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Front Mol Biosci. 2016 Dec 27;3:85. doi: 10.3389/fmolb.2016.00085. eCollection 2016.

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

Author information

1
Department of Computer Science and Genome Center, University of California, Davis Davis, CA, USA.
2
Department of Structural Biology, Stanford UniversityStanford, CA, USA; SLAC National Accelerator Laboratory, Stanford PULSE InstituteMenlo Park, CA, USA.
3
Unit of Structural Dynamics of Macromolecules, UMR 3528 du Centre National de la Recherche Scientifique, Institut Pasteur Paris, France.

Abstract

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:

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

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