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Date of Award

Summer 2023

Document Type

Masters Thesis

Department or Program Affiliation


Degree Name

Master of Science (MS)



First Advisor

McCarty, Jay

Second Advisor

Antos, John M.

Third Advisor

Kowalczyk, Tim


Biochemistry has seen advancements in methods and understanding of the inner workings of proteins, yet biochemists struggle to see real time reaction pathways of protein intermediates. This is where computational chemistry comes in and fills in the holes in knowledge through the use of Quantum Mechanical (QM) models. QM chemistry alone does not give results in a reasonable timescale to predict protein chemistry in a reasonable amount of time. Computational chemistry methods such as Quantum mechanical (QM)/ Molecular Mechanical (MM) (QM/MM), allow us to split the in-silico system into two regions that utilize a fast MM force field region and slow, but a chemically accurate, (QM) region. Our project will utilize docking programs and QM/MM methods to give accurate results in a reasonable timeframe to show the intermediate pathway in the Sortase A/B enzyme, meta-stable and stable intermediate information on the ligand and Sortase B enzyme structure. Several docking suites: AutoDock, FlexPepDock, a manual docking procedure, and a predicted folded structure from AlphaFold will be used to dock the Bacillus anthracis Sortase B (baSrtB) ligand to the active site of the enzyme. baSrtB simulation is supplemented by single point energy calculations of specific frames of structures to be used as a reference to compare to the Free Energy Surface (FES) results. This thesis will show that we have successfully modeled the Sortase B from Bacillus anthracis showing the accurate intermediate pathway.




Computational Chemistry, PLUMED, CP2K, Sortase, QM/MM, Docking


Western Washington University

OCLC Number


Subject – LCSH

Computational chemistry; Quantum chemistry; Enzymes




masters theses




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