Molecular Dynamics Simulations of Intrinsically Disordered Proteins and Biomolecular Assemblies

This dissertation describes four projects using computer simulations to study the molecules of life.
The first project aims to better understand how adhesive junctions between cells form, and the role of protein dynamics in this process.
The second aims to design a new biomaterial that can be used in therapy after a traumatic brain injury.
Here, again, protein dynamics is likely to play a pivotal role.
The third aims to understand how the distinct members of an evolutionary family of proteins, all with the same basic shape, can assemble into very different complexes.
The final project aims to understand how RNA interacts with the surface of an ancient protein.
While these problems come from diverse areas of biology, the methodological approach used for all questions is the same: given an initial set of atomic coordinates, a computer program predicts how those atoms will move over time, thereby simulating the molecular dynamics of the system.
This technique can give an atomically-detailed, femtosecond-by-femtosecond view of otherwise-murky biological processes.