Molecular Dynamics Simulations Of Trans-inhibition Of Methionine Uptake Transporter MetNI

The body’s cells need to uptake nutrients from the environment, while discharge metabolites and wastes, so as to maintain a dynamic balance, which is extremely important to the body’s health. Transport across membrane can be passive or active. Passive transport is a movement of biochemical and other atomic or molecular substances across cell membranes. It is the net movement of material from an area of high concentration to an area with lower concentration. Active transport is the movement of molecules across a cell membrane in the direction against their concentration gradient, going from a low concentration to a high concentration. Active transport requires trans-membrane protein energy for ATP and trans-membrane protein transporters, which gradually become eager to study. ATP (ATP-binding cassette) transporters constitute one of the largest super family in organism. They use the energy from nucleotide binding and hydrolysis to translocate substrate across cell membranes. ABC transporters diverged very early into two classes that correlate with the direction of substrate transport. In importers, TMDs and NBDs reside on separate subunits while in exporters, TMDs are fused to NBDs. ATP binding and hydrolysis would drive the opening and closing motion of nucleotide-binding sites, and guide the reorientation of the translocation pathway.In this study, the methionine uptake transporter MetNI as an ABC importer can uptake of D-and L-methionine. During the process of translocation across cell membrane, methionine uptake transporter MetNI transport system can be regulated by many facts. One example is trans-inhibition, which terms the feedback inhibition of transporter activity resulted from accumulation of transported substrate during the translocation process. This type of inhibition results in the decrease of the transport rates as the concentration of substrate increases.Computational simulation has its own advantages over experiments in protein dynamics studies. It can trace the position and velocity of every atom at every moment and interprets every state on the conformational transition pathway with high accuracy. In this study, we investigate the mechanism of trans-inhibition effect at atomic resolution on Escherichia coli methionine uptake transporter MetNI, using molecular dynamics (MD) simulations. By performing MD simulations for a total of 6μs on the methionine-binding and methionine-free states of MetN subunits, we discover that the binding-induced allosteric effects on C2 domain result in a significant change of conformational flexibility and inter-domain movements. Moreover, the binding of methionine stabilizes an NBD separated conformation, shifting the conformational equilibrate away from the active state of ATP hydrolysis, which eventually disrupts the transport process. In addition, we also propose some key amino acid residues that might be involved in the allosteric regulation pathway. The turn of β 2-β 3 in C2 domain and the rigid body motions of linker to C2 and linker to NBD, might play critical roles in the allosteric regulation process. Our work will deepen our understanding of the activity of the regulatory mechanism of ABC transporter family.