Abstract
Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods. We developed a fragment-based approach to model protein-bound ssRNA, based on the structure of the protein and the sequence of the RNA, without any prior knowledge of the RNA binding site or the RNA structure. The conformational diversity of each fragment is sampled by an exhaustive RNA fragment library that was created from all the existing experimental structures of protein-ssRNA complexes. A systematic and detailed analysis of fragment-based ssRNA docking was performed which constitutes a proof-of-principle for the fragment-based approach. The method was tested on two 8-homo-nucleotide ssRNA-protein complexes and was able to identify the binding site on the protein within 10 Å. Moreover, a structure of each bound ssRNA could be generated in close agreement with the crystal structure with a mean deviation of ~1.5 Å except for a terminal nucleotide. This is the first time a bound ssRNA could be modeled from sequence with high precision.
Highlights
RNA participates in most processes leading to genome expression and its regulation [1, 2], mainly in association with proteins [3,4]
Our fragment-based docking protocol can be described in 5 steps: (i) The RNA sequence is cut in overlapping trinucleotides; (ii) each trinucleotide is represented by a sequence-specific ensemble of conformers in an exhaustive fragment library built from all experimental protein-RNA
The protocol was tested on the two non-redundant single-stranded RNA (ssRNA)-protein complexes of the PDB containing two RNA recognition motif” (RRM) motifs bound to an homopolymer ssRNA: (i) a crystallographic structure of the sex-lethal protein bound to a 5’-GUUGUUUUUUUU ssRNA (PDB ID 1B7F, 2.6 Å resolution) and a crystallographic structure of the poly(A)-binding protein bound to a 5’AAAAAAAAA ssRNA (PDB ID 1CVJ, 2.6 Å resolution), which constitute canonical cases of protein-RNA complexes [27,28]
Summary
RNA participates in most processes leading to genome expression and its regulation [1, 2], mainly in association with proteins [3,4]. Protein-RNA interactions are involved in several neurodegenerative diseases [5] and cancers [6]. Understanding such interaction and the design of drug molecules requires the three-dimensional structure of protein-RNA complexes [7]. In many cases the protein bound RNA molecule is able to adopt a great variety of conformations. The structure determination of complexes containing flexible single-stranded (ss)RNA is a major challenge. Protein-RNA docking methods could help to generate at least models of such interactions. The first task in docking is to sufficiently sample the space of possible conformations and relative orientations (i.e. poses) of the components so as to include near-native structures. Similar to existing protein-protein docking methods [8,9], most current protein-RNA docking methods consist of docking rigid structures of unbound RNAs or their domains [10,11], with no or very limited conformational sampling of the RNA conformations prior to docking
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