Amino acid binding to nanotube: Simulation of membrane protein channels by computational methods

Abstract

The importance of ionic channels is due to the passage of ions across the cell membrane which is based on electrochemical gradients. The structure of ionic channels often includes one or several central cores which makes up the pore. The direct electron transfer between the enzyme and unmodifi ed electrode is usually prohibited due to shielding of the redox active sites by the protein shells. Monte Carlo simulation have been used to investigate protein folding pathways with some success. Monte Carlo was originally developed for calculating equilibrium properties of physical systems .In calculations we optimized the geometry and defi ned Potential Energy of the nanotube structure by performing molecular mechanics calculation using MM+ force fi eld, if too large a time step is used in Monte Carlo simulation, it is possible to have a basic instability in the equations that result in a molecule blowing apart, we need small time steps to preserve integration accuracy, however in the Monte Carlo time step 50 femtoseconds (0.05ps) was appropriate. next step we calculated the Vibrational modes of the tube by applying the semi-empirical molecular orbital method. In this paper, we have studies the stability of CNT-Amino acids clusters using by semi-empirical method and investigation of vibrational frequencies and electrical properties. In the more the potential energy increases the more the conductivity of nanochannels decreases and we chose the least energy among nanotube and amino acid complexes. Also the more energy we use, the more conductivity we will have; therefore, we choose the complex which conducts the most current.