Abstract
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic experimental structure solving, despite essential to the understanding of these functions, is often difficult and expensive. Docking approaches that have been developed for proteins are often challenging to adapt for RNA because of its inherent flexibility and the structural data available being relatively scarce. In this study we adapted the RosettaDock protocol for protein-RNA complexes both at the nucleotide and atomic levels. Using a genetic algorithm-based strategy, and a non-redundant protein-RNA dataset, we derived a RosettaDock scoring scheme able not only to discriminate but also score efficiently docking decoys. The approach proved to be both efficient and robust for generating and identifying suitable structures when applied to two protein-RNA docking benchmarks in both bound and unbound settings. It also compares well to existing strategies. This is the first approach that currently offers a multi-level optimized scoring approach integrated in a full docking suite, leading the way to adaptive fully flexible strategies.
Highlights
Protein-RNA interactions often play a major role in the cell
They are involved in many processes such as replication, mRNA transcription or regulation of RNA levels and control the operation of key cellular machineries such as the RNA induced silencing complex (RISC)
We show that the obtained RosettaDock RNA protocol performs better than in the previous attempts [49] in a semi-rigid body approach for both bound and unbound docking and can undoubtedly be used for successful protein-RNA predictions
Summary
Protein-RNA interactions often play a major role in the cell They are involved in many processes such as replication, mRNA transcription or regulation of RNA levels and control the operation of key cellular machineries such as the RNA induced silencing complex (RISC). They are good candidates for therapeutic studies [1]. Despite the wide interest and advances in structural biology for RNA and protein-RNA complexes, the number of structures available in the PDB is relatively small (a few thousand for RNA molecules and around a thousand for protein-RNA complexes). Both the modelling and the prediction of protein-RNA interactions remain a challenge [13]
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