Analysis of protein structural motifs in terms of sets of codes representing local structures

J. An, Hiroshi Wako, A. Sarai

Research output: Contribution to journalArticle

Abstract

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.

Original languageEnglish
Pages (from-to)905-910
Number of pages6
JournalMolecular Biology
Volume35
Issue number6
DOIs
Publication statusPublished - 2001 Nov

Fingerprint

Amino Acid Motifs
Proteins
Cluster Analysis
Amino Acid Sequence

Keywords

  • Delaunay tessellation
  • Motif
  • Three-dimensional structure

ASJC Scopus subject areas

  • Genetics

Cite this

Analysis of protein structural motifs in terms of sets of codes representing local structures. / An, J.; Wako, Hiroshi; Sarai, A.

In: Molecular Biology, Vol. 35, No. 6, 11.2001, p. 905-910.

Research output: Contribution to journalArticle

@article{3970871cbd2f461e93c368075103823e,
title = "Analysis of protein structural motifs in terms of sets of codes representing local structures",
abstract = "An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.",
keywords = "Delaunay tessellation, Motif, Three-dimensional structure",
author = "J. An and Hiroshi Wako and A. Sarai",
year = "2001",
month = "11",
doi = "10.1023/A:1013250721578",
language = "English",
volume = "35",
pages = "905--910",
journal = "Molecular Biology",
issn = "0026-8933",
publisher = "Maik Nauka-Interperiodica Publishing",
number = "6",

}

TY - JOUR

T1 - Analysis of protein structural motifs in terms of sets of codes representing local structures

AU - An, J.

AU - Wako, Hiroshi

AU - Sarai, A.

PY - 2001/11

Y1 - 2001/11

N2 - An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.

AB - An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.

KW - Delaunay tessellation

KW - Motif

KW - Three-dimensional structure

UR - http://www.scopus.com/inward/record.url?scp=0035566642&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035566642&partnerID=8YFLogxK

U2 - 10.1023/A:1013250721578

DO - 10.1023/A:1013250721578

M3 - Article

VL - 35

SP - 905

EP - 910

JO - Molecular Biology

JF - Molecular Biology

SN - 0026-8933

IS - 6

ER -