The survival of cells depends on the continuous input, storage, and transition of free energy to drive the normal work cycle of such molecular machinery as transporters, channels, and other MPs. What role do electrostatic interactions play in these energy conversion processes? For energy conversion processes other than light energy conversion, is there any “mysterious” phenomenon that classical physics cannot understand? This chapter will discuss the structural dynamics of MP complexes related to the energy conversion between the three major energy systems, namely, redox potential, transmembrane electrochemical potential, and ATP. We will focus on ATP synthase, introduce its simplified model, and propose a mechanistic hypothesis for the proton pump in respiratory chain complex I based on its known structural information.