Hydration of protein-RNA recognition sites.
Bottom Line: Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction do not make any.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.
Affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.Show MeSH
Related in: MedlinePlus
Mentions: Of all the water–RNA H-bonds, the ribose contributes about 45% (14 per interface), whereas the phosphate and the bases contribute 30% (9 per interface) and 25% (7 per interface), respectively. This contribution differs in direct protein–RNA H-bonds, where the phosphate group contributes slightly more (36% or 7 H-bonds per interface) than the bases or the ribose (both contribute about 32% or 6 H-bonds per interface). Among the different bases, guanine and uracil are more frequently found in water-mediated H-bonds than adenine and cytosine. Similar trend is observed for different bases involved in direct H-bonds. Polar groups in all the four bases are frequently found as acceptors in water-mediated H-bonds rather than donors (Figure 3B). The relative contributions of ribose, phosphate and bases in water-mediated H-bonds across different classes are shown in Figure 4. It shows that the ribose contributes twice more than the phosphate and even thrice more than the bases in interfaces with tRNA. Similar trend is observed in interfaces with duplex RNA. In interfaces with ribosomal proteins, contributions of the ribose and the phosphate are almost identical, and each of them contributes more than the bases. In contrast, contributions of the sugar and the bases are almost identical, and each of them contributes more than the phosphate in interfaces with single-stranded RNA.
Affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.