A three dimensional (3-D) physical model of ribosome movement in protein synthesis

In this study, we propose new concepts of Active Potential Energy Well, Specificity and Non-Specificity of the wells. We perform these concepts to establish a 3-D physical model and to elucidate how a complete functional ribosome traps an aminoacyl tRNA, and how it moves along the mRNA template in the elongation of protein synthesis. In our model, we first introduce concepts of reduced mass and relative coordinates of a two objects system. Then we simplify a ribosome movement along mRNA in protein synthesis. We also introduce concepts of active objects and active controls in this study. Our model is based on quantum mechanics, thermal dynamics and the published biochemical data.