Using pulsed EPR in the structural analysis of integral membrane proteins

Pulsed EPR methods, such as PELDOR (or DEER) and ESEEM have emerged as powerful tools for assessing membrane protein conformation, folding, oligomerisation and dynamics. PELDOR distance measurements can provide quantitative information on the conformational equilibria of membrane proteins, dovetailing well with techniques such as X-ray crystallography and cryo-EM. ESEEM spectroscopy can offer deuterium (or solvent) accessibility quantification at a single residue level. An inherent limit placed on membrane protein studies is the need to remove the protein from its natural membrane environment. However, recent developments in the membrane protein field provide lipid scaffolds that mimic that environment, to limit the impact of protein solubilisation and offer flexibility of choice in lipid composition, a key factor in the functional integrity of membrane proteins. Additionally, computational tools can be used to aid spin-labelling experiments, or tailored to incorporate experimentally derived PELDOR distance restraints to reveal the complete conformational ensemble of membrane proteins. In this chapter, we will focus on the application of pulsed EPR in the study of membrane proteins, highlighting case studies including our work on mechanosensitive ion channels. We will discuss experimental considerations, and introduce some of the computational tools that can be used in combination with pulsed EPR methods.