Computational Modeling of Glycolipid-Glycoprotein Complexes: Methods and Applications

Abstract

The human innate immune response to a Gram-negative bacterial infection involves detection of lipopolysaccharides (LPS), also known as endotoxins, which comprise the bacterial outer cell wall. Distinct from mammalian glycolipid structures, LPS have a conserved chemical pattern that is recognized by the pattern recognition receptor complex formed by myeloid differentiation protein 2 (MD-2) and toll-like receptor 4 (TLR4). While there is a clear correlation between endotoxin acylation and elicited agonist or antagonist responses, the 3D structural basis of this relationship remains unclear and difficult to characterize experimentally. In order to explore, at atomic-resolution, the effects of a range of chemically distinct endotoxins on the structure and dynamics of their MD-2·endotoxin complexes, a series of variably acylated lipid A molecules from E. coli and N. meningitidis in complex with human MD-2 were examined. This included the development and validation of appropriate molecular dynamics force fields to study complex (lipid, carbohydrate and protein) systems. Through these computational developments, in concert with experimental data, specific structural and dynamic features that control dimerization of TLR4 molecules were identified. As dimerization is central to the release of downstream chemical mediators, the results provide a structural foundation for the ability of endotoxins to act as either agonists or antagonists of the TLR4 pathway. Additionally, methods for biologically-relevant characterization of dynamic glycolipid-glycoprotein systems will be discussed.