MurD ligase from Escherichia coli: C-terminal domain closing motion

Abstract

MurD (UDP- N-acetylmuramoyl- l-alanine: d-glutamate ligase), a three domain bacterial protein, catalyzes a highly specific incorporation of the d-glutamate into the cytoplasmic intermediate UDP- N-acetyl-muramoyl- l-alanine (UMA) utilizing ATP hydrolysis to ADP and P i. This reaction is part of the biosynthetic pathway enabling bacterial peptidoglycan synthesis. During our previous investigations of this complex dynamic antibacterial target, Targeted Molecular Dynamics (TMDs) simulations were performed (Perdih et al., Proteins: Struct. Funct. Bioinf., 2007) in order to examine the UMA and ATP substrates binding process and gain insights into the structural changes that occur during the conformational transitions of the C-terminal domain from the experimentally determined open structures to its active closed conformation. Off-path simulation (OPS) technique, an extension of the well-established Replica Path Method (RPATh), was applied to compare the relative energy of the two by C-terminal domain closing motions generated by TMD simulations. The first C-terminal domain closing process commenced from the experimental open structure in which this domain is located out-of plane to the N-terminal and central domains (open structure pdb:1EEH). In the second trajectory the conformational movement is confined to this plane only (open structure pdb:1E0D). The obtained results indicated that the C-terminal domain movement occurring from the out-of-plane starting structure is coupled with much higher energy changes compared to the motion of this domain within this plane which is more freely available to the enzyme. The results nicely corroborate experimental findings from recent structural studies. The study offers valuable information for novel structure-based virtual screening campaigns exploiting protein conformational flexibility.