E. J. Deeds

Modeling reveals the strength of weak interactions in stacked ring assembly

The paper develops a mathematical model of stacked trimer assembly, revealing that strong interaction affinities can lead to kinetic trapping, suggesting evolutionary pressure for weaker interactions in stacked ring structures.

In vitro reconstitution of the M.tb proteasome core particle reveals conserved aspects of bacterial proteasome assembly

This study reconstitutes the M.tb proteasome core particle in vitro, revealing conserved assembly pathways across bacteria and enabling inhibitor screening.

Docking-based long timescale simulation of cell-size protein systems at atomic resolution

This study combines protein docking and Monte Carlo simulations to achieve long-timescale atomic-resolution simulations of cell-sized protein systems.

Understanding the Separation of Timescales in Rhodococcus erythropolis Proteasome Core Particle Assembly

This study uses MD simulations to show how the propeptide regulates the separation of timescales in Rhodococcus erythropolis proteasome assembly by blocking or allowing dimerization.

Robustness and the evolution of length control strategies in the type III secretion system and flagellar hook

This study models the ruler mechanism of length control in bacterial structures and finds it allows for longer average lengths with less variance compared to the substrate switching mechanism.