Molecular Basis of pH-dependent HIV gp120 Differences Revealed Using BESI

Abstract

Abstract Research in the field of HIV transmission has yet to provide a vaccine for the imponderable virus. Though progress has been made to extend the life of those chronically infected, a solution to the transmission of the disease outside of abstinence is still no where to be found. Previous laboratory studies involving electrostatic surface charge analysis revealed the sensitivity of gp120 to changes in pH across levels consistent with those found in the human body. A prototype computational approach was developed and found to agree with laboratory results. We previously refined the process and utilized additional methods to determine a system capable of classifying Env structures through machine learning techniques. We have expounded upon the analytical procedure to encompass the residue level and expanded the process to include minimization steps to ensure the integrity of the protein structures. Additionally, the process has been enhanced with advanced data compression techniques to allow for more in depth analysis of the systems. In this research we continue to validate previous work in several studies as well as increase the returned knowledge through a new technique that reveals what we hypothesize to be the mechanistic residues responsible for the binding process.