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: The dataset consists of 89 X-ray structures of protein–RNA complexes with resolution 2.6 Å or better (Supplementary Table S1), reporting a total of 19 327 crystallographic waters bound to them. We have identified 2440 waters (∼13% of all the bound crystallographic waters) bound at the interface, contributing to the recognition process. Thus, an average protein–RNA complex contains about 217 bound waters, of which, 27 (equivalent to 11 per 1000 Å2 of B) are at the interface (Table 1). The number of interface waters ranges from 4 to 116, and tends to increase with B (Figure 1), although the correlation between them is mediocre (Pearson correlation coefficient R = 0.49). Exceptionally, the interface between RNA-dependent RNA polymerase of bacteriophage phi6 and a 6 nt RNA (PDB id: 1UVI) contains only two waters. Here, the small RNA molecule interacts with the core region of the polymerase, which is almost dehydrated (47). On the other hand, the interface between arginyl-tRNA synthetase and its cognate tRNA (Arg) (PDB id: 1F7U) contains 116 waters, highest in this dataset. This complex contains 588 bound waters, and it has been observed that a large number of water-mediated interactions confer a high adaptability to the interface while providing the required specificity and affinity in the recognition process (48). The wide range of the number of interface waters may be attributed to the inconsistent representation of the solvent position in the crystallographic studies, which is evident by the presence of fewer molecules in low-resolution X-ray structures (18). However, this range remains wide, 4–64, in a 1.8 Å subset, suggesting strongly that in spite of the inconsistent reporting there are real differences between protein–RNA interfaces in terms of hydration. On an average, interfaces with tRNA are more than twice larger than those with ribosomal proteins and single-stranded RNA (Table 1). Although the interfaces with tRNA contain the highest number of water molecules, their surface density is less due to the large size of their interfaces. Among the different classes, interfaces with tRNA are less hydrated (9.3 water molecules per 1000 Å2 of B) compared to interfaces with single-stranded RNA (11.0 per 1000 Å2 of B) or duplex RNA (12.4 per 1000 Å2 of B). In contrast, interfaces with ribosomal proteins are most hydrated (14.5 per 1000 Å2 of B). This lowest density of immobilized waters at the tRNA interfaces is justified by their relatively more hydrophobic nature compared to the other three classes (Table 1). ANOVA (analysis of variance) test was performed to find the statistical significance in the differences in mean number of interface waters of four classes. The P-value (at α = 0.05 level of significance) obtained is 0.0091, rejecting the hypothesis (mean values are same in all the four classes).
Affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.