Abstract
We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein–RNA interfaces to probe the binding hot spots at protein–RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein–protein and protein–RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein–RNA recognition sites with desired affinity.
Highlights
Majority of cellular functions are governed by macromolecular interactions, and macromolecules are under constant evolutionary pressure for selecting their partners in a crowded cellular environment
Comparing the bound and the unbound structures of the protein–RNA complexes, we identified three possible hydration sites at the interface: (i) water preservation site (WP), where a protein polar group makes the same H-bond with a water molecule in the bound and in the unbound structures; (ii) hydrated site (WH), where a protein polar group in the bound structure makes Hbond(s) with a water molecule, which is absent in the unbound structure; and (iii) dehydrated site (WD), where a protein polar group in the unbound structure makes Hbond(s) with a water molecule, which is absent in the bound
Comparing the bound and the unbound structures of the components involved in protein–RNA complexes, we identified three sites at the protein surface that interact with the interface waters: water preservation site (WP), hydrated site (WH) and dehydrated site (WD)
Summary
Majority of cellular functions are governed by macromolecular interactions, and macromolecules are under constant evolutionary pressure for selecting their partners in a crowded cellular environment. Conserved residues have often been used to determine the oligomeric state of the proteins [7], and are subject to the drug targets [5]. They have been extensively used to discriminate between the transient and the obligate protein–protein complexes [8], as well as between the biological contact and the crystal-packing protein–protein interfaces [9,10]. It has been shown that the evolutionary conserved residues often contribute significantly to the binding free energy [2,10,12]; they are not distributed evenly at the recognition site [5,11,13]
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