PhD Final Oral: Hyuntae Na

Event
Speaker: 
Hyuntae Na
Friday, April 15, 2016 - 2:30pm to 4:30pm
Location: 
Snedecor 2102
Event Type: 

Proteins are essential structural and functional units in cells. Proteins form stable and yet
somewhat flexible 3-D structures and often function by interacting with other molecules. Their
functional behaviors are determined by their 3-D structures as well as their dynamics. Protein
dynamics studies are thus very important.

One of the most powerful computational methods for studying protein dynamics is normal
mode analysis (NMA). The low frequency modes especially are of great interest for many protein
dynamics studies. Although it provides analytical solutions to a protein’s collective motions,
classical NMA is cumbersome to use and may become even prohibitive when the system being
studies is too large. Many simplified NMA models have been developed, which use extremely
simplified structural models and/or coarse-grained potentials. However, the dynamics given by
such models may not always be fully realistic.

In this dissertation, I have alleviated these problems by addressing the following sequence
of questions: (1) what is the contribution of inter-residue (inter-atom) forces to protein normal
modes; (2) how to remove the cumbersome energy minimization step in NMA while preserving
most of the accuracy of the model; (3) how to efficiently construct coarse-grained structural
models from all-atom models while maintaining the accuracy in dynamics. Additionally, using
my new models as well as the classical NMA, I have closely examined the vibrational spectrum of
globular proteins in the whole frequency range, and have found a connection with experimental
observations. Finally, as an application of normal modes, the last part of this thesis presents a
novel approach in which normal modes are used to identify what breathing motions of myoglobin
dynamically open ligand migration channels. The results are in an excellent agreement with
molecular dynamics simulation results and experimentally determined ligand entry rates.
 

Category: 
Tags: