Electronic Thesis and Dissertation Repository

Degree

Doctor of Philosophy

Program

Biochemistry

Supervisor

Dr. Wing-Yiu Choy

Abstract

Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in

protein-protein interaction networks. Many are involved in cancer, aging and

neurodegenerative diseases. The structure and dynamics of IDPs is intimately related to their

interactions with binding partners. Because IDPs are inherently flexible and do not have a

single conformation, conventional methods and conditions for determining structure and

dynamics of globular proteins may not be directly applicable. Nuclear magnetic resonance

(NMR) spectroscopy is one of the primary techniques characterizing the structures and

dynamics of IDPs, but one cannot rely solely on NMR data. A primary aim of this work was

to use Molecular Dynamics (MD) simulations in conjunction with NMR and other

biophysical techniques to achieve a deeper understanding of the structure and dynamics of

IDPs. To establish suitable parameters and force field choice for simulating IDPs, extensive

MD simulations were performed and the results were compared to experimental data. Using

computational and experimental techniques, the interactions between peptides from 9

disordered proteins with a common target were interrogated. The findings allowed us to

determine key factors in modulating the affinities of the various interactions and highlighted

the importance of molecular recognition fragments (MoRFs) in IDP target recognition and

binding. IDP binding was also investigated from the perspective of the binding partner. The

backbone resonances of the ~32 kDa target were assigned and the binding interface was

mapped in the presence of a peptide from a disordered binding partner. Chemical shift

changes distant from the interaction site indicated that IDP binding is a complex process,

which should be studied from the perspectives of the partner and target. Because IDPs are

highly sensitive to environmental conditions, the effects of molecular crowding on the

dynamics of IDPs were also investigated. I found that crowding might have differential

effects on the conformational propensities of distinct regions of some IDPs. This information

will help to understand the behavior of IDPs in cellular environments and to determine

suitable conditions for accurately studying them. This work has helped to improve the

understanding of how IDP structure and dynamics relate to target binding.

multi_peptide_comparison.mp4 (253820 kB)
Chapter 2 supplemental video 1

99sb_star_rep2_0_to_400ns_time_labels.mp4 (1010728 kB)
Chapter 2 supplemental video 2

VideoS2.mpg (2085 kB)
Chapter 3 supplemental video 2

VideoS1.mpg (5760 kB)
Chapter 3 supplemental video 1


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