Knowledge of the structure and dynamics of cellular protein complexes is essential for understanding their functionally relevant interactions. In Gram-negative bacteria, the complex machinery associated with the type II secretion system (T2SS) polymerises inner membrane pseudopilin proteins into thin filaments, to export substrates such as toxins, hydrolases and cytochromes. Here, computational simulations were used to study proteins from the Klebsiella oxytoca T2SS, focusing on the substrate pullulanase PulA, the major pseudopilin PulG, and the putative chaperone PulM.

Chapter 3 contains an in silico study of both post-translationally acylated PulA (lipoPulA) and non-acylated PulA (PulANA) in association with a lipid bilayer, representing an approximation of the biological state prior to secretion; this study examined PulA dynamics and the possible role of the acyl tail in protein-membrane interactions before secretion. Novel insights into the interactions of a key residue necessary for Type 2 secretion were gained via simulations performed on a PulANA D2S variant, extending prior in vitro results. In Chapter 4, PulA was simulated in conditions closer to the physiological environment, using counter-ions to investigate the possible effect of the high periplasmic calcium concentration on protein conformation and lipid interactions prior to secretion. In Chapter 5, variants of the major pseudopilin PulG containing one transmembrane helix were simulated, demonstrating N-terminal interactions made possible by wild-type methylation of residue Phe1. Simulations of several monomeric PulG variants provided insight into the roles of the essential residue Glu5 and Phe1 methylation, previously identified by experimental work to be important. Simulations of the PulG dimer demonstrated the dynamic nature of the membrane-embedded dimer interface, and showed how computational analysis can predict in vivo contacts. Finally, Chapter 6 extended the T2SS studies to coarse-grained methods, sampling possible conformations and predicting the PulG-PulM interface within the membrane, prior to PulG presentation to the remaining secretion apparatus.