19-08-2014, 10:35 AM
The computer simulation of molecules to predict their properties has a short history compared with experimental methods and only in recent decades computer simulation have become a widely used tool, particularly in studies of proteins and nucleic acids. Molecular modeling involves the use of computational methods for simulating/predicting the three-dimensional structures and physicochemical properties of molecules. Relatively few studies have been made of the structure of the reverse micelles despite their potential importance in a wide range of applications such as oil recovery and protein extraction from aqueous solution and as media for catalytic reactions. (Bandyopadhyay S. et. al., 2000)
The computer simulation of molecules to predict their properties has a short history compared with experimental methods and only in recent decades computer simulation have become a widely used tool, particularly in studies of proteins and nucleic acids. Molecular modeling involves the use of computational methods for simulating/predicting the three-dimensional structures and physicochemical properties of molecules. Relatively few studies have been made of the structure of the reverse micelles despite their potential importance in a wide range of applications such as oil recovery and protein extraction from aqueous solution and as media for catalytic reactions. (Bandyopadhyay S. et. al., 2000)
Molecular modeling is a tool to understand the interactions among atoms, ions and molecules.
Molecular mechanics (MM) calculations optimize the input geometry of the molecular system by using empirical equations, parameters of which are derived from X-ray crystal structure data-bank. (Rigby et al., 1981). A set of these parameters is called as force field. The motion of molecules at a given temperature and pressure condition is studied by molecular dynamics (MD), which solves Newton’s equation of motion for every molecule of the system. The force acting on each molecule at time‘t’ is calculated from the potential energy of that molecule at time 't' which in turn is calculated from MM calculations. (Allen and Tildesley., 1987)
In the present work, Molecular dynamics (MD) simulation have been carried out on a three dimensional model. This model consists of monolayer of an anionic surfactant, sodium-di-(2-ethylhexyl) sulfosuccinate (AOT) at the interface between hexane and aqueous solution containing a polypeptide molecule. This model is used to predict the mechanism of protein transfer from an aqueous phase to a reverse micellar organic phase. The molecular modeling software used was MS Modeling v3.2.0.0. Initially, the interface consisted of a uniform monolayer of 64 erect surfactant (AOT) molecules. A 1ns (nanoseconds) trajectory was generated at NVT ensemble i.e. at constant volume and at constant temperature (T=300K). The simulation predicts the deformation of the interface and relative mass transfer of polypeptide molecule.
Future work involves molecular dynamic simulations and investigations on electrostatic interaction between polypeptides and surfactant molecules