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2.2 Ion Mobility Mass Spectrometry: the Moq-Tof This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Investigation of Protein‐Ion Interactions by Mass Spectrometry and Ion Mobility Mass Spectrometry Yana Berezovskaya PhD The University of Edinburgh 2012 To the memory of my Mother "Confidence is what you have before you understand the problem." Woody Allen Acknowledgements Acknowledgements I would like to thank my supervisor Dr Perdita E. Barran for making my distant‐future‐when‐more‐important‐things‐are‐taken‐care‐of plan to pursue a PhD a reality. I am also grateful for a generous conference allowance, both domestic and international. Thank you for preferentially tasking me with handling most delicate and expensive (!) parts of the instruments from day one of my PhD project. I am grateful to my collaborator Prof. Dek Woolfson and his people (Craig Armstrong and Aimee Boyle) at the University of Bristol, who provided synthetic peptides for the studies described in Chapters 3 and 4. Thank you for all things related to in‐solution analysis and your valuable feedback and discussions. I would like to thank the members of the Barran research group, past and present, for their help, support and cheerful company. I am grateful to all the technical personnel, both internal and external, for their vast research‐enabling capabilities. A lot of time has been saved and frustration spared thanks to your knowledge and professionalism. i Acknowledgements I am indebted to my parents for the wonderful childhood they gave me, for developing my personality, and for their numerous sacrifices to ensure my education. My thanks and eternal gratitude are directed to my husband, Dr Lev Sarkisov for his most professional guidance, discussions, support, advice and reality checks. Thank you for invaluable Linux scripts that made the analysis of the data in Chapter 5 possible. Thank you for always being there for me. I would like to thank my cat Loki for being an unceasing source of positive emotions. Thank you for getting me out of my chair at the desk during my thesis write‐up: your persistence and accurate timing in demanding food and attention have kept my days structured. ii Declaration Declaration This thesis is submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy at the University of Edinburgh. Unless otherwise stated, this work is my own and has not been submitted for any other degree or professional qualification. ………………………………………………………….. Yana Berezovskaya 2012 iii Abstract Abstract Protein‐ion interactions play an important role in biological systems. A considerable number of elements (estimated 25 – 30) are essential in higher life forms such as animals and humans, where they are integral part of enzymes involved in plethora of cellular processes. It is difficult to overestimate the importance of thorough understanding of how protein‐ion interplay affects living cell in order to be able to address therapeutic challenges facing humanity. Presented to the reader’s attention is a gas‐phase biophysical analysis of peptides’ and proteins’ interactions with biologically relevant ions (Zn2+ and I–). This investigation provides an insight into conformational changes of peptides and proteins triggered by ions. Mass spectrometry and ion mobility mass spectrometry are used in this work to probe peptide and protein affinities for a range of ions, along with conformational changes that take place as a result of binding. Observation of peptide and protein behaviour in the gas phase can inform the investigator about their behaviour in solution prior to ionisation and transfer from the former into the latter phase. Wherever relevant, the gas‐phase studies are complemented by molecular dynamics simulations and the results are compared to solution phase findings (spectroscopy). Two case studies of protein‐ion interactions are presented in this thesis. Firstly, sequence‐to‐structure relationships in proteins are considered via iv Abstract protein design approach using two synthetic peptide‐based systems. The first system is a synthetic consensus zinc finger sequence (vCP1) that is responsive to zinc: it adopts a zinc finger fold in the presence of Zn2+ by coordinating the metal ion by two cysteines and two histidines. This peptide has been selected as a reference for the zinc‐bound state and a simple model to refine the characterisation method in preparation for analysis of a more sophisticated second system – dual conformational switch. This second system (ZiCop) is designed to adopt either of the two conformations in response to a stimulus: zinc finger or coiled coil. The reversible switch between the two conformational states is controlled by the binding of zinc ion to the peptide. Interactions of both peptide systems with a number of other divalent metal cations (Co2+, Ca2+ and Cu2+) are considered also, and the differences in binding and switching behaviour are discussed. Secondly, protein‐salt interactions are investigated using three proteins (lysozyme, cytochrome c and BPTI) using variable temperature ion mobility mass spectrometry. Ion mobility measurements were carried out on these proteins with helium as the buffer gas at three different drift cell temperatures – ‘ambient’ (300 K), ‘cold’ (260 K) and ‘hot’ (360 K), and their conformational preferences in response to HI binding and temperature are discussed. The work of this thesis has been covered in the following publications and presentations. Papers: 1 Berezovskaya, Y.; Armstrong, C. T.; Boyle, A. L.; Porrini, M.; Woolfson, D. N.; Barran, P. E. (2011). Metal binding to a zinc‐finger peptide: a v Abstract comparison between solution and the gas phase. Chemical Communications 47, 412‐414 (work described in Chapter 3). 2 Berezovskaya, Y.; Porrini, M.; Nortcliffe, C.; Armstrong, C. T.; Woolfson, D. N.; Barran, P. E. (2012). Ion mobility mass spectrometry as a tool for synthetic biology: a case study on the zinc finger fold versus coiled coil interactions. In preparation (work described in Chapter 4). 3 Berezovskaya, Y.; Porrini, M.; Barran, P. E. (2012). The effect of salt adductation on the conformations of three model proteins is revealed by variable temperature ion mobility mass spectrometry. Submitted to International Journal of Mass Spectrometry (work described in Chapter 5). Presentations: 4 BMSS (British Mass Spectrometry Society) Annual Meeting, Cardiff, UK, 2011, oral: “Metal ions and mass spectrometry assist synthetic biology”. 5 ARF (Analytical Research Forum), Manchester, UK, 2011, oral: “Ion‐ mobility mass spectrometry: a tool for synthetic biology”. 6 ASMS (American Society for Mass Spectrometry) Annual Meeting, Denver, USA, 2011, oral: “Metal ions and mass spectrometry assist synthetic biology”. 7 University of Edinburgh School of Chemistry 2nd year Postgraduate Student Presentation, Edinburgh, UK, 2010, oral: “Ion‐mobility mass vi Abstract spectrometry: a tool for synthetic biology” (second place in competition) . 8 ACS (American Chemical Society) Fall Meeting, Boston, USA, 2010, oral: “Metal binding of model Cys2His2 zinc‐finger peptides”. 9 BMSS (British Mass Spectrometry Society) Annual Meeting, Cardiff, UK, 2010, poster: “Metal binding of model Cys2His2 zinc finger peptide in the gas phase”. 10 ARF (Analytical Research Forum), Loughborough, UK, 2010, poster: “Metal binding of model Cys2His2 zinc finger peptide in the gas phase”. 11 IMSC (International Mass Spectrometry Conference), Bremen, Germany, 2009, oral: “Peptides designed to switch their conformation by metal binding”. 12 ARF (Analytical Research Forum), Kent, UK, 2009, poster: “Ion‐mobility mass spectrometry study of a peptide designed to switch its conformation by metal binding”. vii Abbreviations Abbreviations 3D three‐dimensional Ac acetate (salt) APCI atmospheric pressure chemical ionisation API atmospheric pressure ionisation ATD arrival time distribution AUC analytical ultracentrifugation BPTI bovine pancreatic tryptic inhibitor CCS collision cross section CD circular dichroism CID collision‐induced dissociation CS charge state CV compensation voltage; collision voltage DC direct current DMS differential mobility spectrometry DNA deoxyribonucleic acid EDD electron detachment dissociation EHSS exact hard sphere scattering ESI electrospray ionisation ETD electron transfer dissociation FAB fast atom bombardment FAIMS high‐field asymmetric waveform ion mobility spectrometry viii Abbreviations Fmoc fluorenylmethyloxycarbonyl (chloride): protecting group for amines HBTU O‐benzotriazole‐N,N,N’,N’‐tetramethyl‐uronium (hexafluoro‐phosphate): peptide coupling reagent HPLC high‐performance liquid chromatography i.d. internal diameter IE injection energy IM ion mobility IM‐MS ion mobility mass spectrometry IMS ion mobility spectrometry
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