Natural Modulators of Amyloid Formation in Alzheimer's Disease
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Natural modulators of amyloid formation in Alzheimer’s disease Sirwan M. Amin Al-Jaf A Thesis Submitted for the degree of Doctors of Philosophy July 2016 University of Sheffield Department of Molecular Biology and Technology For Sirwan’s Family; Mother, father, wife, children, brothers and sisters. Abstract Alzheimer’s disease (AD) is the most common cause of dementia, and the deposition of amyloid β (Aβ) peptide in the AD brains is a hallmark of the disease. Other amyloidogenic proteins like Transthyretin (TTR) and human Cystatin C (hCC) can modulate the aggregation of Aβ. These two proteins are proposed to play a role in the pathophysiology of AD as they are found co-deposited in amyloid deposits in the brains of AD patients, most notably at the cell surface. Animal models and cell line assays showed protective roles for TTR and hCC against Aβ-induced toxicity, and Aβ fibril formation is inhibited through interaction with TTR and hCC. This study investigated the mechanism of in vitro interaction of TTR with Aβ. The ability of WT TTR to inhibit Aβ fibrillisation in the presence of Aβ binding surfaces was higher than in the presence of non-binding surfaces. Then, the interaction between different TTR mutants with different multimeric stabilities and different alloforms of Aβ showed that TTRs with less stable tetramers and unfolded monomers are the best inhibitors of Aβ fibrillisation. Analysing the thioflavin T curves of Aβ aggregation in the presence of TTRs and the interaction of TTRs with different forms of Aβ showed that the interaction between the two proteins occurs mainly through binding to early nucleating species of Aβ rather than to the monomer. The dose-dependent inhibition of Aβ fibrillisation and the promotion of amorphous aggregates by hCC were validated. However, the previous suggestion of simple monomer to monomer interaction between Aβ and hCC was not confirmed. Instead, a proposed hCC binding to oligomeric species of Aβ was supported by the observed hCC interaction with different aggregated species of Aβ. The dimeric form of hCC was found to be a less effective inhibitor compared to WT monomer, indicating that the active site could be the hydrophobic loops involved in dimerisation and protease inhibition. This interpretation was supported, as mutation of hydrophobic residues in the active site significantly reduced the intensity of hCC to inhibit Aβ fibrillisation. We showed that these two proteins are mainly inhibit Aβ fibrillisation through interaction with the early aggregated structures of Aβ (some form of oligomers). As it is known that oligomers are responsible for Aβ toxicity in vivo, the potential of these two proteins to be used as natural modulators is supported by this study. Acknowledgements First and foremost I must thank my supervisor Rosie Staniforth who has been wonderful, both for supervising my PhD in the first place and for all her guidance, support and encouragement throughout the last four years, especially during the painful writing up process. I would also like to thank my advisors Jon Waltho, John Rafferty and Mike Williamson for all their help and guidance. Andrea Hounslow has been amazing, assisting me with the NMR experiments and analysis. Thank you also to Svet Tzokov for all of his help with EM. Thank you also to amyloid group, particularly Abi, Pete, Amy, Liam and Alex. Abi has been simply a great colleauge, she was always around for a help and a part of my research has been based on her work, for which I am very grateful. The NMR group have been great; it would be impossible to name everybody (and I would undoubtedly forget someone), but thank you all so much for the help and advice. Thank you also to the NMR group Nicky, Claire, Luke and Angus. Thanks for all the excellent cakes, I have enjoyed Friday cakes a lot. Outside the lab, I have met many wonderful people since moving to Sheffield, but special thanks must go to Taib, Isam, Salar, and Omed. I’m so glad I met you all, and I definitely wouldn’t have made it through without you all. Outside the university, I would like to thank Sarwat, Sartip and Barzan, especially Sarwat for his help at the early days on arriving to UK and been a great friend all the time. Thank you to my wonderful family, to Mum, Dad and the whole family (brothers and sisters) for all their love and support, it means so much to me and I am truly grateful. Thanks to The Higher Committee for Education Development in Iraq, for sponsoring my PhD. Thanks to my friends and university colleagues back home, they were always happy to help for anything I needed there. Last but not least, thank you to my wonderful wife, Srwa, for companionship, as I made her to live away of her family and friends for 4 years, putting up with me and for always believing in me. I couldn’t have done it without you. Table of contents Contents Pages Chapter 1: Introduction .................................................................................................. 1 Background ............................................................................................................................. 1 1. 1. Classification of Amyloid ................................................................................................ 2 1. 2. Alzheimer’s disease ......................................................................................................... 4 1. 3. The structure of amyloid ................................................................................................ 6 1. 4. Atomic-level structural determination .......................................................................... 8 1.4. 1. X-Ray Fibre Diffraction ............................................................................................. 8 1.4.2. Microscopy Techniques ............................................................................................ 9 1.4.3. Cryo-electron microscopy ....................................................................................... 10 1.4.4. Hydrogen-deuterium exchange (HX) ...................................................................... 12 1.4. 5. Limited proteolysis ................................................................................................. 13 1.4. 6. Solid-state nuclear magnetic resonance spectroscopy ............................................ 14 1. 5. Amyloid probing .......................................................................................................... 15 1. 5. 1. Congo red ................................................................................................................ 15 1. 5. 2. Thioflavin T (ThT) .................................................................................................. 16 1. 6. Definitions of amyloid structures ................................................................................. 16 1. 6. 1. Amyloid fibril ......................................................................................................... 16 1. 6. 2. Protofilament ........................................................................................................... 17 1. 6. 3. Amyloid intermediates ............................................................................................ 17 1. 6. 3. 1. Protofibrils .......................................................................................................... 17 1. 6. 3. 2. Annular aggregates ............................................................................................. 18 1. 6. 3. 3. Oligomers ............................................................................................................ 18 1. 6. 3. 4. Aβ-derived diffusible ligands (ADDLs). ............................................................ 19 1. 6. 4. Amorphous aggregate ............................................................................................. 19 1. 6. 5. Amyloid fibril seed ................................................................................................. 19 1. 7. Transformation to the amyloid-forming competent state ......................................... 20 1. 8. Mechanism of fibril formation ..................................................................................... 22 1. 9. Kinetic models ............................................................................................................... 23 1.10. Alzheimer’s disease and related proteins ....................................................................... 27 1. 10. 1. Transthyretin (TTR) .................................................................................................. 27 1. 10. 1. 1. TTR amyloidosis ............................................................................................... 28 1. 10. 1. 2. TTR and Aβ ...................................................................................................... 29 1. 10. 2. Human Cystatin C ..................................................................................................... 33 1. 10. 2. 1. Cystatin C amyloidosis ..................................................................................... 33 1. 10. 2. 2. Cystatin C and Aβ ............................................................................................. 35 1. 10. 2. 3. Genetic studies .................................................................................................. 36 1. 10. 2. 4. Mechanisms of neuroprotection ........................................................................ 37 1. 10. 3. Neuroserpin