Confronting Fusion Protein-Based Membrane Protein Topology Mapping with Reality: The Escherichia coli ClcA H+/Cl− Exchange Transporter

The topology of bacterial inner membrane proteins is commonly determined using topology reporters such as alkaline phosphatase and green fluorescent protein fused to a series of C-terminally truncated versions of the protein in question. Here, we report a detailed topology mapping of the Escherichia coli inner membrane H+/Cl− exchange transporter ClcA. Since the 3-D structure of ClcA is known, our results provide a critical test of the reporter fusion approach and offer new insights into the ClcA folding pathway.