Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations

Abstract

Lassa virus can cause dreadful human hemorrhagic disease, for which there is no effective therapy. A recent study points out that the amino (N)-terminal domain of Lassa virus nucleoprotein (NP) plays an important role in viral RNA synthesis and firstly solved the X-ray crystal structures of NP complexed with the capped Deoxythymidine triphosphate (dTTP) analog, but the binding mode of m7GpppG to the N domain of NP, which is required for viral RNA transcription, has not been studied. In this study, molecular dynamics (MD) simulations have been carried out to investigate the characters of dTTP binding to two forms of NP, i.e. the NP without the C domain and the full-length NP model, using two different force fields, ff03 and ff99SB, respectively. Our calculated results show that the truncated model is reasonable and can replace the full protein model in the following MD simulations, and that ff99SB combined with the general AMBER force field is more suitable for sampling the structure of small molecule NP complex. From the comparisons of stability of hydrogen bonds between small molecule and protein in the dTTP and Uridine 5′-Triphosphate complexes, one finds that the stable hydrogen bonds between the second phosphate group of small molecules and two residues, Thr178 and Arg323, are critical for cap analogs binding to the N domain of NP. Additionally, docking method combined with MD simulations have been applied to predict the binding mode of m7GpppG to NP; and the hydrogen bond analysis and the binding free energy decomposition method (MM/GBSA) are conducted to study the interactions in the putative binding mode. The calculated results are expected to provide guidance for drug development.