Building Graphs to Describe Dynamics, Kinetics and Energetics in the D-Ala:D-Lac Ligase Vana

Abstract

The D-Ala:D-Lac ligase VanA, plays a very important role into the resistance to vancomycin, as it allows the bacteria to replace the synthesis of D-Ala:D-Ala by the synthesis of D-Ala-D-Lac in the bacterial wall, thus making obsolete the role of vancomycin. The reaction catalyzed by VanA requires the opening of the omega-loop to let the substrates entering the active site. Previous molecular dynamics simulations have shown the spontaneous opening of omega-loop in the presence of a crystallographic disulphide bridge. Here, the conformational landscape of VanA is further explored in the absence of the bridge and by using the enhanced sampling approach temperature-accelerated molecular dynamics (TAMD). This analysis has permitted to reveal a description of the conformational space of VanA, where the internal mobility and various opening modes of omega-loop play a major role. The other important feature is the correlation of the omega-loop motion with the movements of the opposite domain. The relative mobility of these two regions is observed in the conformational space analysis and their coupling is demonstrated by the communities analysis of the protein structure. The observations made on the VanA dynamics and conformations permit to propose some residues interactions to be important for the kinetics of the omega-loop opening. Also, the various graph network analyses performed here provide a panel of methods to describe a protein function in the frame of a larger system-oriented network.