Construction and equilibration of nitrate/nitrite antiporter NARK

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Presenter(s)

Michael Swing, Zeyna Aouad

Abstract or Description

Protein modeling at the atomistic level proves crucial in the study of how proteins interact within a controlled environment. These protein models are generated and visualized using Visual Molecular Dynamic (VMD) software and the files can be used to simulate the mechanism of action of a protein in response to changes in environmental variables. The energy and trajectories of these interactions between the atoms can be calculated using dynamic equations found in Nanoscale Molecular Dynamics (NAMD) software. Collectively, this research demands mastery in the understanding of how to properly execute, through terminal commands, certain input and output files necessary to successfully simulate the proteins. This project sought to develop and refine skills relevant in constructing protein models for future projects relating to complex protein-membrane simulations. Protein models of the nitrate/nitrite antiporter NARK were generated, solvated, ionized, and minimized to a stable low-energy state. The atom trajectories of the minimization step were used to run the system through a 0.5 nanoseconds (ns) equilibration of the protein and the results were plotted to determine the volume and energy states.