ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow

Abstract

Recent progress in molecular biology has revealed that many non-coding RNAs regulate gene expression or catalyze biochemical reactions in tumors, viruses and several other diseases. The tertiary structure of RNA molecules and RNA-RNA/ protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. Current RNA drugs are split into two groups: antisense RNA molecules and aptamers. In this report, we present a novel workflow to predict RNA tertiary structures and RNA-RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. In this study, three analytical workflows for comprehensive structural analysis of RNA are introduced: (1) prediction of the tertiary structure of RNA; (2) prediction of the structure of RNA-RNA complexes and analysis of their interactions; and (3) prediction of the structure of RNA-protein complexes and analysis of their interactions. In an RNA-protein case study, we modeled the tertiary structure of pegaptanib, an aptamer drug, and performed docking calculations of the pegaptanib-vascular endothelial growth factor complex using a fragment of the interaction site of the aptamer. We also present molecular dynamics simulations of the RNA-protein complex to evaluate the affinity of the complex by mutating bases at the interaction interface. The results provide valuable information for designing novel features of aptamer-protein complexes.

Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study

“…The photo‐crosslink is maintained throughout the simulations, and the average photo‐crosslinking distance from the 5 μs simulations is 6.0 ± 1.2 Å. The average photo‐crosslinking distance using the same definition reported in a previous MD simulation study over 1.5 ns of simulation time was 4.5 ± 0.7 Å 36 . It has been reported that the formation of the photo‐crosslink requires π stacking of U14 and the Cys10‐Cys27 disulfide bond 24 .…”

“…The average photo-crosslinking distance using the same definition reported in a previous MD simulation study over 1.5 ns of simulation time was 4.5 ± 0.7 Å. 36 It has been reported that the formation of the photo-crosslink requires π stacking of U14 and the Cys10-Cys27 disulfide bond. 24 Based on large changes in chemical shifts in NMR spectra of HBD induced by Macugen binding, it was suggested that Macugen interacts with two regions in HBD.…”

“…35 The initial structure of Macugen with native nucleic acid bases (i.e., without any modifications as in therapeutic Macugen) was taken from an earlier work. 36 The initial structure of the HBD-Macugen complex was built based on the interaction between HBD and Macugen also from earlier experiments. 20,24 For the preparation of each system, a cuboidal TIP3P 28 water box with a minimum distance of 10 Å from any atom in the solute to the edge of the periodic box around the surface of free HBD, free Macugen, and HBD-Macugen complex was added to mimic the aqueous environment.…”

“…The initial structure of HBD was taken from the NMR structure (PDB entry: 2VGH) 35 . The initial structure of Macugen with native nucleic acid bases (i.e., without any modifications as in therapeutic Macugen) was taken from an earlier work 36 . The initial structure of the HBD‐Macugen complex was built based on the interaction between HBD and Macugen also from earlier experiments 20,24 .…”

Systematic bio-fabrication of aptamers and their applications in engineering biology

“…3 D). Molecular docking technique analyzes the interaction forces between aptamers and target molecules through a variety of computational methods, and reveals this binding form between aptamer and target molecule [ 76 ]. Compared with the secondary structure prediction, molecular docking technology may be more intuitive and reliable.…”