Multiscale Modeling of Enzymatic Efficiency in Multienzyme Complex: Effect of Interenzyme Distance, Crowding Effect and Side Reactions

Molecular association is one of the most fundamental principles of chemistry and biology. Biomolecular complexes need to colocalize sequential catalytic and chemical processes such that the intermediates are precisely positioned to diffuse efficiently. The relative distance and orientation between the active sites within these complexes may affect the intermediate binding, which may also be different under different cell environments. In this work, we used Brownian dynamics simulations to model an intermediate substrate association in the tryptophan biosynthesis pathway in <i>Escherichia coli</i> (<i>E. coli</i>) for investigating potential advantages of using TrpCF bifunctional enzyme which fuses phosphoribosyl anthranilate isomerase (PRAI) and indoleglycerol phosphate synthase (IGPS). We focused on transporting a product of PRAI, 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate (CdRP), which is also the substrate of in IGPS. We report the average association time and direct binding percentage when the substrate concentration is 10.0 μM as an estimated physiological concentration in cells. Our results suggest that final product synthesis efficiency can be achieved by optimizing the interenzyme distance and by properly aligning the orientation of the active sites. In addition, the intermolecular interactions between the substrate and macromolecule crowders largely affected the transportation of a substrate. The overall rate of product synthesis enhancement in a multienzyme complex depends on the distance between enzymes when the substrate leaking phenomenon exists. Our work highlights the importance of the enzyme spatial organization in regulating the production efficiency of a product in multienzyme complexes, broadens implications in synthesis processes under complex cell environments, and brings biophysical insights into the enzyme-substrate association and understanding of target ligand/substrate kinetics.