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