Solvation and Binding of the Membrane Enzyme Pagp By Detergents and Lipids

Abstract

The solvation of membrane proteins by detergents is a necessary step for structure determination by NMR and X-ray crystallography, and yet this process remains poorly understood. The severe under-representation of membrane proteins amongst proteins of known structure is a direct consequence of the difficulties associated with the solubilization of the large hydrophobic faces presented by this important class of proteins. The prominence of these membrane proteins as important drug targets provides a strong impetus for the rational design of new detergents or cofactors to assist the solubilization of hydrophobic faces while maintaining structural integrity. To this end, we begin by investigating the process of detergent self-aggregation, utilizing molecular dynamics simulations to characterize the atomic interactions that underlie the dynamic aggregation of detergents in aqueous solution. We determine the critical micelle concentration and the equilibrium aggregation number based on generalized ensemble methods and, separately, thermodynamic cycles involving non-physical order parameters that are more computationally efficient. Next, we apply similar methods to study the aggregation of detergents around the bacterial outer membrane enzyme and virulence factor PagP. These studies shed light on the process of protein self aggregation in solution and the atomistic mechanisms by which detergents may prevent protein precipitation at high concentrations. Finally, we draw functional conclusions for PagP, an acyltransferase that binds and catalyses its own lipid solvent.