Western Michigan University ScholarWorks at WMU Dissertations Graduate College 5-2007 Bioengineering of Protein Nanotubes and Protein Nanomaterial Composites Thilak Kumara Mudalige Western Michigan University Follow this and additional works at: https://scholarworks.wmich.edu/dissertations Part of the Chemistry Commons Recommended Citation Mudalige, Thilak Kumara, "Bioengineering of Protein Nanotubes and Protein Nanomaterial Composites" (2007). Dissertations. 899. https://scholarworks.wmich.edu/dissertations/899 This Dissertation-Open Access is brought to you for free and open access by the Graduate College at ScholarWorks at WMU. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks at WMU. For more information, please contact [email protected]. BIOENGINEERING OF PROTEIN NANOTUBES AND PROTEIN- NANOMATERIAL COMPOSITES by Thilak Kumara Mudalige A Dissertation Submitted to the Faculty of The Graduate College in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Department of Chemistry Western Michigan University Kalamazoo, Michigan M ay 2007 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number: 3265909 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. ® UMI UMI Microform 3265909 Copyright 2007 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Copyright by Thilak Kumara Mudalige 2007 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS First, I would like to thank my research advisors Professor Subra Muralidharan and Professor Brian C. Tripp for their guidance, support, dedication and patience trough my research. Next, I would like to gratefully thank my committee members Professor Yirong M o, Professor Dongil Lee and Professor Nora Berrah for taking time to review my work and for valuable advice. I would also like to thank the help and advice from Professor Karim Essani and Professor Robert Eversole o f the Biological Sciences Department. This work would not have been possible without the love and affection o f my parents and my wife Sulari. This research was supported by the Nanotechnology Research and Computation Center at Western Michigan University, Michigan Life Science Corridor, W. M. Keck Foundation, and Western Michigan University President’s Innovation Fund. Thilak Kumara Mudalige 11 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. TABLE OF CONTENTS ACKNOWLEDGMENTS .......................................... ............................................. ii LIST OF TABLES ............................................................................................... ix LIST OF FIGURES.................................... x CHAPTER I. INTRODUCTION .......................................................... 1 Central Hypothesis ................................................................................ 1 Scope o f This Research Dissertation.................................................... 1 Bionanotube in Nanotechnology.............. 2 Advantages of Bacterial Flagella over Other Systems........................ 3 Structure of Bacterial Flagella.............................................................. 6 II. GENERATION AND CHARACTERIZATION OF INORGANIC AND ORGANIC NANOTUBES ON BIOENGINEERED FLAGELLA OF MESOPHILIC BACTERIA ............................................. 11 Introduction..................... 11 Experimental Methods .................................................. 12 Materials and Methods........................................................... 12 Preparation of FliTrx Engineered Loop Peptide Flagella for Use as Nanotube Scaffolds........................................................... 13 Synthesis o f Silica Nanotubes on Cationic Arginine-Lysine Loop Flagella Scaffold................... 17 Synthesis o f Titanium Dioxide Nanotubes on Tyrosine- Serine-Glycine Loop Flagella Scaffold......................................... 18 iii Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Table of Content— Continued CHAPTER Synthesis o f Hydroxyapatite Nanotubes on Anionic Aspartate-Glutamate Loop Flagella Scaffold............................... 18 Synthesis o f Polyaniline Nanowires on Anionic Aspartate- Glutamate Loop Flagella Scaffold................................................ 19 Results and Discussion ............................................... 20 Silica Biomineralization on Cationic Arginine-Lysine Loop Flagella Scaffolds........................................................................... 20 Titania Biomineralization on Phenolic Tyrosine Loop Flagella Scaffold.......................................... 23 Hydroxyapatite Biomineralization on Anionic-Aspartate- Glutamate Flagella Scaffold.......................................................... 26 Polyaniline Biomineralization on Anionic Aspartate- Glutamate Flagella Scaffold.......................................................... 29 Conclusion......................... 29 m. EXCITON ENERGY TRANSFER IN SELF-ASSEMBLED QUANTUM DOTS ON BIOENGINEERED BACTERIAL FLAGELLA NANOTUBES ....................................................................... 32 Introduction........................................................................................... 32 Materials and Methods ........................................... 34 Results and Discussion ......................................................................... 37 Conclusion............................................................................................. 45 IV. SELF-ASSEMBLY OF METAL NANOPARTICLES AND NANOTUBES ON BIOENGINEERED FLAGELLA SCAFFOLDS 46 Introduction........................................................................................... 46 Experimental Methods ......................................................................... 49 iv Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Table of Content— Continued CHAPTER M aterials ........................................................................................ 49 Engineering of FliTrx Flagella Loop Peptide Variants for Use as Bionanotube Scaffolds and Templates.......................... 49 Generation of Nanoparticle Arrays and Nanotubes on Flagella with Peptide Loops.......................................................... 51 Generation of Gold Nanoparticle Arrays on Histidine Loop Flagella........................................................................................... 51 Covalent Attachment of Gold Nanoparticles to Arginine- Lysine Loop Flagella................................. 52 Generation of Copper Nanoparticle Arrays and Nanowires on Histidine Loop Flagella............................................................ 53 Generation of Copper Nanoparticle Arrays and Nanowires on Histidine Loop Flagella............................................... 53 Generation of Palladium and Cadmium Nanoparticles on Aspartic Acid-Glutamic Acid Loop Flagella............................... 55 Generation of Silver Nanowires on Aspartic Acid-Glutamic Acid Loop Flagella............... 55 Results and Discussion .................................................................... 55 Generation of Gold Nanoparticle Arrays on Histidine Loop Flag ella........................................................... 56 Covalent Attachment of Gold Nanoparticles to Arginine- Lysine Loop Flagella.............................. 60 Generation of Copper Nanoparticle Arrays and Nanowires on Histidine Loop Flagella.......................................... 63 Generation of Cobalt Nanoparticles on Histidine Loop Flagella. ............................. 6 6 v Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Table of Content—Continued CHAPTER Generation of Palladium and Cadmium Nanoparticles on Aspartic Acid-Glutamic Acid Loop Flagella............................... 6 8 Generation of Silver Nanowires on Aspartic Acid-Glutamic Acid Loop Flagella ................................................................. 69 Conclusion.......................... 70 V. BIOENGINEERED FLAGELLA PROTEIN NANOTUBES WITH CYSTEINE LOOPS: SELF-ASSEMBLY AND MANIPULATION IN AN OPTICAL TRAP ....................................... 74 Introduction........................................................................................... 74 Experimental Methods ........................................................................ 75 M aterials ........................................................................................ 75 Construction of FliTrx Polycysteine