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Structure based approach for understanding organism specific recognition of protein-RNA complexes
BACKGROUND: Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes has been a challenging task in molecular and computational biology. In earlier works, the recognition mechanisms have been studied for a specific complex o...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352265/ https://www.ncbi.nlm.nih.gov/pubmed/25886642 http://dx.doi.org/10.1186/s13062-015-0039-8 |
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author | Nagarajan, Raju Chothani, Sonia Pankaj Ramakrishnan, Chandrasekaran Sekijima, Masakazu Gromiha, M Michael |
author_facet | Nagarajan, Raju Chothani, Sonia Pankaj Ramakrishnan, Chandrasekaran Sekijima, Masakazu Gromiha, M Michael |
author_sort | Nagarajan, Raju |
collection | PubMed |
description | BACKGROUND: Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes has been a challenging task in molecular and computational biology. In earlier works, the recognition mechanisms have been studied for a specific complex or using a set of non–redundant complexes. In this work, we have constructed 18 sets of same protein-RNA complexes belonging to different organisms from Protein Data Bank (PDB). The similarities and differences in each set of complexes have been revealed in terms of various sequence and structure based features such as root mean square deviation, sequence homology, propensity of binding site residues, variance, conservation at binding sites, binding segments, binding motifs of amino acid residues and nucleotides, preferred amino acid-nucleotide pairs and influence of neighboring residues for binding. RESULTS: We found that the proteins of mesophilic organisms have more number of binding sites than thermophiles and the binding propensities of amino acid residues are distinct in E. coli, H. sapiens, S. cerevisiae, thermophiles and archaea. Proteins prefer to bind with RNA using a single residue segment in all the organisms while RNA prefers to use a stretch of up to six nucleotides for binding with proteins. We have developed amino acid residue-nucleotide pair potentials for different organisms, which could be used for predicting the binding specificity. Further, molecular dynamics simulation studies on aspartyl tRNA synthetase complexed with aspartyl tRNA showed specific modes of recognition in E. coli, T. thermophilus and S. cerevisiae. CONCLUSION: Based on structural analysis and molecular dynamics simulations we suggest that the mode of recognition depends on the type of the organism in a protein-RNA complex. REVIEWERS: This article was reviewed by Sandor Pongor, Gajendra Raghava and Narayanaswamy Srinivasan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13062-015-0039-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4352265 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-43522652015-03-08 Structure based approach for understanding organism specific recognition of protein-RNA complexes Nagarajan, Raju Chothani, Sonia Pankaj Ramakrishnan, Chandrasekaran Sekijima, Masakazu Gromiha, M Michael Biol Direct Research BACKGROUND: Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes has been a challenging task in molecular and computational biology. In earlier works, the recognition mechanisms have been studied for a specific complex or using a set of non–redundant complexes. In this work, we have constructed 18 sets of same protein-RNA complexes belonging to different organisms from Protein Data Bank (PDB). The similarities and differences in each set of complexes have been revealed in terms of various sequence and structure based features such as root mean square deviation, sequence homology, propensity of binding site residues, variance, conservation at binding sites, binding segments, binding motifs of amino acid residues and nucleotides, preferred amino acid-nucleotide pairs and influence of neighboring residues for binding. RESULTS: We found that the proteins of mesophilic organisms have more number of binding sites than thermophiles and the binding propensities of amino acid residues are distinct in E. coli, H. sapiens, S. cerevisiae, thermophiles and archaea. Proteins prefer to bind with RNA using a single residue segment in all the organisms while RNA prefers to use a stretch of up to six nucleotides for binding with proteins. We have developed amino acid residue-nucleotide pair potentials for different organisms, which could be used for predicting the binding specificity. Further, molecular dynamics simulation studies on aspartyl tRNA synthetase complexed with aspartyl tRNA showed specific modes of recognition in E. coli, T. thermophilus and S. cerevisiae. CONCLUSION: Based on structural analysis and molecular dynamics simulations we suggest that the mode of recognition depends on the type of the organism in a protein-RNA complex. REVIEWERS: This article was reviewed by Sandor Pongor, Gajendra Raghava and Narayanaswamy Srinivasan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13062-015-0039-8) contains supplementary material, which is available to authorized users. BioMed Central 2015-03-07 /pmc/articles/PMC4352265/ /pubmed/25886642 http://dx.doi.org/10.1186/s13062-015-0039-8 Text en © Nagarajan et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Nagarajan, Raju Chothani, Sonia Pankaj Ramakrishnan, Chandrasekaran Sekijima, Masakazu Gromiha, M Michael Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title | Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title_full | Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title_fullStr | Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title_full_unstemmed | Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title_short | Structure based approach for understanding organism specific recognition of protein-RNA complexes |
title_sort | structure based approach for understanding organism specific recognition of protein-rna complexes |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352265/ https://www.ncbi.nlm.nih.gov/pubmed/25886642 http://dx.doi.org/10.1186/s13062-015-0039-8 |
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