Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2013 Fatty acid and polyketide synthesis enzymes: sequences, structures, and mechanisms David Cantu Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Bioinformatics Commons, Chemical Engineering Commons, and the Chemistry Commons Recommended Citation Cantu, David, "Fatty acid and polyketide synthesis enzymes: sequences, structures, and mechanisms" (2013). Graduate Theses and Dissertations. 13020. https://lib.dr.iastate.edu/etd/13020 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Fatty acid and polyketide synthesis enzymes: sequences, structures, and mechanisms by David C. Cantu A dissertation submitted to the graduate faculty in partial fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY Major: Chemical Engineering Program of Study Committee Peter J. Reilly, Major Professor Laura R. Jarboe Robert L. Jernigan Monica H. Lamm Basil J. Nikolau Iowa State University Ames, Iowa 2013 Copyright © David C. Cantu, 2013. All rights reserved. ii TABLE OF CONTENTS Acknowledgments......................................................................................................................v Chapter 1: Introduction..............................................................................................................1 Chapter 2: Overview of methods...............................................................................................3 Chapter 3: ThYme: a database for thioester-active enzymes Abstract..........................................................................................................................9 Introduction....................................................................................................................9 Identifying and populating families.............................................................................12 Content.........................................................................................................................12 Database organization and features.............................................................................13 Updates........................................................................................................................14 Experimentally characterized sequences.....................................................................14 Sequences with multiple domains................................................................................14 Similarity to other enzyme databases..........................................................................15 Conclusion...................................................................................................................16 March 2013 update......................................................................................................16 References....................................................................................................................16 Figures..........................................................................................................................18 Chapter 4: Thioesterases: A new perspective based on their primary and tertiary structures Abstract........................................................................................................................19 Introduction..................................................................................................................19 Identification of thioesterase families..........................................................................20 Identification of thioesterase clans...............................................................................24 ThYme database...........................................................................................................25 Results and discussion.................................................................................................26 iii Thioesterases in existing databases and previous classifications................................37 Concluding remarks.....................................................................................................39 Acknowledgments........................................................................................................39 References....................................................................................................................39 Tables...........................................................................................................................44 Figures..........................................................................................................................51 Chapter 5: Phylogenetic characterization of an acyl-ACP thioesterase family Abstract........................................................................................................................52 Introduction..................................................................................................................52 Phylogenetic and statistical analysis methods.............................................................54 Results and discussion.................................................................................................55 Comments on published paper and conclusions..........................................................57 Acknowledgements......................................................................................................58 References....................................................................................................................58 Tables...........................................................................................................................60 Figures..........................................................................................................................61 Supplementary Information.........................................................................................62 Chapter 6: Investigation of a thioesterase mechanism by QM/MM metadynamics simulation Abstract........................................................................................................................68 Introduction..................................................................................................................68 Computational methods...............................................................................................70 Results and discussion.................................................................................................74 Conclusions..................................................................................................................78 Acknowledgments........................................................................................................79 References....................................................................................................................79 Tables...........................................................................................................................81 Figures..........................................................................................................................82 Supplementary Information.........................................................................................86 iv Chapter 7: Structural classification and properties of ketoacyl reductases, hydroxyacyl dehydratases, and enoyl reductases Abstract........................................................................................................................88 Introduction..................................................................................................................88 Computational methods...............................................................................................90 Results and discussion.................................................................................................90 Conclusions..................................................................................................................99 References....................................................................................................................99 Tables.........................................................................................................................102 Figures........................................................................................................................107 Chapter 8: Acyl carrier protein structural classification and normal mode analysis Abstract......................................................................................................................109 Introduction................................................................................................................109 Results and discussion...............................................................................................110 Computational methods.............................................................................................118 Concluding remarks...................................................................................................120 Acknowledgments......................................................................................................121