = "10.2174/092986608785849164",
language = "English",
volume = "15",
pages = "956--963",
journal = "Protein and Peptide Letters",
issn = "0929-8665",
publisher = "Bentham Science Publishers B.V.",
number = "9",

}

TY - JOUR

T1 - TOP-IDP-scale

T2 - A new amino acid scale measuring propensity for intrinsic disorder

AU - Campen, Andrew

AU - Williams, Ryan M.

AU - Brown, Celeste J.

AU - Meng, Jingwei

AU - Uversky, Vladimir N.

AU - Dunker, A.

PY - 2008/9

Y1 - 2008/9

N2 - Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(so | χ) and P(sd | χ) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(so | χ) and P(sd | χ) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute's power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10%. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/ disindex.php).

AB - Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(so | χ) and P(sd | χ) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(so | χ) and P(sd | χ) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute's power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10%. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/ disindex.php).

KW - Amino acid scale

KW - Conditional probability

KW - Intrinsic disorder

UR - http://www.scopus.com/inward/record.url?scp=52249124593&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=52249124593&partnerID=8YFLogxK

U2 - 10.2174/092986608785849164

DO - 10.2174/092986608785849164

M3 - Article

C2 - 18991772

AN - SCOPUS:52249124593

VL - 15

SP - 956

EP - 963

JO - Protein and Peptide Letters

JF - Protein and Peptide Letters

SN - 0929-8665

IS - 9

ER -