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Title: MACiE : the computer representation, analysis and classification of enzymatic reaction mechanisms
Author: Holliday, Gemma Louise
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2006
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Here we describe the development of MACiE, a unique and fully searchable database for enzyme reaction mechanisms and other relevant enzymatic data. Our database holds the reaction mechanism for individual enzymes; this includes the overall reaction and the multiple steps that may be involved in the mechanism of action. The data are held in both ISIS/Base and CML (an XML application) formats. For this purpose we have developed CMLReact, an extension to CML designed specifically for holding chemical reactions, and CMLSnap, an application for producing animated reaction mechanisms. We show that MACiE will help us to better understand the chemistry of enzymes. MACiE will help answer questions ranging from how nature best uses her arsenal of amino acids to how individual amino acids act in any given situation. We have shown that cysteine and histidine are the most catalytically active residues and that tyrosine and cysteine are the most versatile residues. We have also examined the types of chemical mechanism used in nature, finding that whilst the actual reactions performed are incredibly complex, enzymes mainly function through general acid/base catalysis. We have examined the classification of enzyme reaction mechanisms using a fingerprint to describe the chemical changes occurring. We also show that is possible to use this fingerprint to predict chemical mechanism. Finally we have shown that the problem of classifying enzymes by their mechanism is far from trivial and suggest some ways forward.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available