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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.

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

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Hydration pattern in protein–RNA interfaces. In each diagram, the protein chain is shown as molecular surface and the RNA chain is shown as ribbon. The interface region is colored blue, and the interface water molecules are represented by red sphere. (A) A ‘wet’ interface between arginyl-tRNA synthetase and its cognate tRNA (1F7U; dr = 0.84). (B) A ‘dry’ interface between ribosomal protein L1 and mRNA (2HW8; dr = 1.18). (C) A ‘wet’ interface between FAB and duplex RNA (2R8S; dr = 0.95). (D) A ‘dry’ interface between CspB and single-stranded RNA (3PF4; dr = 1.46).
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Figure 5: Hydration pattern in protein–RNA interfaces. In each diagram, the protein chain is shown as molecular surface and the RNA chain is shown as ribbon. The interface region is colored blue, and the interface water molecules are represented by red sphere. (A) A ‘wet’ interface between arginyl-tRNA synthetase and its cognate tRNA (1F7U; dr = 0.84). (B) A ‘dry’ interface between ribosomal protein L1 and mRNA (2HW8; dr = 1.18). (C) A ‘wet’ interface between FAB and duplex RNA (2R8S; dr = 0.95). (D) A ‘dry’ interface between CspB and single-stranded RNA (3PF4; dr = 1.46).

Mentions: Depending on the spatial distribution of the interface waters, macromolecular interfaces can be distinguished into ‘wet’ and ‘dry’ categories (25). We used dr (as described in the ‘Materials and Methods’ section) to quantify the ‘dry’ and ‘wet’ protein–RNA interfaces. Figure 5 shows the spatial distribution of the interface waters in four protein–RNA complexes. Interfaces with tRNA and duplex RNA are generally ‘wet’ with an average dr of 0.86 and 0.98, respectively, whereas the interfaces with ribosomal proteins and single-stranded RNA are ‘dry’ with an average dr of 1.17 and 1.07, respectively (Table 2). The interface of arginyl-tRNA synthetase and its cognate tRNA (PDB id: 1F7U) contains 116 waters. They are distributed throughout the interface, making it ‘wet’ (dr = 0.84; Figure 5A). All the tRNA interfaces in this dataset are ‘wet’ with dr between 0.67 and 1.00. On the other hand, all the interfaces with ribosomal proteins are ‘dry’ with dr >1.0. This is evident in the ribosomal protein L1–mRNA interface (PDB id: 2HW8), where the waters are distributed along the periphery of the interface, making it ‘dry’ (dr = 1.18; Figure 5B). With few exceptions, majority of the interfaces involving duplex RNA are ‘wet’ with an average dr of 0.98. This is evident in the Fab–RNA interface (PDB id: 2R8S) where the waters are distributed throughout the interface, making it ‘wet’ (dr = 0.95; Figure 5C). In spite of few exceptions, majority of the interfaces involving single-stranded RNA are ‘dry’ with an average dr of 1.07. Figure 5D shows a ‘dry’ interface between cold shock protein B and single-stranded RNA (PDB id: 3PF4) where the waters are distributed along the periphery of the interface (dr = 1.46). The distribution of the dr values for the 89 interfaces is shown in the Supplementary Figure S4. A two-tailed t-test (at α = 0.05 level of significance) shows that there is a significant difference (P-value 2.34E-18) between the ‘dry’ and ‘wet’ interfaces separated by cut-off value 1.0.


Hydration of protein-RNA recognition sites.

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

Hydration pattern in protein–RNA interfaces. In each diagram, the protein chain is shown as molecular surface and the RNA chain is shown as ribbon. The interface region is colored blue, and the interface water molecules are represented by red sphere. (A) A ‘wet’ interface between arginyl-tRNA synthetase and its cognate tRNA (1F7U; dr = 0.84). (B) A ‘dry’ interface between ribosomal protein L1 and mRNA (2HW8; dr = 1.18). (C) A ‘wet’ interface between FAB and duplex RNA (2R8S; dr = 0.95). (D) A ‘dry’ interface between CspB and single-stranded RNA (3PF4; dr = 1.46).
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Figure 5: Hydration pattern in protein–RNA interfaces. In each diagram, the protein chain is shown as molecular surface and the RNA chain is shown as ribbon. The interface region is colored blue, and the interface water molecules are represented by red sphere. (A) A ‘wet’ interface between arginyl-tRNA synthetase and its cognate tRNA (1F7U; dr = 0.84). (B) A ‘dry’ interface between ribosomal protein L1 and mRNA (2HW8; dr = 1.18). (C) A ‘wet’ interface between FAB and duplex RNA (2R8S; dr = 0.95). (D) A ‘dry’ interface between CspB and single-stranded RNA (3PF4; dr = 1.46).
Mentions: Depending on the spatial distribution of the interface waters, macromolecular interfaces can be distinguished into ‘wet’ and ‘dry’ categories (25). We used dr (as described in the ‘Materials and Methods’ section) to quantify the ‘dry’ and ‘wet’ protein–RNA interfaces. Figure 5 shows the spatial distribution of the interface waters in four protein–RNA complexes. Interfaces with tRNA and duplex RNA are generally ‘wet’ with an average dr of 0.86 and 0.98, respectively, whereas the interfaces with ribosomal proteins and single-stranded RNA are ‘dry’ with an average dr of 1.17 and 1.07, respectively (Table 2). The interface of arginyl-tRNA synthetase and its cognate tRNA (PDB id: 1F7U) contains 116 waters. They are distributed throughout the interface, making it ‘wet’ (dr = 0.84; Figure 5A). All the tRNA interfaces in this dataset are ‘wet’ with dr between 0.67 and 1.00. On the other hand, all the interfaces with ribosomal proteins are ‘dry’ with dr >1.0. This is evident in the ribosomal protein L1–mRNA interface (PDB id: 2HW8), where the waters are distributed along the periphery of the interface, making it ‘dry’ (dr = 1.18; Figure 5B). With few exceptions, majority of the interfaces involving duplex RNA are ‘wet’ with an average dr of 0.98. This is evident in the Fab–RNA interface (PDB id: 2R8S) where the waters are distributed throughout the interface, making it ‘wet’ (dr = 0.95; Figure 5C). In spite of few exceptions, majority of the interfaces involving single-stranded RNA are ‘dry’ with an average dr of 1.07. Figure 5D shows a ‘dry’ interface between cold shock protein B and single-stranded RNA (PDB id: 3PF4) where the waters are distributed along the periphery of the interface (dr = 1.46). The distribution of the dr values for the 89 interfaces is shown in the Supplementary Figure S4. A two-tailed t-test (at α = 0.05 level of significance) shows that there is a significant difference (P-value 2.34E-18) between the ‘dry’ and ‘wet’ interfaces separated by cut-off value 1.0.

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