Mechanistic insights into proteins association through molecular dynamics
Chua, Khi Pin
Date of Issue2017
Interdisciplinary Graduate School (IGS)
NTU Institute for Health Technologies
The study of proteins' structures and dynamics is critical to understanding the question of "What is Life?". Human body, for example, contains innumerable proteins working in tandem to perform biological functions necessary for human survival. This thesis attempts to shed insights into various types of association and aggregation processes between proteins and peptides. In the first part of this thesis, we first look into the aggregation process of human islet amyloid polypeptide (hIAPP) and a small fragment of prion protein (106-126). These are two structurally and sequentially distinct peptides that were found to aggregate in experiments (Gal et al. JACS 2013, 135, 13582-9). We discovered that the two peptides adopt highly polymorphic complex and can potentially form beta-sheet rich structures. The second part of this thesis looks into the binding process of a profilin sequence from Arabidopsis Thaliana (AtPRF3) with a short polyproline peptide. Our binding energy analysis was consistent with that of experiments (Manuscript in preparation) and we were able to provide insights into the binding mechanism in atomistic details. Several important interactions were found such as the CH-pi stacking and electrostatic attraction/repulsion. Lastly, this thesis concludes with a project investigating two short peptides from sucker ring teeth (SRT) proteins that differ only by a single amino acid. One of the peptides was able to form hydrogel in water while the other could not. By using large scale simulation together with coarse-grained modelling, we discovered fibril-like structures containing beta-sheets.