Interdisciplinary research has become a mature approach for the development of novel, integrated solutions for many complex problems in basic science and applied technology. The convergence of biology and nanotechnology is particularly promising from an engineering perspective. This dissertation will use computer simulations to investigate the structure-function of the P-type ATPases, a class of vital biological transmembrane proteins. A detailed understanding of protein function at the atomic level and associated time scale is not only important for biomedical research but also vital for the design and development of engineering applications, such as self-assembling molecular devices. This work’s methodology will show that significant insight into the structure-function relationship of ion-motive ATPases can be derived by a combination of simulation tools and analysis techniques including molecular dynamic trajectories, steric pathway analysis, and electrostatic calculations.