Abstract: Allosteric signaling, the phenomenon of an effector molecule to modulate the activity at a distal active site, has been known for some half a century in molecules such as proteins. However, how that signal is transmitted remains a debated topic. One method posited to identify a network of residues transmitting the signal is sector analysis. This identifies a group of residues covarying evolutionarily; these residues are termed a sector. Based on this, our lab has developed a similar method, MD sectors, based on the covariance of the residues in molecular dynamics (MD) simulations. Examining the networks from model systems such as PDZ and p53 has indicated that the networks themselves change based on the liganded state, and we have called upon MD simulations to gain insights into this observation. However, to perform such analysis, the convergence of the simulations is imperative. To this end, our current project focuses on both streamlining our pipeline analysis and evaluating the extent to which convergence has been ascertained. Here, we present the steps used in our analysis, as well as the development of metrics to assess the convergence of the trajectories to ensure the robustness of the conclusions.
PosterLive Poster Session:
Thursday, July 29th 1:45-3:45pm EDT