IDPM: an online database for ion distribution in protein molecules

Abstract Background Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case...

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Main Authors: Xilun Xiang, Haiguang Liu
Format: Article
Language:English
Published: BMC 2018-03-01
Series:BMC Bioinformatics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12859-018-2110-9
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spelling doaj-e134b071370c477cbeaf73a684e53c0a2020-11-25T00:36:58ZengBMCBMC Bioinformatics1471-21052018-03-0119111210.1186/s12859-018-2110-9IDPM: an online database for ion distribution in protein moleculesXilun Xiang0Haiguang Liu1Complex Systems Division, Beijing Computational Science Research CenterComplex Systems Division, Beijing Computational Science Research CenterAbstract Background Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case basis is valuable, it is also important to study the ion-protein interaction statistically. From experimentally determined structures, it is possible to examine the ion distribution around each amino acid. Such distributions can reveal relation between ions and amino acids, so it is desirable to carry out a systematic survey of ‘ion-amino acid’ pairing interaction and share the information with a publicly available database. Results The survey in the Protein Data Bank (PDB) revealed that approximately 40% of molecules records contain at least one ion. To reduce the bias resulted from protein redundancy, the statistics were extracted from a non-redundant dataset by excluding the proteins with similar sequences. Based on the structures of protein molecules and the location of ions, the statistical distributions of ions around each proteinogenic amino acid type were investigated and further summarized in a database. To systematically quantify the interactions between ions and each amino acid, the positions of ions were mapped to the coordinate system centered at each neighboring amino acid. It was found that the distribution of ions follows the expected rules governed by the physicochemical interactions in general. Large variations were observed, reflecting the preference in ‘ion-amino acid’ interactions. The analysis program is written in the Python programming language. The statistical results and program are available from the online database: ion distribution in protein molecules (IDPM) at http://liulab.csrc.ac.cn/idpm/. Conclusion The spatial distribution of ions around amino acids is documented and analyzed. The statistics can be useful for identifying ion types for a given site in biomolecules, and can be potentially used in ion position prediction for given structures.http://link.springer.com/article/10.1186/s12859-018-2110-9Ion distributionProteinStatistical analysisDatabase
collection DOAJ
language English
format Article
sources DOAJ
author Xilun Xiang
Haiguang Liu
spellingShingle Xilun Xiang
Haiguang Liu
IDPM: an online database for ion distribution in protein molecules
BMC Bioinformatics
Ion distribution
Protein
Statistical analysis
Database
author_facet Xilun Xiang
Haiguang Liu
author_sort Xilun Xiang
title IDPM: an online database for ion distribution in protein molecules
title_short IDPM: an online database for ion distribution in protein molecules
title_full IDPM: an online database for ion distribution in protein molecules
title_fullStr IDPM: an online database for ion distribution in protein molecules
title_full_unstemmed IDPM: an online database for ion distribution in protein molecules
title_sort idpm: an online database for ion distribution in protein molecules
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2018-03-01
description Abstract Background Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case basis is valuable, it is also important to study the ion-protein interaction statistically. From experimentally determined structures, it is possible to examine the ion distribution around each amino acid. Such distributions can reveal relation between ions and amino acids, so it is desirable to carry out a systematic survey of ‘ion-amino acid’ pairing interaction and share the information with a publicly available database. Results The survey in the Protein Data Bank (PDB) revealed that approximately 40% of molecules records contain at least one ion. To reduce the bias resulted from protein redundancy, the statistics were extracted from a non-redundant dataset by excluding the proteins with similar sequences. Based on the structures of protein molecules and the location of ions, the statistical distributions of ions around each proteinogenic amino acid type were investigated and further summarized in a database. To systematically quantify the interactions between ions and each amino acid, the positions of ions were mapped to the coordinate system centered at each neighboring amino acid. It was found that the distribution of ions follows the expected rules governed by the physicochemical interactions in general. Large variations were observed, reflecting the preference in ‘ion-amino acid’ interactions. The analysis program is written in the Python programming language. The statistical results and program are available from the online database: ion distribution in protein molecules (IDPM) at http://liulab.csrc.ac.cn/idpm/. Conclusion The spatial distribution of ions around amino acids is documented and analyzed. The statistics can be useful for identifying ion types for a given site in biomolecules, and can be potentially used in ion position prediction for given structures.
topic Ion distribution
Protein
Statistical analysis
Database
url http://link.springer.com/article/10.1186/s12859-018-2110-9
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AT haiguangliu idpmanonlinedatabaseforiondistributioninproteinmolecules
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