title: Hydration of protein-RNA recognition sites.
abstract: We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively 'dry' than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2'OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.
authors.forename: Amita
authors.initials: A
authors.lastname: Barik
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India r.bahadur@hijli.iitkgp.ernet.in.
authors.forename: Ranjit Prasad
authors.initials: RP
authors.lastname: Bahadur
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D014867:Water; D012313:RNA; D012343:RNA, Transfer
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