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Structural Position Correlation Analysis (SPCA) for Protein Family

BACKGROUND: The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by tw...

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Autores principales: Du, Qi-Shi, Meng, Jian-Zong, Wang, Cheng-Hua, Long, Si-Yu, Huang, Ri-Bo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230615/
https://www.ncbi.nlm.nih.gov/pubmed/22163002
http://dx.doi.org/10.1371/journal.pone.0028206
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author Du, Qi-Shi
Meng, Jian-Zong
Wang, Cheng-Hua
Long, Si-Yu
Huang, Ri-Bo
author_facet Du, Qi-Shi
Meng, Jian-Zong
Wang, Cheng-Hua
Long, Si-Yu
Huang, Ri-Bo
author_sort Du, Qi-Shi
collection PubMed
description BACKGROUND: The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by two or three catalytic residues with the collaboration of several functional residues at key positions. Communication signals are conducted in a position network, adjusting the biological functions in the protein family. METHODOLOGY: A computational approach, namely structural position correlation analysis (SPCA), is developed to analyze the correlation relationship between structural segments (or positions). The basic hypothesis of SPCA is that in a protein family the structural conservation is more important than the sequence conservation, and the local structural changes may contain information of biology functional evolution. A standard protein P((0)) is defined in a protein family, which consists of the most-frequent amino acids and takes the average structure of the protein family. The foundational variables of SPCA is the structural position displacements between the standard protein P((0)) and individual proteins P(i) of the family. The structural positions are organized as segments, which are the stable units in structural displacements of the protein family. The biological function differences of protein members are determined by the position structural displacements of individual protein P(i) to the standard protein P((0)). Correlation analysis is used to analyze the communication network among segments. CONCLUSIONS: The structural position correlation analysis (SPCA) is able to find the correlation relationship among the structural segments (or positions) in a protein family, which cannot be detected by the amino acid sequence and frequency-based methods. The functional communication network among the structural segments (or positions) in protein family, revealed by SPCA approach, well illustrate the distantly allosteric interactions, and contains valuable information for protein engineering study.
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spelling pubmed-32306152011-12-09 Structural Position Correlation Analysis (SPCA) for Protein Family Du, Qi-Shi Meng, Jian-Zong Wang, Cheng-Hua Long, Si-Yu Huang, Ri-Bo PLoS One Research Article BACKGROUND: The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by two or three catalytic residues with the collaboration of several functional residues at key positions. Communication signals are conducted in a position network, adjusting the biological functions in the protein family. METHODOLOGY: A computational approach, namely structural position correlation analysis (SPCA), is developed to analyze the correlation relationship between structural segments (or positions). The basic hypothesis of SPCA is that in a protein family the structural conservation is more important than the sequence conservation, and the local structural changes may contain information of biology functional evolution. A standard protein P((0)) is defined in a protein family, which consists of the most-frequent amino acids and takes the average structure of the protein family. The foundational variables of SPCA is the structural position displacements between the standard protein P((0)) and individual proteins P(i) of the family. The structural positions are organized as segments, which are the stable units in structural displacements of the protein family. The biological function differences of protein members are determined by the position structural displacements of individual protein P(i) to the standard protein P((0)). Correlation analysis is used to analyze the communication network among segments. CONCLUSIONS: The structural position correlation analysis (SPCA) is able to find the correlation relationship among the structural segments (or positions) in a protein family, which cannot be detected by the amino acid sequence and frequency-based methods. The functional communication network among the structural segments (or positions) in protein family, revealed by SPCA approach, well illustrate the distantly allosteric interactions, and contains valuable information for protein engineering study. Public Library of Science 2011-12-05 /pmc/articles/PMC3230615/ /pubmed/22163002 http://dx.doi.org/10.1371/journal.pone.0028206 Text en Du et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Du, Qi-Shi
Meng, Jian-Zong
Wang, Cheng-Hua
Long, Si-Yu
Huang, Ri-Bo
Structural Position Correlation Analysis (SPCA) for Protein Family
title Structural Position Correlation Analysis (SPCA) for Protein Family
title_full Structural Position Correlation Analysis (SPCA) for Protein Family
title_fullStr Structural Position Correlation Analysis (SPCA) for Protein Family
title_full_unstemmed Structural Position Correlation Analysis (SPCA) for Protein Family
title_short Structural Position Correlation Analysis (SPCA) for Protein Family
title_sort structural position correlation analysis (spca) for protein family
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230615/
https://www.ncbi.nlm.nih.gov/pubmed/22163002
http://dx.doi.org/10.1371/journal.pone.0028206
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