Modeling the Stability of the High-Density Lipoprotein Particle by Examining the Protein-to-Protein Binding Strengths.

    Author Name(s)

    Cynthia Fernandez

    Faculty Advisor(s)

    William Munroe

    Abstract

    Our research focuses on modeling the stability of the human High-Density Lipoprotein (HDL) particle and understanding its characteristics. As we did protein-protein docking, we were able to dock HDL-associated proteins to apoAI (the main structural protein of HDL) as 3D models through the ICM Molsoft modeling program and obtain certain parameters such as their delta G values. This program models protein-protein docking interactions taken from the protein’s 3D structure protein data bank (PDB) file. Protein–protein docking is the computational prediction of potential binding strengths among the targeted proteins that occur in living organisms. Through our findings, we tested the protein-protein docking between a large number of proteins and apoAI using ICM Molsoft to calculate a set of delta G values to compare the differences in how these proteins interact. All of these delta G values for the selected proteins are the minimum value of their relative docking site. The delta G values obtained fell in different ranges with the smallest value of -385.9 to the largest value of 113.24 kcal/mol. We found that the values greater than -200 kcal/mol were the proteins with a greater binding energy, which include Angiotensinogen at -283.3 kcal/mol and apoB-100 at -385.9 kcal/mol. The research we are conducting reflects how these proteins interact in their environment. By determining the range of these delta G values it can be considered that delta G determines the stability of any given protein–protein complex, or, otherwise, the binding affinity of a protein to a given receptor.

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