Structural Comparison of Human Beta Defensin Type 3 in Vacuum, Implicit and Explicit Solvents using NAMD, FMO-DFTB3 and CHARMM

Abstract

The primary defense system of the human body for fending off invasive organisms, such as bacteria, viruses and fungi, is known as the “Immune System”. Although the immune system is comprised of specialized cells and tissues, one crucial component that is located in the stomach and intestine lumen, as well as the epidermis, are epithelial cells. Pertaining to secretion and protection, epithelial cells release an antimicrobial peptide in the mucus bilayer known as “Human Beta Defensins”, or noted as HBD’s, and are tasked in the warning, resistance and amelioration of foreign organisms.
The method of recording HBD’s performance during attacks on foreign organisms is accomplished through different simulation techniques that monitor the stability, motion and dynamics of HBD interaction with its surrounding environment. This is done by employing energy calculations, root mean squared deviations, root mean squared fluctuations and other parallel calculations. The three types of simulation that will be used throughout the research are: Nano Molecular Dynamics (NAMD), Chemistry at Harvard Molecular Mechanics (CHARMM) and Fragment Model Orbital method using Density Functional Tight Binding (FMO-DFTB3). Virtual Molecular Dynamics (VMD) is also utilized for the visualization of structural changes While each of the program’s computational techniques vary, the predicted results will show an overlap in HBD - environment interactions. As well, Preliminary results show an overlap in vacuum and explicit results. Ergo, the operating purpose is to monitor and compare the structure of HBD-3 in a vacuum and implicit and explicit solvents using NAMD, FMO-DFTB3 and CHARMM respectively.