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PDFOpen Access (License Unspecified), Open Access
Thesis
Molecular simulations of monomeric sarcosine oxidase
Master of Science (M.S.), Drexel University
Jun 2010
DOI:
https://doi.org/10.17918/etd-3291
Abstract
Monomeric sarcosine oxidase (MSOX) is a flavoenzyme that catalyzes the oxidation of sarcosine to form formaldehyde, glycine and hydrogen peroxide. MSOX also reduces molecular oxygen. There is no channel detected by experiment that transports oxygen from the protein surface to the buried active site for oxygen reduction. The main purpose of this work is to determine the oxygen transport channels in MSOX using molecular simulations. Here we used two methods: Molecular Dynamics (MD) and Single-sweep free energy reconstruction. Our results show that there exist two different pathways to the oxygen activation site: the so called si-side and re-side entry pathways. Between these two, the si-side entry pathway is more thermodynamically favorable. This highlights the efficiency of MSOX because the substrate and O2 access the catalytic center via two distinct pathways.
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Details
- Title
- Molecular simulations of monomeric sarcosine oxidase
- Creators
- Shyno Mathew - DU
- Contributors
- Cameron F. Abrams (Advisor) - Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Master of Science (M.S.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Resource Type
- Thesis
- Language
- English
- Academic Unit
- Chemical (and Biological) Engineering [Historical]; College of Engineering (1970-2026); Drexel University
- Other Identifier
- 3291; 991014632551304721