BPS2026 – Modeling AAC1 nucleotide transport using molecular dynamics simulations

Proteins have flexible three-dimensional structures which can adopt multiple conformations. Understanding how small molecules interact with protein conformational landscapes beyond the ground state structure is essential to understanding protein-ligand interactions. Such interactions are integral to the functioning of membrane transporter proteins, but the mechanistic details vary widely. ATP/ADP carrier protein 1 (AAC1) transports ATP and ADP across the inner mitochondrial membrane, but does not transport AMP, GTP, or GDP despite their structural similarity. Furthermore, it interconverts between the two terminal states of the nucleotide transport pathway only in the presence of its ATP or ADP substrates. Its structure has been experimentally determined in two conformations believed to represent these transport pathway endpoints, but the precise mechanism of nucleotide transport and existence of metastable intermediate states remains unknown. Existing simulation studies using different nucleotides suggest that AAC1 substrate selectivity is only partially explained by differences in nucleotide binding affinity. A model of the transport process is therefore needed to uncover the full structural determinants of selectivity and the mechanism by which ATP and ADP lower the energy barrier to protein conformational change. AAC1 nucleotide transport has thus far only been simulated using externally applied forces to pull the protein from one state to the other in a manner not equipped to identify the true biological transition pathway. This work will use molecular dynamics simulations with metadynamics to map the conformational transition pathway of AAC1, identifying the structural basis for nucleotide selectivity and nucleotide-catalyzed protein conformational change. Understanding the mechanism of nucleotide selectivity in AAC1 will also shed light on the potential mechanisms of other AAC-family proteins.