Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

Cécilia Hognon; Tom Miclot; Cristina Garcia Iriepa; Antonio Francés-Monerris; Stephanie Grandemange; Alessio Terenzi; Marco Marazzi; Giampaolo Barone; Antonio Monari

The hypothesis is based on the identification of G4 sequences in key host mRNA that encode proteins involved in different signaling pathways such as apoptoting or survival signaling, [31] [32] [33] [34] [35] [36] [37] [38] these proteins could induce a controlled cellular death of infected cells slowing down or stopping the infection, or promote cell survival to delay apoptosis by producing antiviral cytokines. 37 However, the removal of the mRNA necessary to produce these signaling factors by viral SUD may impair the apoptosis/survival response pathways allowing massive cell infection. 28, 37 In this letter, we report an extended all-atom molecular dynamics (MD) study of the interactions produced between a dimeric SUD domain and a short RNA G4 sequence. The crystal structure of the protein (pdb 2W2G) and of the oligonucleotide (pdb 1J8G) 39 have been chosen coherently with the experimental work performed by Tan et al. 28 Equilibrium MD has allowed to assess some of the hypothesized complexation modes between G4 and SUD, while also highlighting the most important interactions patterns at an atomistic level, and the effects of G4 in maintaining the dimer stability. Furthermore, to better sample the multidimensional conformational space and to quantify the strength of the interactions coming into play, the free-energy surface has been explored using enhanced sampling methods. A two-dimensional (2D) free energy profile has been computed along two coordinates defining the distance between the centers of mass of G4 and one SUD domain . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.07.029447 doi: bioRxiv preprint 6 (G4-SUD A ), and the two SUD domains (SUD A -SUD B ), respectively. The corresponding 2D potential of mean force (PMF) was obtained using a recently developed combination of extended adaptative biased force (eABF) 40 and metadynamics, 41 hereafter named meta-eABF. 42 Both protein and RNA have been described with the amber force field 43 including the bsc1 corrections, 44, 45 and the MD simulations have been performed in the constant pressure and temperature ensemble (NPT) at 300K and 1 atm. All MD simulations have been performed using the NAMD code 46 and analyzed via VMD, 47 the G4 structure has also been analyzed with the 3DNA suite. 48, 49 More details on the simulation protocol can be found in Supplementary Information (SI). The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.07.029447 doi: bioRxiv preprint 7