Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps

Abstract

Transmembrane proteins include membrane channels, pores, and receptors and, as such, comprise an important part of the proteome, yet our knowledge about them is much less complete than about soluble, globular proteins. An important aspect of transmembrane protein structure is their exact position within the lipid bilayer, a feature hard to investigate experimentally at the atomic level. Here we describe MemBlob, a novel approach utilizing difference electron density maps obtained by cryo-EM studies of transmembrane proteins. The idea behind is that the nonprotein part of such maps carries information on the exact localization of the membrane mimetics used in the experiment and can be used to extract the positional information of the protein within the membrane. MemBlob uses a structural model of the protein and an experimental electron density map to provide an estimation of the surface residues interacting with the membrane.