Computational Analysis of Wild-type and Selenium-Incorporated Down-regulated Proteins in E. coli

The addition of heavy metal amino acid analogs has long been a standard augmentation of X‐ray crystallography to solve the phase problem associated with smaller atoms such as carbon, nitrogen, and sulfur. Unfortunately, the addition of such analogs, like selenomethionine (SeMet), brings about unprecedented negative implications concerning the growth of the exposed cell cultures. The negative impact of growth is due to the cytotoxic effects of selenium‐incorporation, either partial or complete, as seen by a proteomic analysis performed by Broderick and Boles in 2013. It is apparent that there are a marked number of completely down‐regulated key enzymes in these exposed cell cultures. Many aspects of the down‐regulation cannot be experimentally tested; thus, computational methodology can be utilized to provide unique insight into the cellular processes and the cytotoxic effects of selenium on proteins in vivo . An AMBER14 force field has been modified to properly model selenium atoms in the protein structure. This modification allows for the analysis of protein stability and protein/substrate interactions of the mutant variant down‐regulated enzymes.