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Biomolecular Simulations Group

Shadi A Badiee

Shadi A Badiee


Shadi A Badiee is a second year PhD student in Cell and Molecular Biology. She earned her Bachelor's degree in Molecular and Cellular Biology - Genetics from University of Yazd, Iran (Class of 2015), and her Master's degree in Molecular Biotechnology and Bioinformatics from University of Milan, Italy (Class of 2020). Shadi’s Master’s thesis was “Improving the Efficiency of Metadynamic Metainference Simulations”. She enjoys traveling, playing basketball and spending time with her family.


Molecular dynamics investigation of the influenza hemagglutinin conformational changes

Hemagglutinin (HA) is an antigenic glycoprotein found on the surface of the influenza viruses. HA, a homotrimeric protein, mediates the fusion of viral membrane and that of the host cell. The HA is synthesized as inactive HA0 and is cleaved to HA1 and HA2 by host proteases. When the pH within the endosome drops, the HA2 protein undergoes a large conformational change, while HA1 moves away, releasing the fusion peptide. In this study we have investigated the conformational changes of HA2 trimer under various pH conditions using all-atom molecular dynamics simulations. We have used a combination of microsecond-level unbiased simulations and nonequilibrium biased simulations within an enhanced sampling scheme. The equilibrium simulations particularly compare the initial stages of HA2 conformational changes in the absence and presence of HA1 while the nonequilibrium simulations compare various mehchanisms involving cooperative vs sequential conformational changes of HA2 trimer in the absence of HA1. These simulations provide a detailed dynamic picture of pH-dependent HA2 conformational changes in influenza hemagglutinin protein.

Copyright © 2015, Biomolecular Simulations Group, Department of Chemistry and Biochemistry, University of Arkansas.
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