Author: Amrita Roy; Liangzhong Lim; Shagun Srivastava; Jianxing Song
Title: Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations Document date: 2016_9_28
ID: l82aakrk_31
Snippet: We also attempted to assess the dynamics of Zika and Dengue NS2B-NS3pro complexes in the closed conformation. To achieve this, we performed MD simulations up to 100 ns on the crystal structures of Zika (5LC0) (25) and Dengue (3U1I) (31) NS2B-NS3pro complexes with the small molecule inhibitors removed. We remove the small molecule inhibitors because: 1) we aimed to find whether the removal of the small molecules would trigger a difference in dynam.....
Document: We also attempted to assess the dynamics of Zika and Dengue NS2B-NS3pro complexes in the closed conformation. To achieve this, we performed MD simulations up to 100 ns on the crystal structures of Zika (5LC0) (25) and Dengue (3U1I) (31) NS2B-NS3pro complexes with the small molecule inhibitors removed. We remove the small molecule inhibitors because: 1) we aimed to find whether the removal of the small molecules would trigger a difference in dynamic instability for Zika and Dengue complexes. 2) Currently the force-field parameters for simulating small molecules are still not universally established. Fig 6A and 6B show the root-mean-square deviations (RMSD) trajectories averaged over four independent MD simulations respectively for NS3pro and NS2B of both Zika and Dengue complexes in the closed form. Interestingly, for the closed conformation without inhibitors, Dengue complex is more dynamic than the Zika one. While the Dengue NS3pro has author/funder. All rights reserved. No reuse allowed without permission.
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