Author: Pervushin, Konstantin; Tan, Edward; Parthasarathy, Krupakar; Lin, Xin; Jiang, Feng Li; Yu, Dejie; Vararattanavech, Ardcharaporn; Soong, Tuck Wah; Liu, Ding Xiang; Torres, Jaume
Title: Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel Document date: 2009_7_10
ID: 1e102wrc_56
Snippet: A symmetrical ETM homo-pentameric structure was reconstructed (Fig. S1 , A-C) starting with a backbone model based on orientational data from site-specific infrared dichroism (SSID), which defined helix tilt and rotational pitch angles for residues L21, A22, F23, and V24 [38] . The ETM a-helix built from NMR data was superimposed onto the pentamer skeleton to obtain the full atomic description of the model. This model was subjected to energy mini.....
Document: A symmetrical ETM homo-pentameric structure was reconstructed (Fig. S1 , A-C) starting with a backbone model based on orientational data from site-specific infrared dichroism (SSID), which defined helix tilt and rotational pitch angles for residues L21, A22, F23, and V24 [38] . The ETM a-helix built from NMR data was superimposed onto the pentamer skeleton to obtain the full atomic description of the model. This model was subjected to energy minimization to resolve steric clashes, following which, inter-helical NOEs (Table S2) were used as constraints in molecular dynamics (MD) simulations to refine the structure. Inter-helical NOE constraints were applied one by one; only when the system reached equilibrium, another constraint was added. Upon inclusion of all inter-helical constraints, the refined final model was compatible with both site specific infrared dichroism and NMR data.
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