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https://hdl.handle.net/10356/96407
Title: | Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations | Authors: | Han, Nanyu Mu, Yuguang |
Keywords: | DRNTU::Science::Biological sciences::Microbiology::Bacteria | Issue Date: | 2013 | Source: | Han, N., & Mu, Y. (2013). Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations. PLoS ONE, 8(4). | Series/Report no.: | PLoS ONE | Abstract: | Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. | URI: | https://hdl.handle.net/10356/96407 http://hdl.handle.net/10220/9875 |
ISSN: | 1932-6203 | DOI: | 10.1371/journal.pone.0060995 | Schools: | School of Biological Sciences | Rights: | © 2013 The Author(s). | Fulltext Permission: | open | Fulltext Availability: | With Fulltext |
Appears in Collections: | SBS Journal Articles |
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File | Description | Size | Format | |
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1. Plasticity of 150-Loop in Influenza Neuraminidase.pdf | 1.41 MB | Adobe PDF | View/Open |
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