Comparison in structural stability between chain A and B of CLC-ec1 exchanger by using MD simulation

The CLC-type exchangers have been extensively studied in recent years. CLC-ec1, whose crystal structure is known and several experimental and theoretical hot spots have been identified, but the structural stability in true solution environment of this protein has not been provided. In this paper, we analyzed the structural stability of CLC-ec1 protein by using the atomistic molecular dynamics (MD) simulation. The simulation result indicates that there exists no inevitable correlation between chain A and chain B in expressing their biological function. Chain A has smaller average C_α displacement value than that of chain B. The calculated electrostatic binding free energy and its fluctuation of chain A are also smaller. These results indicate that chain A has more stable structure than chain B in physical essence. It is to say that chain A may be more reliable than chain B in expressing their biological function. This work proposes a new topic on future experimental and theoretical investigations for biologists and biophysicists.