Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

Yin-Chen Hsieh (1) , Frédéric Poitevin (2, 3) , Marc Delarue (4) , Patrice Koehl (1)

1 UC Davis - University of California [Davis]
2 Stanford University
3 Stanford PULSE Center
4 Dynamique structurale des Macromolécules / Structural Dynamics of Macromolecules

Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis. We describe the elements of DD-NMA that are relevant to the analysis of large systems, such as virus capsids. In particular, we introduce our implementation of simplified elastic networks and justify their parametrization. Using DD-NMA, we illustrate the importance of packing interactions within the virus capsids on the dynamics of the E proteins of DENV and ZIKV. We identify differences between the computed atomic fluctuations of the E proteins in DENV and ZIKV and relate those differences to changes observed in their high resolution structures. We conclude with a discussion on additional analyses that are needed to fully characterize the dynamics of the two viruses.

Keywords: normal modes; elastic network models; Zika; Dengue; proteins; viruses

Domains: Bioinformatics [q-bio.QM]

Yin-Chen Hsieh, Frédéric Poitevin, Marc Delarue, Patrice Koehl. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids. Frontiers in Molecular Biosciences, 2016, 3, pp.85. ⟨10.3389/fmolb.2016.00085⟩. ⟨pasteur-02174598⟩