Molecular Dynamic Simulations
Although the nuclear receptors share large homologous segments, their individual sequences can produce large differences in structure in 3D space. Therefore, to create a glucocorticoid biosensor adapted from the existing estrogen receptor- based intein splicing construct developed by Buskirk et al. 2004, we knew that we could gain valuable insight by determining the appropriate length and flexibility of our linkers between the glucocorticoid receptor and the intein. We have achieved this through modeling with PyMol and performing molecular dynamic simulations of the root-mean-square deviation of atomic position. Dr. Campbell of the Department of Biomedical and Molecular Sciences has kindly agreed to run the simulations based on PyMol images we submitted to the Queen’s University Cluster Computer.
The molecular dynamics simulation performed consist of the N-terminal of the RecA intein (shown in blue), and the C-terminal of the RecA intein (shown in red), separated by an N-terminal linker with the sequence GPGGSG, the Ligand Binding domain of the Glucocorticoid Receptor bound to the agonist Dexamethasone, and then a C-Terminal linker with the sequence GGSGAS. The two halves of the trans-intein and are not immediately associated with each other and therefore not able to splice.
After 100 nanoseconds of simulation, it can be seen that the linkers are of sufficient length such that the N terminal of the intein, shown in blue and the C terminal of the intein shown in red, may form a favorable interaction.
Therefore, from the above media it can be seen that the N-terminal linker GPGGSG, and C-Terminal linker GGSGAS, which were originally adapted from Buskirk et al. 2004, are sufficient in length and flexibility to form a favourable interaction, and therefore are in close enough proximity to perform an intein splicing event for an agonist-bound glucocorticoid receptor ligand binding domain.