The Dynamics of Protein Interaction Networks By Chi Nam Ignatius Pang A thesis submitted for the degree of Doctor of Philosophy in Biotechnology January 2010 School of Biotechnology and Biomolecular Sciences The University of New South Wales Table of Contents Originality Statement....................................................................................... iii Copyright Statement........................................................................................ iv Authenticity Statement..................................................................................... v Acknowledgements ......................................................................................... vi Publications.................................................................................................... viii Book chapter:................................................................................................... ix Abstract ............................................................................................................. x Dedication........................................................................................................ xii 1 Introduction ................................................................................................. 1 1.1 Protein-protein interactions ................................................................................2 1.2 Technologies for the discovery of protein-protein interactions ...........................4 1.3 Protein interaction networks .............................................................................11 1.4 Integrating protein-protein interaction data with genomics and proteomics data 19 1.5 Proteomic technology to quantify protein absolute abundance, half-lives, and translation rate...........................................................................................................20 1.6 Post-translational modifications........................................................................28 1.7 Different methods of detecting post-translational modifications .......................31 1.8 Aims of this thesis ............................................................................................35 2 Are protein complexes made of cores, modules and attachments?.... 36 3 High throughput protein-protein interaction data: clues for the architecture of protein complexes ................................................................ 37 i 4 Surface accessibility of protein post-translational modifications........ 38 5 Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications ....................... 39 6 Proteins deleterious on overexpression are associated with high intrinsic disorder, specific interaction domains and low abundance........ 40 7 Discussion ................................................................................................. 42 7.1 The role of domain-domain interactions in the formation of stable protein complexes .................................................................................................................43 7.2 Using high-throughput interaction data to determine the architecture of protein complexes .................................................................................................................46 7.3 The role of surface accessibility in post-translational modifications .................47 7.4 Identification of arginine- and lysine-methylation using peptide mass spectra.50 7.5 Exploring the function of arginine and lysine methylation in the proteome of S. cerevisiae ..................................................................................................................53 7.6 Interaction domains and high intrinsic disorder favours interaction promiscuity 55 7.7 Tight regulation of protein abundance prevents promiscuous protein-protein interactions ................................................................................................................56 8 Conclusions............................................................................................... 59 9 References................................................................................................. 61 10 Appendices.............................................................................................. 97 10.1 Appendix I - Publications................................................................................97 10.2 Appendix II - Book Chapters ..........................................................................98 10.3 Appendix III - Publication highlights ...............................................................99 ii Originality Statement I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgment is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project’s design and conception or in style, presentation and linguistic expression is acknowledged. Chi Nam Ignatius Pang School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW 2052 Australia January 2010 iii Copyright Statement I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorize University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation. Chi Nam Ignatius Pang School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW 2052 Australia January 2010 iv Authenticity Statement I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format. Chi Nam Ignatius Pang School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW 2052 Australia January 2010 v Acknowledgements I would like to sincerely thank the following people, who have assisted me throughout my thesis: Professor Marc Wilkins, my supervisor, for being an inspirational teacher and an incredible scientist. The thesis has certainly improved from your ideas and critical reviews, and I have learnt a lot from you. Thank you for proofreading my thesis so many times, which would have been an arduous task for anyone. Thank you for supporting me as a friend, and helping me though the many difficulties I encountered throughout the past 4 years. Dr. Rohan Williams, my co-supervisor, for being a helpful mentor throughout my studies. Your challenging questions and critical comments have helped sharpen many ideas in my thesis. Thank you for your constant support. Dr. Mark Tanaka, for being a panel member for my annual reviews, and taking precious time to chair these important meetings. Dr. Elisabeth Gasteiger, for building the FindMod bulk submission webpage. It is the most critical software for chapter 5, and without it the project would not have come so far. Thank you very much. Dr. Anne-Claude Gavin, for personal correspondence and facilitating access to the Cellzome peptide mass data. Dr. Andrew Hayen, for providing technical help on statistics and programming in R. Dr. Mark Cowley, for giving me countless advice on Linux and R programming. Thank you for assisting me with the illustration of Figure 2 in Chapter 4. Liang Ma, for charging ahead with the analysis of proteins deleterious upon overexpression. I like this paper very much. Thank you! Angela Lek, for writing the Perl scripts for acquiring the domain-domain interactions from iPfam. James Krycer, for contributing to two chapters of my thesis. Your help was important for my thesis. Thank you! Simone Li, for your help in visualizing protein-protein interactions in GEOMI. Thank you for verifying the GO terms analysis in chapter 5. It was just what we needed to tackle the difficult reviewers' comments. Yose Widjaja and Dr. Tim Lambert, for giving me the opportunity to contribute to the paper on the Interactorium. The visualization is very high-tech and it is like science fiction becoming reality. Dr. Merridee Wouters and Dr. Richard George, for your supervision at the Victor Chang Cardiac Research Institute, and for your help with writing the Scooby-Domain paper. Weit-Tse Hsu, for the opportunity to work with you on the paper. vi Tim Couttas, for