Molecular Dynamics Simulations Provide Insights into Structure and Function of Amadoriase Enzymes

Abstract

Background. Enzymatic assays based on Fructosyl Amino Acid Oxidases (FAOX) represent a potential, rapid and economical strategy to measure glycated hemoglobin (HbA1c), which is in turn a reliable method to monitor the insurgence and the development of diabetes mellitus. However, the engineering of naturally occurring FAOX to specifically recognize fructosyl-valine (the glycated N-terminal residue of HbA1c) has been hindered by the paucity of information on the tridimensional structures and catalytic residues of the different FAOX that exist in nature, and in general on the molecular mechanisms that regulate specificity in this class of enzymes. Objective. In this study, we use molecular dynamics simulations and advanced modeling techniques to investigate five different relevant wild-type FAOX (Amadoriase I, Amadoriase II, PnFPOX, FPOX-E and N1-1-FAOD) in order to elucidate the molecular mechanisms that drive their specificity towards polar and nonpolar substrates. Specifically, we compare these five different FAOX in terms of overall folding, ligand entry tunnel, ligand binding residues and ligand binding energies. Methods. We used a combination of homology modeling and molecular dynamics simulations to provide insights into the structural difference between the five enzymes of the FAOX family. Results. We first predicted the structure of the N1-1-FAOD and PnFPOX enzymes using homology modelling. Then, we used these models and the experimental crystal structures of Amadoriase I, Amadoriase II and FPOX-E to run extensive molecular dynamics simulations in order to compare the structures of these FAOX enzymes and assess their relevant interactions with two relevant ligands, f-val and f-lys. Conclusions. Our work will contribute to future enzyme structure modifications aimed at the rational design of novel biosensors for the monitoring of blood glucose levels.