In-silico Models of Steady-State Ternary Complexes of Phenylacetaldehyde Dehydrogenase
By: Julio Espinosa Robles
Department: Cellular & Molecular Biology
Faculty Advisor: Dr. George Gassner
Phenylacetaldehyde dehydrogenase (NPADH) is an enzyme involved in the metabolism of styrene, oxidizing phenylacetaldehyde to phenylacetate. Phenylacetaldehyde, however, is not the only the only substrate this enzyme is able to accept as it can also oxidize other aldehydes, and this has made it a great candidate as a biocatalyst with applications in green chemical synthesis and bioremediation. AutoDock Vina is a tool that simulates the interactions between a substrate and enzyme, the resulting model showing the possible final locations of the substrate in the enzyme-substrate complex as well as the affinity for the ligand at each possible location. NPADH follows a sequential ternary-complex reaction mechanism where NAD+ is the first substrate to bind, followed by the aldehyde that will be oxidized, so these models were created with NAD+ already bound to the enzyme. Three different substrates have been used to create docking models: cinnamaldehyde, ortho-nitrobenzaldehyde, and para-nitrobenzaldehyde. The KM of the enzyme for each substrate has also been found; the cinnamaldehyde having the lowest KM at 2.17µM, para-nitrobenzaldehyde being the highest at 19.9µM, and ortho-nitrobenzaldehyde having a value in-between at 9.15µM. The Michaelis-Menten equation shows that KM is inversely related to an enzyme’s affinity for its substrate under steady-state conditions, a smaller KM corresponds to a higher affinity. The KM values have been converted to steady-state binding energies that better reflect the enzyme’s affinity for the substrate and may allow for the models created through AutoDock Vina to be evaluated, the expectation being that the binding energies given by AutoDock Vina should follow a similar pattern as the converted affinities obtained from the experimental KM values.