Microscopic Insights into a Ligand Escape Pathway and Energetics in Leucine-Isoleucine-Valine Binding Protein

Periplasmic binding proteins (PBPs) are a large family of receptors and transporters present in Gram-negative bacteria, which play a pivotal role in cellular transport. PBPs have a distinct two-domain architecture that undergoes large conformational transitions through hinge motion. In particular, leucine-isoleucine-valine binding protein (LIVBP) can sense specific amino acid side chains and undergoes a transition from an open conformation to a closed conformation, which is traditionally viewed as a ligand-induced conformational change. Although many studies focused on conformational fluctuations of LIVBP, the same attention was not paid to the microscopic and energetic aspects of ligand escape. Here, μs long atomistic molecular dynamics and well-tempered metadynamics simulations are used to understand the role of the ligand (namely, isoleucine) in the conformational transition/selection of the LIVBP. Furthermore, the pathway, energetics, and sequence of events during ligand escape/unbinding are unveiled from a microscopic perspective. The ligand escape is a two-step process in which the domain separation precedes the ligand escape. However, the reverse is also observed. Water is found to play an important role in the ligand unbinding process as well as in providing stability to the closed conformation, in the absence of the ligand, by forming bridging hydrogen bonds between two domains.