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Structure based approach for understanding organism specific recognition of protein-RNA complexes.

Nagarajan R, Chothani SP, Ramakrishnan C, Sekijima M, Gromiha MM - Biol. Direct (2015)

Bottom Line: 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.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.This article was reviewed by Sandor Pongor, Gajendra Raghava and Narayanaswamy Srinivasan.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. nagabioinfostar@gmail.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Normalized binding propensity of nucleotides in different organisms.
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Fig2: Normalized binding propensity of nucleotides in different organisms.

Mentions: We have computed the normalized binding propensity of nucleotides in E. coli, H. sapiens, S. cerevisiae, thermophiles and archaea, and the results are presented in FigureĀ 2. We observed that the propensity is high for adenine in H. sapiens and archaea, uracil in S. cerevisiae and cytosine in E. coli and thermophilies. Cytosine has the propensity of more than one in 4 of the 5 considered groups. The propensity of guanine lies between the propensities of other nucleotides in all organisms. This analysis also emphasizes different modes of recognition by different organisms. However, it is noteworthy that the difference in propensity among the four nucleotides in different organisms is less than that of 20 amino acid residues.Figure 2


Structure based approach for understanding organism specific recognition of protein-RNA complexes.

Nagarajan R, Chothani SP, Ramakrishnan C, Sekijima M, Gromiha MM - Biol. Direct (2015)

Normalized binding propensity of nucleotides in different organisms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4352265&req=5

Fig2: Normalized binding propensity of nucleotides in different organisms.
Mentions: We have computed the normalized binding propensity of nucleotides in E. coli, H. sapiens, S. cerevisiae, thermophiles and archaea, and the results are presented in FigureĀ 2. We observed that the propensity is high for adenine in H. sapiens and archaea, uracil in S. cerevisiae and cytosine in E. coli and thermophilies. Cytosine has the propensity of more than one in 4 of the 5 considered groups. The propensity of guanine lies between the propensities of other nucleotides in all organisms. This analysis also emphasizes different modes of recognition by different organisms. However, it is noteworthy that the difference in propensity among the four nucleotides in different organisms is less than that of 20 amino acid residues.Figure 2

Bottom Line: 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.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.This article was reviewed by Sandor Pongor, Gajendra Raghava and Narayanaswamy Srinivasan.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. nagabioinfostar@gmail.com.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus