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RNA structural features at the interface of RNA-protein complexesAuthor: K Sanjana Karanth Date: 2019-11-08 Report no: IIIT/TH/2019/126 Advisor:Abhijit Mitra AbstractRNA molecules show enzymatic activities and several other complex functionalities in living systems. Several of the functional RNAs exist as RNA-protein complexes and in order to achieve specific biological goals, RNAs and proteins often interact with each other at the cellular level. The ribosome is the largest and one of the most well known examples of such complexes. Studies on RNA-protein interactions predominantly have focused on structural properties of RNA binding proteins. Even though the conventional approach to investigate the RNA-protein interface region includes studies on non-covalent interactions, binding affinity and surface properties of the interacting RNA and protein, detailed struc- tural studies of the interacting RNA, at a molecular level, are mostly neglected. However, some recent RNA-centric research reveals the involvement of small RNA structural motifs, role of sugar O2’ atom and the importance of nucleobase specific interactions in the RNA-protein interface region.In our present work, we have re-visited the nucleobase specific interactions, identified within a eukaryotic 80S ribosome (Saccharomyces cerevisiae or yeast), with a resolution of 2.9Å, which includes 4 chains of ribosomal RNAs interacting with 81 protein chains in each biological assembly. Here, specif-ically we have explored the structural features of RNA interacting with protein at the interface, in terms of different types of non-covalent interactions between them, the canonical and non canonical base pairs made by interface RNA residues, and their involvement in secondary structural motifs like internal and hairpin loops. A detailed statistical and contextual analysis of all the observed interface RNA residues have been carried out and reported here. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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