DETERMINATION OF STRUCTURAL STABILITY AND CATALYTIC ACTIVITY OF G6PD VARIANTS USING MOLECULAR DYNAMIC SIMULATION (MDS) APPROACH

Abstract

BackgroundGlucose‐6‐phosphate dehydrogenase (G6PD) is a known housekeeping enzyme that is important in the pentose phosphate pathway (PPP) and essential for basic cellular function. G6PD also aids in producing compounds to prevent build‐up of reactive oxygen species (ROS) within the red blood cells. Glucose‐6‐phosphate dehydrogenase deficiency (G6PDD) is a known hereditary mutation and X‐linked recessive genetic disorder that have affected over 400 million people worldwide. More than 186 G6PD variants have been characterized that affect enzyme catalytic activities and biochemical reactions leading to various clinical phenotypes.ObjectivesThe intention of this study was to investigate the genotype‐phenotype correlations of selected G6PD mutations via structural analysis and molecular dynamic simulation analysis (MDSA) tools.MethodESPript 3.0 software was used for multiple sequence alignments of G6PD from human and from other organisms. PyMOL molecular visualization tool was also used to shown and evaluate structural changes in ten selected variants of the protein.ResultsMultiple sequence alignment of G6PD from human and three other organisms, namely; Trypanasoma cruzi, Mycobacterium avium and Leuconostoc mesenteroides revealed three conserved regions. The findings of this study suggested that mutation to residues that are unable to adopt a cis conformation would lead to an extremely high activation energy barrier for the enzyme to adopt the correct transition state during the enzymatic reaction. The protein was subjected to several computational approaches as described in previous part. The simulation data from the molecular dynamic simulation helps to determine the protein dynamics through stability and flexibility of G6PD native and mutation.The native G6PD have high RMSD average value than Class I, class II and class III mutation, thus, have low structure stability. The G163D has the lowest RMSD value thus have the most stable structure through simulation. From RMSF analysis, the residue at 310 until 320 (loop 1), 374 until 388 (loop2), 408 until 414 (loop 3) and 424 until 434 (loop 4) responsible for structure flexibility and stability. The loop regions produce larger fluctuation thus, providing the flexibility to the structure.Findings from molecular dynamic analysis reported here will be more valuable if comparison to kinetic data of the mutants are made. Simulation of the enzyme dimer form could stipulate the relationship between structural changes and enzymatic activity of G6PD variants.Support or Funding InformationResearch Center, King Fahad Medical City, Riyadh, KSA