Normal Mode Analysis of Collective Excitations in a Lipoxygenase Proton Tunneling Reaction

Soybean lipoxygenase (SLO) supports a proton tunneling reaction that proceeds across a 2.8 A tunneling distance, but the precise way it achieves this active site geometry is unknown. One says its its vibrational normal modes can efficiently channel thermal energy from surface residues to the active site and correctly position the linoleic acid substrate to allow the reaction to take place; one such pathway has already been found by experimentalists. To further explore this phenomenon, we will use the AmberTools software package to perform an all-atom normal mode analysis of SLO. We can find the most influential normal modes by computing the power spectrum between atom pairs of interest, such as the heavy atoms involved in the proton tunneling reaction. We can then look through the most interesting of these modes to see which describe long-range, delocalized excitations of the protein, and further study these pathways that help channel thermal energy to the active site and enable the proton tunneling reaction to occur.