Exploring conformational transitions in membrane proteins with memento.

Abstract

Despite rapid advances in cryo-EM delivering structures of membrane transport proteins at an unprecedented rate, they are typically solved in one conformational state. Whilst conformational flexibility can be inferred from static end-state structures, the interconversion mechanisms between states are often beyond the scope of direct experimentation. Given the dynamical nature of the processes in question, many studies have attempted to explore conformational transitions using molecular dynamics. However, ensuring proper convergence and reversibility in the predicted transitions is extremely challenging. In this work, we present an approach that we term “MEMENTO” (morphing end states by modelling ensembles with independent Topologies) to generate paths that alleviate starting state dependence (hysteresis) in the construction of conformational free energy profiles. MEMENTO utilises template-based structure modelling to restore physically reasonable protein conformations based on coordinate interpolation (morphing), and we apply it in conjunction with replica-exchange umbrella sampling to sample likely transitions. We demonstrate how the method works via application to well-characterized test cases (deca-alanine and adenylate kinase) before discussing its use in transporter proteins. We also suggest that extended end-state sampling combined with MEMENTO can aid the discovery of collective variables for umbrella sampling on a case-by-case basis.