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Electronic Control of Protein Interactions Mark Anthony Sellick

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Electronic Control of Protein Interactions Mark Anthony Sellick 1 Electronic Control of Protein Interactions Mark Anthony Sellick Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Centre for Doctoral Training in Molecular-Scale Engineering School of Electronic and Electrical Engineering September 2016 2 3 The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. © 2016 The University of Leeds and Mark Anthony Sellick The right of Mark Anthony Sellick to be identified as Author of this work has been asserted by Mark Anthony Sellick in accordance with the Copyright, Designs and Patents Act 1988. 4 5 Acknowledgements I would first like to acknowledge my supervisor Professor Christoph Wälti for his invaluable guidance and support during my studies. Doctor Steven Johnson and Doctor Simon White, the other members of the coiled coil team, have also been integral to this project and I thank them for their assistance and friendship. I would also like to thank Doctor Franziska Thomas and Professor Dek Woolfson for their insights and assistance designing and synthesising the peptides used in this work. I must also thank all the members of the Bioelectronics Group, past and present, for their expertise and friendship over the years. Thanks also to the members of the various biology and chemistry groups in Leeds and Bristol for helping the confused physicist who could occasionally be found in their labs asking odd questions and trying not to break anything. Thanks also go to my friends in the original cohort of the Centre for Doctoral Training in Molecular Scale Engineering: Will, Billa, Andy, Scott and Olly. I could not have asked for a better group of friends to go through the CDT experience with. Finally and most importantly, thank you to my family, and particularly my wife Laura, for their unwavering love and support. 6 7 Abstract This thesis details work carried out with the aim of demonstrating electronic control of protein interactions. A pair of coiled coil peptides including an acidic peptide and an alkaline peptide were designed and synthesised. Characterisation studies were carried out in solution using CD and FRET, which showed that heterodimers were preferentially formed at neutral and weakly alkaline pH and that homodimers of the alkaline peptide were preferentially formed at strongly alkaline pH. This demonstrated that the peptides had pH dependent binding behaviour, as intended. Characterisation was then performed using FRET, SPR, and CD with the alkaline peptide immobilised on surfaces. It was shown that the pH dependent binding behaviour was retained, with the acidic peptides dissociating from the alkaline peptide monolayer only above a certain alkaline binding pH. This binding pH was typically lower than the pH at which homodimer preferentially formed in solution and could be changed by varying the concentration and pH at which the monolayers were formed. This led to the conclusion that the binding pH depended on the density of the monolayer. Experiments were performed to demonstrate that the pH of a solution in the vicinity of an electrode could be changed electrochemically and measured using optical techniques. It was shown that the pH changes immediately at the electrode surface were significantly larger than those observed further into the solution. Monolayers of heterodimers were then immobilised on electrodes via the alkaline peptide and it was demonstrated that the acidic peptide could be removed from the monolayer by application of a current to the electrode. Control experiments demonstrated that the removal of the acidic peptide was caused by the pH change at the electrode surface that was induced by the current application. Electronic control of protein interactions was therefore demonstrated. 8 9 Table of contents Acknowledgements ....................................................................................................................... 5 Abstract ......................................................................................................................................... 7 Table of contents ........................................................................................................................... 9 List of tables and illustrative material ......................................................................................... 13 List of abbreviations ................................................................................................................... 17 1. Introduction ............................................................................................................................. 19 1.1. Aim of this work .............................................................................................................. 19 1.2. Motivation ........................................................................................................................ 19 1.3. Previous work in the field ................................................................................................ 22 1.4. Overview .......................................................................................................................... 23 1.5. References ........................................................................................................................ 24 2. Background and literature review ........................................................................................... 27 2.1. Introduction ...................................................................................................................... 27 2.2. Electrochemical pH control ............................................................................................. 27 2.2.1. Measurement of electrochemical pH changes .......................................................... 28 2.2.2. Applications of electrochemical pH changes ............................................................ 31 2.3. Proteins and peptides ....................................................................................................... 32 2.4. Coiled coils ...................................................................................................................... 35 2.4.1. Coiled coil design principles ..................................................................................... 39 2.4.2. Coiled coil monolayers ............................................................................................. 47 2.4.3. Applications of coiled coils ...................................................................................... 48 2.5. References ........................................................................................................................ 55 3. Experimental techniques ......................................................................................................... 69 3.1. Introduction ...................................................................................................................... 69 3.2. Peptide synthesis .............................................................................................................. 69 3.2.1. Solid phase peptide synthesis .................................................................................... 69 3.2.2. High performance liquid chromatography (HPLC) .................................................. 70 3.2.3. Mass spectrometry .................................................................................................... 72 3.3. Peptide characterisation ................................................................................................... 74 3.3.1. Circular dichroism spectroscopy (CD) ..................................................................... 74 3.3.2. Förster resonance energy transfer (FRET) ................................................................ 78 3.3.3. Confocal laser scanning microscopy (CLSM) .......................................................... 80 3.3.4. Surface plasmon resonance spectroscopy (SPR) ...................................................... 81 3.3.5. Concentration determination by UV spectroscopy ................................................... 82 3.4. Electrochemistry .............................................................................................................. 83 3.4.1. The electrochemical cell ........................................................................................... 83 10 3.5. References ........................................................................................................................ 83 4. Peptide design, synthesis, and solution characterisation ......................................................... 87 4.1. Introduction ...................................................................................................................... 87 4.2. Materials and methods ...................................................................................................... 87 4.2.1. Peptide synthesis and labelling .................................................................................. 87 4.2.2. Peptide purification ................................................................................................... 88 4.2.3. Mass spectrometry ....................................................................................................
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