Dynamic Gating Mechanism of the b0,+AT-Mediated Arg Transport: Insights from ASMD Simulations

Heteromeric amino acid transporters (HATs) mediate essential amino acid flux across membranes, but the molecular dynamics of substrate translocation remain poorly defined for many family members. Here, using conventional and adaptive steered molecular dynamics (cMD and ASMD) simulations, we identify residue W230 in the b0,+AT transport channel as a dynamic gate that regulates arginine (Arg) influx through side chain flipping. By integrating dynamic network analysis with dynamical cross-correlation of residue motions, we show that regulatory signals propagate from the Arg binding site through transmembrane helix 5 (TM5), a connecting loop, and TM6 to reach W230. We propose a dynamic gating mechanism for b0,+AT - mediated amino acid transport. Arg binding at V186 triggers signal propagation that enhances cooperative interactions between W230 and Arg, driving the side chain flipping of W230. Our findings reveal a dynamic gating mechanism underlying b0,+AT - dependent Arg transport and suggest that residue-triggered side chain reorientation may represent a conserved and efficient strategy in transporter function. Author SummaryAmino acids are the essential building blocks of life, and their transport across cell membranes is vital for nutrition and cellular signaling. Heteromeric amino acid transporters (HATs) mediate this process, yet how they physically move substrates through the protein at the atomic level remains poorly understood. In this study, we used advanced computer simulations to observe, in unprecedented detail, how b0,+AT--a key HAT member--transports the amino acid arginine. Our simulations revealed that a single residue, tryptophan 230 (W230), functions as a molecular gate: its side chain flips open to allow arginine to pass and then closes behind it, ensuring one-way traffic into the cell. We further discovered that the initial binding of arginine sends a signal through specific structural elements (helices and loops) to trigger this gate opening. This work not only uncovers a dynamic gating mechanism for b0,+AT but also suggests that similar side-chain flipping events may represent a common and efficient strategy used by other transporters to control substrate movement. Our findings provide a new framework for understanding transporter function and could inform future drug design targeting these critical membrane proteins.