Chapter 9. Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels
Résumé
Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of ∼ 25 OMPs are currently known, the relationship between structure, dynamics and function is often unclear. Furthermore, relatively little is known about the effect of the local environment on the protein dynamics. Over the past 10 years or so, molecular dynamics simulations have been successful in revealing insights into aspects of outer membrane proteins that are difficult to study with experimental methods alone. Indeed in some cases simulations have aided the interpretation of structural data e.g. the apparent discrepancy between the x-ray structure of OmpA from E. coli and the observed conductance data. Simulations have also been employed to design mutants of OMPs with desired properties, e.g mutants of OmpG that may serve as components of stochastic biosensors.
In general, more OMPs have been studied via MD simulations than perhaps any other family of membrane protein, yielding a wealth of information that provides an ideal complement to experimental determined data.