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Access Type

WSU Access

Date of Award

January 2022

Degree Type


Degree Name



Biochemistry and Molecular Biology

First Advisor

Zhe Yang


Molecular dynamics simulation allows for the simulation of proteins with precise control over what ligands are present at what sites. The conformational ensemble of a protein can be obtained from MD simulation with and without binding at an allosteric site and compared between to gain insight at what effects binding at an allosteric site has on a protein’s structure. SMYD2, a critical regulator of cellular processes, was recently found to have a novel secondary binding site with allosteric effects on its activity. The discovery of an allosteric site has implications for drug design in the inhibition of SMYD2 to treat cancer. Understanding the mechanism that this allosteric site affects SMYD2 by could help guide development of allosteric inhibitor drugs for SMYD2. Molecular dynamics can generate conformational ensembles of SMYD2 with and without binding at its novel allosteric site to gain insight into its allosteric mechanism.

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