Abstract
BackgroundProtein-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.ResultsWe 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.ConclusionBased 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.ReviewersThis article was reviewed by Sandor Pongor, Gajendra Raghava and Narayanaswamy Srinivasan.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0039-8) contains supplementary material, which is available to authorized users.
Highlights
IntroductionUnderstanding the recognition mechanism of protein-Ribonucleic acid (RNA) complexes has been a challenging task in molecular and computational biology
Protein-Ribonucleic acid (RNA) interactions perform diverse functions within the cell
We have investigated the organism specific recognition of protein-RNA complexes based on various sequence and structure based features such as binding propensity, preference of residues at conserved positions, binding segments, binding motifs, neighboring residues and interacting amino acid-nucleotide pairs
Summary
Understanding the recognition mechanism of protein-RNA complexes has been a challenging task in molecular and computational biology. The recognition mechanisms of protein-RNA complexes and their functional importance have been mainly elucidated by three-dimensional structure determination of proteinRNA complexes [2] along with other molecular biology experiments such as site directed mutagenesis, fluorescence resonance energy transfer (FRET) imaging, etc. The availability of protein-RNA complex structures in PDB [6] has enabled researchers to develop secondary databases [7,8] and to analyze the binding sites in terms of atomic contacts, amino acid composition, preference of residues, secondary structures, solvent accessibility, electrostatic interactions, hydrophobic contacts, hydrogen bonding, cation-π, stacking and van der Waals interactions [3,9,10]. Fornes et al reviewed the applications of knowledge-based potentials for evaluating the models of protein-RNA interactions along with other complexes [12]
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