Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar protiens

Gek Huey Chua, Arun Krishnan, Kuo Bin Li, Masaru Tomita

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/ functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7% and a precision of 96.75% in cross-validation tests.

Original languageEnglish
Pages (from-to)1245-1267
Number of pages23
JournalJournal of Bioinformatics and Computational Biology
Volume4
Issue number6
DOIs
Publication statusPublished - 2006 Dec

Fingerprint

Multiresolution analysis
Protein Kinases
Conservation
Proteins
Catalytic Domain
Phosphotransferases
Amino Acids
Mutation
Amino acids

Keywords

  • Amino acid index
  • Function
  • Physicochemical properties
  • Structure
  • Wavelet transform

ASJC Scopus subject areas

  • Medicine(all)
  • Cell Biology

Cite this

Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar protiens. / Chua, Gek Huey; Krishnan, Arun; Li, Kuo Bin; Tomita, Masaru.

In: Journal of Bioinformatics and Computational Biology, Vol. 4, No. 6, 12.2006, p. 1245-1267.

Research output: Contribution to journalArticle

@article{438cedbe9df9459a8c755f8343ca7e93,
title = "Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar protiens",
abstract = "Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/ functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7{\%} and a precision of 96.75{\%} in cross-validation tests.",
keywords = "Amino acid index, Function, Physicochemical properties, Structure, Wavelet transform",
author = "Chua, {Gek Huey} and Arun Krishnan and Li, {Kuo Bin} and Masaru Tomita",
year = "2006",
month = "12",
doi = "10.1142/S0219720006002442",
language = "English",
volume = "4",
pages = "1245--1267",
journal = "Journal of Bioinformatics and Computational Biology",
issn = "0219-7200",
publisher = "World Scientific Publishing Co. Pte Ltd",
number = "6",

}

TY - JOUR

T1 - Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar protiens

AU - Chua, Gek Huey

AU - Krishnan, Arun

AU - Li, Kuo Bin

AU - Tomita, Masaru

PY - 2006/12

Y1 - 2006/12

N2 - Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/ functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7% and a precision of 96.75% in cross-validation tests.

AB - Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/ functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7% and a precision of 96.75% in cross-validation tests.

KW - Amino acid index

KW - Function

KW - Physicochemical properties

KW - Structure

KW - Wavelet transform

UR - http://www.scopus.com/inward/record.url?scp=33846520123&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846520123&partnerID=8YFLogxK

U2 - 10.1142/S0219720006002442

DO - 10.1142/S0219720006002442

M3 - Article

VL - 4

SP - 1245

EP - 1267

JO - Journal of Bioinformatics and Computational Biology

JF - Journal of Bioinformatics and Computational Biology

SN - 0219-7200

IS - 6

ER -