title: Structure based approach for understanding organism specific recognition of protein-RNA complexes.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. nagabioinfostar@gmail.com.
authors.forename: Raju
authors.initials: R
authors.lastname: Nagarajan
authors.affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. sonya2611@gmail.com.|Philips Research North America, 345 Scarborough Road, Briarcliff Manor, NY, 10510, USA. sonya2611@gmail.com.
authors.forename: Sonia Pankaj
authors.initials: SP
authors.lastname: Chothani
authors.affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. ramki.rpcr@gmail.com.
authors.forename: Chandrasekaran
authors.initials: C
authors.lastname: Ramakrishnan
authors.affiliation: Global Scientific Information and Computing Center (GSIC), Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. sekijima@gsic.titech.ac.jp.
authors.forename: Masakazu
authors.initials: M
authors.lastname: Sekijima
authors.affiliation: Department of Biotechnology, Bhupat Jyoti Metha School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India. gromiha@iitm.ac.in.
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
mesh_terms: D020816:Amino Acid Motifs; D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003460:Crystallization; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D006801:Humans; D056004:Molecular Dynamics Simulation; D009711:Nucleotides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D013045:Species Specificity; D016963:Thermus thermophilus / Q000737:chemistry / Q000235:genetics
chemical_list: D000596:Amino Acids; D009711:Nucleotides; D010455:Peptides; D016601:RNA-Binding Proteins; D012313:RNA