Structural Insights into the Human Mitochondrial Pyruvate Carrier Complexes

Abstract

Pyruvate metabolism requires the mitochondrial pyruvate carrier (MPC) proteins to transport pyruvate from the intermembrane space through the inner mitochondrial membrane to the mitochondrial matrix. The lack of the atomic structures of MPC hampers the understanding of the functional states of MPC and molecular interactions with the substrate or inhibitor. Here, we develop the de novo models of human MPC complexes and characterize the conformational dynamics of the MPC heterodimer formed by MPC1 and MPC2 (MPC1/2) by computational simulations. Our results reveal that functional MPC1/2 prefers to adopt an inward-open conformation, with the carrier open to the matrix side, whereas the outward-open states are less populated. The energy barrier for pyruvate transport in MPC1/2 is low enough, and the inhibitor UK5099 blocks the pyruvate transport by stably binding to MPC1/2. Notably, consistent with experimental results, the MPC1 L79H mutation significantly alters the conformations of MPC1/2 and thus fails for substrate transport. However, the MPC1 R97W mutation seems to retain the transport activity. The present de novo models of MPC complexes provide structural insights into the conformational states of MPC complexes and mechanistic understanding of interactions between the substrate/inhibitor and MPC proteins.

Consumption and Metabolism of Extracellular Pyruvate by Cultured Rat Brain Astrocytes

“…Mitochondrial uptake is a prerequisite of a subsequent mitochondrial metabolism of pyruvate. To test whether the mitochondrial pyruvate carrier (MPC) is involved in the observed astrocytic pyruvate consumption, we applied UK5099, an inhibitor of the mitochondrial pyruvate carrier [ 23 , 46 , 47 ]. The presence of UK5099 lowered the astrocytic pyruvate consumption in a concentration-dependent manner and completely prevented pyruvate consumption in a concentration of 100 µM (Fig.…”

Identification of Novel Mitochondrial Pyruvate Carrier Inhibitors by Homology Modeling and Pharmacophore-Based Virtual Screening

“…The dimer was constructed in the inward facing position based on structural alignment with the SemiSWEET transporter X-ray structure (PDB: 4X5M) as a template [ 16 ] ( Figure 2 A,B). During our work on this manuscript, Xu, et al, published a homology model of the MPC dimer and a molecular dynamics simulations study on the model [ 27 ]. Comparison of our homology model with the published model revealed high similarity.…”

Experimental Investigations on the Structure of Yeast Mitochondrial Pyruvate Carriers

“…However, because of the lack of sufficient membrane protein structures, the prediction accuracy on membrane proteins is low. Recent literature using RoseTTAFold to calculate the 3D structure of MPCs also showed a different secondary structure from the NMR results [ 13 ]. Though both programs gave the prediction of the tertiary structure of the MPC complex, the differences of the secondary structures between the predictions and experimental results implicate that further structural characterization of the MPC complex is needed.…”

“…Earlier study suggested that MPC1 displays two transmembrane segments with the N- and C-termini projecting into the mitochondrial matrix, whereas MPC2 in mammals and MPC3 in yeast probably consist of three transmembrane helices, with the N-terminus projecting in the matrix and the C-terminus in the intermembrane space [ 12 ]. It was recently predicted by AlphaFold2 and RoseTTAFold that MPC1 and MPC2 both display three transmembrane helices [ 13 ]. So far, the membrane topology of MPC1 and MPC2 is still not fully resolved, as no experimental investigations on the structure of MPCs have been reported.…”