Cellular lives adjust to changes in their environment to continue their bioactivities through various mechanisms governed by enzymatic processes. Adenylate kinase (AKE) enzyme is crucial to Escherichia coli (E. coli) survival and exists at ambient and cold temperatures. Kinetic studies using folding and unfolding concepts showed similar activation rates for AKE and four mutant forms (A37G, A55G, V135G, and V142G) at an ambient and lower temperature. However, we envisaged that a fine ensemble of AKE and mutants would enable better insight into the conformational dynamics as a driving force for optimal reactivity prediction. Such study would enable capturing nearly all the possible conformations of the protein and its mutations with a high level of precision. Protein structure study with an algorithm that could account for electrostatic properties during inhibitor interaction at the active site and conformational fluctuations of the whole protein is still scarce. Here, we study the dynamics of AKE and glycine mutations A37G, A55G, V135G, and V142G using the AMOEBA polarizable force field. Introducing a single conformational entropy-enhancing mutation (such as glycine) at a distal region from the active site on the AKE affects cold adaptation in E. coli. Hence, we aim to investigate the structural and functional allosteric of these AKE mutations when coupled with an inhibitor (AP5). The applied polarizable force field enables the evaluation of conformational dynamics and the residues contributing substantially to the inhibitor interaction at the active site using Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code (ELECTRIC). Electric field simulation in Tinker has been modified to account for hydrogen bond, long-range interaction, water, and other possible electrostatic interactions within a system. We hope that the study provides a better understanding of the cold adaptation allostery at the molecular level. Glycine mutations might significantly lower the binding affinity and increase the catalytic rate of adenylate kinase.

Cold adaptation allostery in Escherichia coli: A molecular dynamics study of Adenylate kinase with AMOEBA polarizable force field

ACS Fall 2021

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.