Investigating The Mechanisms of Active Site Mutations to the 1T9G WT MCAD Protein to Better Understand Medium Chain Acyl-CoA Dehydrogenase Deficiency (MCADD)

Authors

Omar E. Saleh, Nova Southeastern UniversityFollow
Rhea Khatiwala, Nova Southeastern UniversityFollow
Jeremy Ignatius, Nova Southeastern UniversityFollow

Files

Submission Date

Fall 2022

Abstract

Medium-chain Acyl-CoA Dehydrogenase Deficiency (MCADD) is a human disorder that hinders β-oxidation, affecting approximately 1 in 17,000 people in the United States. Once mutated, the Acyl-CoA Dehydrogenase Medium-Chain (ACADM) gene, which is solely responsible for MCADD, is unable to produce enough MCAD enzymes to metabolize medium-chain fatty acids. As a result, fats are not catabolized, causing symptoms of lethargy and hypoglycemia, as well as damage to the brain and liver due to a buildup of unused fatty tissue. The purpose of this project was to investigate the possible and known effects of different amino acid mutations on the human MCAD protein and produce a 3D-printed model to explain the molecular story of MCADD. This model builds on previous bioinformatics and in vivo experiments aimed at revealing the underlying enzymatic mechanisms of MCADD. Using PyMOL, the human wild-type MCAD (PDB ID: 1T9G) had its electron transferring flavoprotein (ETF) complex removed and a single chain from its homotetramer portion isolated for clarity. PyRx was used to dock the substrate, Octanoyl-CoA (PDB ID: CO8) into the slightly mutated enzyme, referencing PDB ID 1EGC. Known mutations from the PDB files and related literature were then compared and analyzed on the modified 1T9G to determine known and possible effects the mutations had, such as helix-helix stability and ligand hydrogen bonding. LigPlot+ was then used to analyze ligand-active site interactions. Jmol was used to cosmetically enhance the modified 1T9G to produce a 3D model for printing. In the model, the mutations were ranked according to known K_M range values (0.4, 0.6), (0.7, 0.9), and 0.9+, which were highlighted in the colors “lightskyblue”, “royalblue”, and “midnightblue”, respectively; unknown K_M values were colored “chartreuse”. All mutations had their side chains shown for further clarity. E376, the catalytic base, was colored “magenta”, the backbone was colored “dimgray”, and the support struts of the model were colored “lightseagreen”. The use of the 3D model was beneficial, enabling model viewers to locate, determine, and hypothesize the mutations and their effects on MCAD, in addition to providing a visual and physical learning aid for researchers, professors, students, and other biomedical professionals. Furthermore, the clarity produced by a physical model ultimately enables further research for MCADD and may assist in the development of a cure for those who unfortunately suffer from this rare condition.

Recommended Citation

Saleh, Omar E.; Khatiwala, Rhea; and Ignatius, Jeremy, "Investigating The Mechanisms of Active Site Mutations to the 1T9G WT MCAD Protein to Better Understand Medium Chain Acyl-CoA Dehydrogenase Deficiency (MCADD)" (2022). Protein Modeling Reports. 7.
https://nsuworks.nova.edu/protein_modeling_reports/7