The simulations were CC-4047 performed in an isothermal-isobaric ensemble. Bond length constraints were applied to all bonds that contained hydrogen atoms based on the LINCS protocol. An integration step of 0.002 ps was allowed in simulations. Electrostatic interactions were GW 4064 treated with Particle Mesh Ewald method with a cutoff of 0.9 nm with grid spacing for the FFT grid < 0.12 nm. A cutoff of 1.2 nm was used in the calculation of van der Waals interaction. The details for all the simulation systems can be found in Table 1. The volume of the 150-cavity was calculated using POVME program. In the initial structure, a 3D-grid that that covered the 150-cavity was created. NA structural snapshots were extracted from the simulation trajectory every 20 ps, and superimposed onto the reference open structure. The previously generated 3D-grid was also superimposed. Grid points overlapping protein atoms in the structural snapshots were systematically deleted. The volume of the 150-cavity was then calculated by a measurement script by counting the remaining grid points. Residues that influenced the volume include all the residues from 147 to 152 in the 150- loop as well as nearby residues coming close to the cavity during the simulations. To investigate the stability of ligands in the binding pocket, a series of normal MD simulations were performed. The drug ZMR and the compound ETT, designed by Mark von Itzstein��s group, were included in the simulations for comparison. In our setup, each protomer of the tetrameric 09N1 protein was bound with an identical ligand, resulting in four trajectories of the same NA-ligand complex in one simulation. Among the four designed compounds, Lig 1 had the smallest RMSD values, indicating the most stable binding. For the other three ligands, the RMSD values in some protomers were higher and fluctuated around 0.5 nm, representing deviation of the ligands from their proposed binding positions. The large RMSD of the three ligands are displayed as the black curve in Figure 7B and 7C and the blue curve in Figure 7D. As expected, ZMR remained stable in its binding pocket with a RMSD value less than 0.2 nm. Although ETT was designed to target the 150-cavity, we found that it was unstable in the
