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Hydration of protein-RNA recognition sites.

Barik A, Bahadur RP - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.

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Number of interface water molecules making zero to four H-bonds to the protein or the RNA component. The bars under ‘0’ H-bond represent the number of water molecules making no H-bond with one partner, but they make H-bonds with the other partner.
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Figure 2: Number of interface water molecules making zero to four H-bonds to the protein or the RNA component. The bars under ‘0’ H-bond represent the number of water molecules making no H-bond with one partner, but they make H-bonds with the other partner.

Mentions: Bridging waters must make at least one H-bond with both the interacting partners. Since water has two donors and two acceptors, tetrahedrally oriented, just two H-bonds will not be specific because the water can potentially rotate to present either a donor or acceptor to the base (27). Therefore, specificity only arises when the water makes more than two H-bonds simultaneously. Figure 2 shows the frequency distribution of interface waters making up to four H-bonds. About 60% of them make one or two H-bonds with the protein polar groups. This percentage increases to 67% with the RNA polar groups. These waters are involved in non-specific recognition, mostly filling up the interface cavities. They also contribute toward maximizing the surface complementarity at the interface (26). Besides, only 6% of the interface waters make three or four H-bonds with the protein polar groups. This percentage increases to 13% with the RNA polar groups. They largely contribute to the specificity in the recognition process, which is exemplified in the interface of arginyl-tRNA synthetase and its cognate tRNA (Arg) (PDB id: 1F7U) (48). This interface contains 116 waters, and 96 of them make at least one H-bond with an interface atom. Delagoutte et al. (48) hypothesized that the water-mediated interactions confer a high adaptability to the interface while providing the required specificity and affinity. We identified a significant number (20%) of waters making three and four H-bonds at this interface, contributing to the specificity of the recognition. In our dataset, 34% of interface waters do not make any H-bond with the protein polar groups, but they make H-bonds with the RNA polar groups. Counter example also exists, however, with a lower fraction of 20%, indicating that waters at the protein–RNA interfaces have preference to make H-bonds with RNA than its partner protein.


Hydration of protein-RNA recognition sites.

Barik A, Bahadur RP - Nucleic Acids Res. (2014)

Number of interface water molecules making zero to four H-bonds to the protein or the RNA component. The bars under ‘0’ H-bond represent the number of water molecules making no H-bond with one partner, but they make H-bonds with the other partner.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150782&req=5

Figure 2: Number of interface water molecules making zero to four H-bonds to the protein or the RNA component. The bars under ‘0’ H-bond represent the number of water molecules making no H-bond with one partner, but they make H-bonds with the other partner.
Mentions: Bridging waters must make at least one H-bond with both the interacting partners. Since water has two donors and two acceptors, tetrahedrally oriented, just two H-bonds will not be specific because the water can potentially rotate to present either a donor or acceptor to the base (27). Therefore, specificity only arises when the water makes more than two H-bonds simultaneously. Figure 2 shows the frequency distribution of interface waters making up to four H-bonds. About 60% of them make one or two H-bonds with the protein polar groups. This percentage increases to 67% with the RNA polar groups. These waters are involved in non-specific recognition, mostly filling up the interface cavities. They also contribute toward maximizing the surface complementarity at the interface (26). Besides, only 6% of the interface waters make three or four H-bonds with the protein polar groups. This percentage increases to 13% with the RNA polar groups. They largely contribute to the specificity in the recognition process, which is exemplified in the interface of arginyl-tRNA synthetase and its cognate tRNA (Arg) (PDB id: 1F7U) (48). This interface contains 116 waters, and 96 of them make at least one H-bond with an interface atom. Delagoutte et al. (48) hypothesized that the water-mediated interactions confer a high adaptability to the interface while providing the required specificity and affinity. We identified a significant number (20%) of waters making three and four H-bonds at this interface, contributing to the specificity of the recognition. In our dataset, 34% of interface waters do not make any H-bond with the protein polar groups, but they make H-bonds with the RNA polar groups. Counter example also exists, however, with a lower fraction of 20%, indicating that waters at the protein–RNA interfaces have preference to make H-bonds with RNA than its partner protein.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.

Show MeSH
Related in: MedlinePlus