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.

Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein

“…On the basis of the calculated RMSF value reflected in Figure 4, the largest fluctuations are observed in the C-termini regions and the loop A (from Ala190 to Thr205) connecting the first two helices H1 and H2 ( 3.2. Binding free energies calculation of three complexes using MM-PBSA method MM-PBSA method Li et al, 2013;Luo et al, 2005;Molina & Hill, 2007;Pastor et al, 1988; was used and 200 snapshots were extracted from the 10 ns of stabilized MD trajectories for the corresponding equilibrium states with a 50 ps interval to evaluate the binding free energies of the three complexes. The calculated relative binding free energy of each complex and their energy contributions using the single trajectory are listed in Table 1 …”

“…MM-PBSA computes the binding free energy using a thermodynamic cycle that combines the molecular mechanical (MM) energies with the continuum solvent approaches. For our investigated systems, the binding free energies between three BH3 α-helices and Mcl-1ΔNΔC were calculated using the MM-PBSA method (Hou, McLaughlin, Lu, Chen, & Wang, 2006;Li, Li, Chen, & Han, 2013;Luo et al, 2005;Molina & Hill, 2007;, which combines MM energies, a continuum solvent Poisson-Boltzmann (PB) model for polar solvation, a solvent accessible surface area (SASA) for nonpolar solvation term, and an additional solute entropy term (TΔS) in Equation (1).The predicted results by MM-PBSA method are directly related to the experimental values, this method was proved to be useful for measuring the binding energies of biomolecular systems Li, Froeyen, & Herdewijn, 2008). The MM-PBSA method can be conceptually summarized as:…”

Influence of RNA Binding on the Structure and Dynamics of the Lassa Virus Nucleoprotein

“…Molecular modeling studies on Lassa have been limited by the lack of structural information, but recent studies have examined the Z protein (21) and NP (22,23). The studies on NP involved calculations of binding between NP and m7GpppN cap (23) and RNA (22).…”

“…Molecular modeling studies on Lassa have been limited by the lack of structural information, but recent studies have examined the Z protein (21) and NP (22,23). The studies on NP involved calculations of binding between NP and m7GpppN cap (23) and RNA (22). In the earlier study, Li et al (23) examined dTTP and m7GpppN binding to the closed conformation of NP to evaluate a proposed cap-snatching mechanism for priming mRNA synthesis (11).…”