Multiscale Modeling of Enzyme-Catalyzed Methanol Production by Particulate Methane Monooxygenase Katherine K
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Louisiana Tech University Louisiana Tech Digital Commons Doctoral Dissertations Graduate School Spring 2013 Multiscale modeling of enzyme-catalyzed methanol production by particulate methane monooxygenase Katherine K. Bearden Follow this and additional works at: https://digitalcommons.latech.edu/dissertations Part of the Biochemistry Commons, Inorganic Chemistry Commons, and the Other Chemical Engineering Commons MULTISCALE MODELING OF ENZYME-CATALYZED METHANOL PRODUCTION BY PARTICULATE METHANE MONOOXYGENASE by Katherine K. Bearden, B.S, M.S. A Dissertation Presented in Partial Fulfillment of the Requirements of the Degree Doctor of Philosophy COLLEGE OF ENGINGEERING AND SCIENCE LOUISIANA TECH UNIVERSITY May 2013 UMI Number: 3573581 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Di!ss0?t&iori Publishing UMI 3573581 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 LOUISIANA TECH UNIVERSITY THE GRADUATE SCHOOL ________________ March 21,2013 Date We hereby recommend that the dissertation prepared under our supervision by Katherine K. Bearden, M.S. __________________________________________________ entitled Multiseale Modeling of Enzyme-Catalyzed ______________________________ Methanol Production by Particulate Methane Monooxygenase ____________________ be accepted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Engineering ______________________ ■Supervisor ofDissertation Research Head of Department Department Recomi Son concurred in: >_ s Advisory Committee Approved: Approved: Directdrof Graduate Studies Dean of theGraduate School Dean of the College GS Form 13 (8/10) ABSTRACT In this work, the conversion of methane to methanol by the particulate Methane Monooxygenase (pMMO) enzyme is investigated using a multi-scale modeling approach. This enzyme participates in carbon cycling and aids in the removal of harmful atmospheric methane, converting it to methanol. The interaction between pMMO and a neighboring enzyme that is present in the same organism is studied, and the unknown pMMO active site is elucidated and tested for methane oxidation towards the production of methanol. Fundamental knowledge of pMMO’s mechanism is not fully understood. Understanding how this enzyme works in nature will provide information towards designing efficient synthetic catalysts through biomimetics, which can mitigate the harmful effects of methane in the atmosphere. These studies could also lead to the development of new synthetic catalysts that could impact the use of methanol as a cleaner, and greener, energy source. The practical application of this study would become fruitful once the mechanism is determined, mimicked, and then applied to create biofuels, synthetically. This work focuses on the fundamental research of the kinetics of an important catalyzed chemical reaction that relates to environmental biocatalysis, and involves atmospheric methane consumption (oxidation) for the production of fuel (methanol). Mimicking these same reactions in industrial settings has the potential to also reduce the harmful effects of methane while producing methanol as a desirable alternative fuel. Although experimental techniques have indicated a region of interest where the reaction is thought to take place, the novelty of this research begins with uniquely studying the interactions between MDH and pMMO by examining the docking regions of the enzymes to deduce an active region. Secondly, reaction mechanisms are proposed, and information about the kinetics of the methane oxidation process reaction is obtained. Transition state structures are determined and energy barriers estimated. Lastly, macroscopic reaction rates are determined through Kinetic Monte Carlo calculations to support the favored reaction pathways and demonstrate real-time oxidation reactions while observing the behavior of the pMMO system. Details from each of these techniques provide information to further the understanding of how pMMO oxidizes methane. APPROVAL FOR SCHOLARLY DISSEMINATION The author grants to the Prescott Memorial Library of Louisiana Tech University the right to reproduce, by appropriate methods, upon request, any or all portions of this Dissertation. It is understood that “proper request” consists of the agreement, on the part of the requesting party, that said reproduction is for his personal use and that subsequent reproduction will not occur without written approval of the author of this Dissertation. Further, any portions of the Dissertation used in books, papers, and other works must be appropriately referenced to this Dissertation. Finally, the author of this Dissertation reserves the right to publish freely, in the literature, at any time, any or all portions of this Dissertation. Authpr- GS Form 14 (8/10) DEDICATION To my parents who taught me the power of prayer and persistence. * TABLE OF CONTENTS ABSTRACT.................................................................................................................................. iii DEDICATION..............................................................................................................................vi LIST OF TABLES...................................................................................................................... xii LIST OF FIGURES...................................................................................................................xiii ACKNOWLEDGMENTS........................................................................................................ xix CHAPTER 1 ...................................................................................................................................1 INTRODUCTION.........................................................................................................................1 1.1 Methane.........................................................................................................................1 1.1.1 Methane as a Pollutant............................................................................................1 1.1.2 Methane Derivative as Fuel ................................................................................... 1 1.1.3 Bioremediation of Methane Performed by Paddy Plants.................................. 3 1.2 Enzymatic Reactions....................................................................................................4 1.2.1 Description and Advantages of Enzymatic Reactions...................................... 4 1.2.2 Metalloenzymes for Small Molecule Catalysis..................................................6 1.3 Dissertation Overview.................................................................................................7 CHAPTER 2 LITERATURE REVIEW.....................................................................................9 2.1 Methanol Dehydrogenase..........................................................................................10 2.1.1 MDH Structure ........................................................................................................11 2.1.2 Oxidation of Methanol by MDH......................................................................... 11 2.1.3 MDH/pMMO Interaction..................................................................................... 12 2.2 Particulate Methane Monooxygenase......................................................................13 vii viii 2.2.1 Two Forms of Methane Monooxygenase..........................................................13 2.3 Structure of pMMO.................................................................................................... 14 2.3.1 Evolution of Structure Composition...................................................................16 2.3.1.1 PDB Energy 1 YEW - Methylococcus capsulatus (Bath)...................... 16 2.3.1.2 PDB Entry 3CHX - Methylococcus trichosporium OB3b..................... 17 2.3.2 Metal Centers.......................................................................................................... 19 2.3.2.1 Monocopper Center......................................................................................20 2.3.2.2 Dicopper Center............................................................................................ 21 2.3.2.3 Tricopper Center........................................................................................... 22 2.4 Overview of Methane Oxidation Mechanism by MMO........................................22 2.4.1 Proposed Mechanisms......................................................................................... 22 2.4.2 Dioxygen Scission and C - H Bond Activation................................................23 2.4.2.1 Dioxygen Scission........................................................................................23 2.4.2.2 C-H Bond Activation....................................................................................24 2.5 pMMO Mechanism .....................................................................................................25