Study About The Conbinational Scoring Function In Protein-RNA Docking And The Cation-pi Interactions On Protein-RNA Interfaces

The protein-RNA interaction is very important in cell life cycle and hassignificant influence in many biological processes. Facing the fact that it is still slowand laborious to obtain three dimensional structures of protein-RNA complexes byexperimental methods, protein-RNA docking, which can predict the3D structures ofcomplexes from the monomer structure, can greatly help the elucidation ofprotein-RNA interactions. While the docking methodology of protein-proteincomplexes has been very well established, there are still few docking and scoringmethods for protein-RNA interactions. One crucial task of protein-RNA docking is todevelop a good scoring function which can distinguish near-native structures fromincorrect structures efficiently. Unfortunately, there is still no such a good scoringfunction up to now.Cation-pi interaction is a new kind of nonbond interaction which exists in manychemical and biological systems. Energy calculation shows that this kind ofinteraction can be as strong as H-bond. And published studies of cation-pi interactionsin biological systems have demonstrated that the cation-pi interaction has significantinfluence on protein stability, protein-ligand recognition and so on. The analysis ofcation-pi interactions on protein-RNA interfaces can not only help us understand themechanism of cation-pi interacions, but also induce new thinking for the design oftargeted drugs. However, there is still few study about cation-pi intercations inprotein-RNA complexes.There are two major parts in this article:(1) The study of protein-RNA scoring functionTo get a good scoring function which can discriminate near-native decoys fromincorrect decoys, we developed a new combinatorial scoring function includingresidue-nucleotide propensity potential, electrostatic interaction and van der Waals’interaction. The weights of different scoring terms were optimized through linearregression. Then, we tested the screening ability of the combinational scoring functionin17non-redundent protein-RNA complexes. The results show that the combinatorialscoring function performs better than residue-nucleotide propensity potential.(2) Cation-pi interactions on protein-RNA interfacesWe analyzed the characteristics of the4RNA bases in forming cation-pi interactions with Na+. Then the cation-pi interactions on282protein-RNA interfacesfrom144protein-RNA complexes were studied systematically. We analyzed thecation-pi interaction numbers and average interaction energy, the propensity ofcation-pi interactions on the kind of amino acid/RNA base, and how the RNAsecondary structure influenc the forming of cation-pi interactions.