title: Molecular architecture of protein-RNA recognition sites.
abstract: The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.
authors.affiliation: a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.
authors.forename: Amita
authors.initials: A
authors.lastname: Barik
authors.affiliation: a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.
authors.forename: Nithin
authors.initials: N
authors.lastname: C
authors.affiliation: a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.
authors.forename: Smita P
authors.initials: SP
authors.lastname: Pilla
authors.affiliation: a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.
authors.forename: Ranjit Prasad
authors.initials: RP
authors.lastname: Bahadur
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D006860:Hydrogen Bonding; D046911:Macromolecular Substances / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity
chemical_list: D000596:Amino Acids; D046911:Macromolecular Substances; D016601:RNA-Binding Proteins; D012313:RNA; D012343:RNA, Transfer
keywords: hydrogen bond; interfaces area; protein-RNA complexes; protein-RNA interfaces; salt bridges; shape complementarity