Structural Modeling of T9SS Outer Membrane Proteins and Their Complexes

Abstract

The type 9 secretion system (T9SS) is a recently discovered machinery that both transports cargo proteins across the Gram-negative bacterial outer membrane and attaches them to lipopolysaccharides on the extracellular surface. Outer membrane proteins (OMPs) are key components of the T9SS and are involved in both steps. In this chapter, we describe a method for the in silico modeling of T9SS OMPs and their complexes, and model validation. This is useful when the production of recombinant OMPs is difficult, and these protocols can also be applied to OMP complexes outside of the T9SS.

Keywords: AlphaFold; AlphaFold multimer; Bacterial envelope; MD simulations; Membrane-embedded β-barrel proteins; OMPs; Protein secretion; T9SS.