A working model for the topology of the Tim23 protein in the mitochondrial inner membrane (IM). (A) The Tim23p contains four predicted TM segments and its amino and carboxyl termini have been shown to face the intermembrane space (IMS). TM segments are indicated by the numbered rectangles, and loops L1 and L3 are proposed to face the matrix as indicated. (B) An HA epitope inserted into loop L2 of Tim23p faces the IMS. Mitochondria were isolated yeast cells expressing Tim23p with the HA epitope in loop L2 from plasmid pAD91 (called I-HA). As controls mitochondria were isolated from wt cells (WT), and cells expressing Tim23p with the HA epitope inserted at its C terminus from plasmid pJE8 (called C-HA). Intact mitochondria were digested with 100 μg/ml proteinase K for 30 min at 0°C, and mitochondria whose OM was disrupted by OS were digested with 50 μg/ml proteinase K. Mitochondrial proteins were immune blotted with antibodies to the amino-terminal domain of Tim23p, the HA epitope, the matrix protein α-MPP, or the OM protein, Tom70p.