Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling

Brownian dynamics (BD) simulations test for channeling of the substrate, glyceraldehyde 3-phosphate (GAP), as it passes between the enzymes fructose-1,6-bisphosphate aldolase (aldolase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). First, BD simulations determined the favorable complexes between aldolase and GAPDH; two adjacent subunits of GAPDH form salt bridges with two subunits of aldolase. These intermolecular contacts provide a strong electrostatic interaction between the enzymes. Second, BD simulates GAP moving out of the active site of the A or D aldolase subunit and entering any of the four active sites of GAPDH. The efficiency of transfer is determined as the relative number of BD trajectories that reached any active site of GAPDH. The distribution functions of the transfer time were calculated based on the duration of successful trajectories. BD simulations of the GAP binding from solution to aldolase/GAPDH complex were compared to the channeling simulations. The efficiency of transfer of GAP within an aldolase/GAPDH complex was 2 to 3% compared to 1.3% when GAP was binding to GAPDH from solution. There is a preference for GAP channeling between aldolase and GAPDH when compared to binding from solution. However, this preference is not large enough to be considered as a theoretical proof of channeling between these proteins.