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Normal mode analysis of Zika virus

Byung Ho Lee1, Soojin Jo1, Moon-Ki Choi1

  • 1School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, South Korea.

Computational Biology and Chemistry
|February 8, 2018
PubMed

Insights

Zika virus (ZIKV) dynamics were simulated using normal mode analysis. This study reveals intrinsic vibrational properties and glycosylation site mobility, offering insights into ZIKV

Area of Science:

  • * Virology
  • * Structural Biology
  • * Computational Biophysics

Background:

  • * Zika virus (ZIKV) poses a global health threat due to its association with microcephaly.
  • * Limited understanding of ZIKV's fundamental viral features and infection mechanisms.
  • * Recent cryo-electron microscopy revealed the mature ZIKV icosahedral shell structure.

Purpose of the Study:

  • * To analyze the dynamic properties of ZIKV from a mechanical perspective using simulations.
  • * To investigate the intrinsic vibrational motions and basic properties of ZIKV's structure.
  • * To gain insights into ZIKV's biological functions and infection mechanisms.

Main Methods:

  • * Performed normal mode analysis (NMA) on a dimeric unit structure of ZIKV (envelope and membrane proteins).
  • * Utilized icosahedral symmetry for efficient simulation of the entire ZIKV shell structure.
  • * Analyzed low-frequency normal modes to capture intrinsic vibrational motions.

Main Results:

  • * Captured intrinsic vibrational motions and defined basic vibrational properties of the ZIKV unit structure.
  • * Simulated the entire ZIKV shell structure with reduced computational cost.
  • * Identified highly mobile glycosylation sites, supporting their importance in ZIKV function.

Conclusions:

  • * NMA provides a method to comprehend ZIKV's dynamic fluctuations.
  • * The study offers insights into the mechanical properties influencing ZIKV's biological functions.
  • * Findings contribute to understanding ZIKV's infection mechanism and potential therapeutic targets.
Keywords:
Elastic network modelGlycosylation siteNormal mode analysisSymmetry constrained elastic network modelZika virus

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