Interplay between membrane curvature and conformational states in ABC transporters

Abstract

Biological membranes are complex functional and structural assemblies involved in several physiological processes. At the molecular level, some processes that involve transmembrane proteins also involve reorganization of the lipid environment, therefore generating membrane curvature. In this research work, we investigate the interplay between membrane curvature and conformational states in ABC transporters, a superfamily of transmembrane proteins involved in substrate translocation and multidrug resistance. By combining computational and experimental approaches, we test a hypothesis that states that proteins of different shapes remodel the lipid environment differently, thus inducing distinctive curvatures. We also work under the hypothesis that proteins with different shapes diffuse differently. To validate our hypothesis, we select the mammalian P-glycoprotein (Pgp), one of the best-characterized and most prevalent ABC transporters, and a bacterial homolog, the Bacillus multidrug resistance ATP (BmrA). Pgp and BmrA not only have common substrates, but also display the same protein shape: an inverted conical shape in the open conformation, and a cylinder-like shape in the closed conformation. Since structures of Pgp are available in two different conformational states, and BmrA can be functionally reconstituted in large amounts, these two ABC transporters are good candidates to test our hypothesis using an integrative approach that combines computer simulations and experiments. In the computational approach, I carried out Coarse-Grained (CG) Molecular Dynamics (MD) simulations at different levels of complexity to study membrane curvature induced by ABC transporters. As part of my work, I developed an open-source tool that allows the calculation of membrane curvature from MD simulations. Our computational results are in very good agreement with the experiments, validating our hypothesis and providing compelling evidence that protein shape is a critical underlying factor in the dynamic interplay between membrane curvature and conformational states in ABC transporters.

Description
Keywords
ABC transporters, Membrane Curvature, MD simulations, Lipid-protein interactions, Martini force field
Citation
Barreto Ojeda, E. (2022). Interplay between membrane curvature and conformational states in ABC transporters (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.