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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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Related in: MedlinePlus

Percentage contribution of (A) amino acid residues, and (B) nucleotide bases to the interface water-mediated H-bonds. One-letter codes of the amino acid residues along with their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (A). One-letter codes of the nucleotide bases and their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (B).
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Figure 3: Percentage contribution of (A) amino acid residues, and (B) nucleotide bases to the interface water-mediated H-bonds. One-letter codes of the amino acid residues along with their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (A). One-letter codes of the nucleotide bases and their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (B).

Mentions: Table 3 and Figure 3A describe the frequency of chemical groups involved in water-mediated H-bonds. The neutral polar side chains of amino acid residues have the highest contribution followed by the charged side chains, and the main chain oxygen and nitrogen. The side chains of the neutral polar amino acids like Asn, Gln, Thr and Tyr are preferable acceptors, while the side chains of His and Ser have no such preferences. Among the charged side chains, Arg and Lys are the major donors, while Asp and Glu are the major acceptors. In contrast to the water-mediated H-bonds, the charged side chains have the highest contribution in the direct H-bonds followed by the neutral polar side chains, and the main chain nitrogen and oxygen.


Hydration of protein-RNA recognition sites.

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

Percentage contribution of (A) amino acid residues, and (B) nucleotide bases to the interface water-mediated H-bonds. One-letter codes of the amino acid residues along with their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (A). One-letter codes of the nucleotide bases and their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (B).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Percentage contribution of (A) amino acid residues, and (B) nucleotide bases to the interface water-mediated H-bonds. One-letter codes of the amino acid residues along with their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (A). One-letter codes of the nucleotide bases and their contribution as the donor (D) or as the acceptor (A) are given along the abscissa in (B).
Mentions: Table 3 and Figure 3A describe the frequency of chemical groups involved in water-mediated H-bonds. The neutral polar side chains of amino acid residues have the highest contribution followed by the charged side chains, and the main chain oxygen and nitrogen. The side chains of the neutral polar amino acids like Asn, Gln, Thr and Tyr are preferable acceptors, while the side chains of His and Ser have no such preferences. Among the charged side chains, Arg and Lys are the major donors, while Asp and Glu are the major acceptors. In contrast to the water-mediated H-bonds, the charged side chains have the highest contribution in the direct H-bonds followed by the neutral polar side chains, and the main chain nitrogen and oxygen.

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