Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 2 of 2
Full-Text Articles in Physical Sciences and Mathematics
Using Qm/Mm Methods To Explore Sortase Enzyme Intermediates, Kinetics, And Stability, Kyle Whitham
Using Qm/Mm Methods To Explore Sortase Enzyme Intermediates, Kinetics, And Stability, Kyle Whitham
WWU Graduate School Collection
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 …
Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso
Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso
WWU Graduate School Collection
In the field of molecular dynamics (MD), a long-standing issue is the time frame required in order to fully observe a chemical reaction. Enhanced sampling methods have been the primary way of overcoming this issue for the past 40 years. In this experiment our goal was to combine new and existing sampling methods in order to create an efficient and accurate way of retrieving kinetics data from simulations. In order to do this, we examined two test cases: the enzymes chorismate mutase and cytosine deaminase. We did this using hybrid quantum mechanics/molecular mechanics simulations coupled with enhanced sampling methods. The …