Relative stability of different conformations and pathways of ligand escape in LIV-binding protein: A molecular dynamics simulation study

Periplasmic binding proteins (PBPs) are a large family of receptors and transporters, present in gram-negative bacteria, which play a pivotal role in transport, chemotaxis and quorum sensing. These class of proteins have a distinct two domain architecture that undergo large conformational transitions through a hinge motion. In particular, Leucine-Isoleucine-Valine (LIV) binding protein can sense these specific side chains and undergoes a transition from a open to a closed conformation which is traditionally viewed as ligand induced conformational change. Here, atomistic molecular dynamics simulations and well-tempered metadynamics simulations are used to understand the role of ligand (namely, Isoleucine) in the conformational transition/selection of the LIV-binding protein. Furthermore, the pathway, energetics, and sequence of events during ligand escape/unbinding are unveiled from a microscopic perspective. Two distinct ligand binding pathways are identified: (i) domain separation followed by ligand escape, and (ii) ligand escape either followed by or synchronous with domain separation. The former is found to be energetically more favorable. Water is found to play an important role in the ligand unbinding process as well as providing stability to the closed conformation in the absence of the ligand, by forming bridging hydrogen bonds between two domains.