Free Energy Calculation for NavAb Channel Using the Crooks Fluctuation Method

Abstract

Membrane proteins such as ion channels, transporters and receptors are among the biologically important proteins. Because membrane proteins allow cells to communicate with their environment. Therefore, membrane proteins are targets for almost all drugs. It is also of scientific interest that membrane proteins play an important role in the control of the life process. Recent developments in experimental and computational sciences have further increased the interest in membrane proteins. The milestone development in this area is the obtaining of the crystal structure of membrane proteins. The crystal structure of the voltage-gated bacterial Nav channel was obtained in 2011 by Payandeh et al. Voltage-gated sodium channels are very important as they initiate the action potential. In this study, the Crooks fluctuation method, which was developed for the calculation of free energy in unbalanced systems, was applied for voltage-gated sodium channels, which is a complex biological system. The results were compared with other calculation methods in the literature.