10.1371/journal.pone.0134879.g008 Nan Wang Nan Wang Jiahong Jiang Jiahong Jiang Xichen Li Xichen Li Hongwei Tan Hongwei Tan Jimin Zheng Jimin Zheng Guangju Chen Guangju Chen Zongchao Jia Zongchao Jia Average conformation of the YhdE closed state with dTTP bound in MD simulation (a) and the YhdE open state with dTTP bound in MD simulation (b). Public Library of Science 2015 Free Energy Calculations YhdE dimerization allosteric communication network Molecular Dynamics Simulation Studies cell metabolism pathway dTTP binding sites YhdE Dimerization YhdE dTTP binding 2015-08-07 03:53:52 Figure https://plos.figshare.com/articles/figure/_Average_conformation_of_the_YhdE_closed_state_with_dTTP_bound_in_MD_simulation_a_and_the_YhdE_open_state_with_dTTP_bound_in_MD_simulation_b_/1506104 <p>The diagram on the left shows the interactions between dTTP and YhdE residues in the binding pocket. The diagram on the right shows two sodium ions that interact with dTTP and I29, E30 at the same time in the MD simulation.</p>