Stability, orientation and position preference of the stem region (residues 689-703) in Hepatitis C Virus (HCV) envelope glycoprotein E2: a molecular dynamics study

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Envelope glycoproteins E1 and E2 are essential for the initial binding and internalization of Hepatitis C Virus (HCV) into host cells. Both glycoproteins have been shown to interact as a non-covalent heterodimer during biosynthesis. In our previous studies, we demonstrated that the unfolding behavior of the E2 TM helix monomer was attributed to the charged Asp728, which was located in the hydrophobic core. The main contribution of Asp was postulated to be located at the helix-helix interface and involved the formation of a salt bridge with the Lys of the E1 envelope glycoprotein. E2 envelope glycoprotein is known to be required for interactions with cellular receptors involved in endocytosis and membrane fusion. In this work, we carried out MD simulations for three E2 structures: (1) a model generated by the n