Journal Title
Title of Journal: J Mol Model
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Abbravation: Journal of Molecular Modeling
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Publisher
Springer-Verlag
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Authors: HaoJen Hsu Wolfgang B Fischer
Publish Date: 2011/05/04
Volume: 18, Issue: 2, Pages: 501-514
Abstract
ORF 3a of human severe acute respiratory syndrome corona virus SARSCoV has been identified as a 274 amino acid membrane protein When expressed in Xenopus oocytes the protein forms channels Based on bioinformatics approaches the topology has been identified to include three transmembrane domains TMDs Since structural models from experiments are still lacking computational methods can be challenged to generate such models In this study a ‘sequential approach’ for the assembly is proposed in which the individual TMDs are assembled one by one This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment The results suggest that bundles are likely with the second TMD facing the putative pore All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossingWBF acknowledges National YangMing University the government of Taiwan and the National Science Council of Taiwan NSC for financial support Thanks to D Willbold Jülich D for valuable discussions We thank the National Center for HighPerformance Computing of Taiwan wwwnchcorgtw for providing computer timePotential energies MOE of the assemblies to generate the monomer Seq1 TMD3 and TMD2 displayed in respect to distance rotational angle 1 rotational angle 2 and tilt a Potential energies of the assemblies of TMD3+TMD2 with TMD1 are shown as for a to form Seq1 b The structure used for further studies is marked by the arrow JPEG 117 kbPotential energies of the assembled tetramers without loops Values for generating all the sequences are shown in dependence of distance left panels rotational angles middle and tilt right panels The arrows indicate models TSeq1 I TSeq2 II TSim III JPEG 137 kb
Keywords:
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