Molecular dynamics of the interaction between the ALS/FTD-associated (GGGGCC)n RNA G-quadruplex structure and the three RRM domains of hnRNP H

Hexanucleotide repeat expansions (HRE), located in the first intron of chromosome 9 open reading frame 72 (C9orf72) are the most common genetic abnormality associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Presence of the HRE may cause various effects to neuronal cells, leading to pathogenicity. One of these is the sequestration of RNA-binding proteins by three-quartet parallel RNA G-quadruplexes (RG4s) formed from repeated (GGGGCC)n sequences on the sense transcripts of the HRE. Multiple studies imply a major role of the sequestration of heterogeneous nuclear ribonucleoprotein H (hnRNP H) in the pathology of ALS/FTD. In this study, molecular docking and molecular dynamics (MD) were used to simulate the interaction of the three RNA recognition motifs (RRMs) of hnRNP H with the RG4. Molecular Mechanics with Generalised Born and Surface Area Solvation (MM-GBSA) and hydrogen bonding analyses of MD simulations were performed. The MM-GBSA analyses revealed that Arg29, Arg150, and Arg299 are important contributors to the binding, consistent with previous observations of arginine-mediated binding of protein to RNA. In addition, our results point to a previously unknown role of the stretch of residues from Lys72 to Tyr82 on hnRNP H for binding the (GGGGCC)n RG4, forming a hydrogen bonding hotspot. Interestingly, the identified residues are not located in the beta sheet, as would be expected of RRMs in general, suggesting that the binding of hnRNP H to this pathological RG4 may be specifically targeted. This has implications for future in vitro studies including but not limited to mutational analysis of these mentioned residues as well as drug development to prevent the sequestration of hnRNP H in ALS/FTD.