Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics

Abstract

Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.

Figure 1

Schematic of experimental setup. The substrate sphere (orange) must diffuse to the active zone of the first enzyme (pink) and then to the active zone of the second enzyme (blue). Shown are the enzyme spheres with the 8 Å radius and the active zones in the 45° orientation. The center of the substrate sphere must encounter the active zone for a reaction to occur.

Figure 2

Probabilities of reactions at changing distances when active zones are in 0° orientation. (A) Probability of the first reaction occurring. The probability is fairly constant except when the active zone centers are only 5 Å apart. The close proximity of the enzyme spheres may hinder the substrate ability to encounter the active site. (B) Probability of second reaction given that first reaction occurred. Close proximity of the active zones leads to effective reaction pathway, with the charged active zones being more efficient until ∼25 Å separation. (C) Probability of second (overall) reaction. The effect of shielding the first active zone can clearly be seen. In general, the closer active zones lead to a more effective pathway, with the charged active zones being significantly more efficient at the closer distances.

Figure 3

Probabilities of reactions at rotated active zone orientations when active zones are at 10 Å distance. (A) Probability of the first reaction occurring. The probability is fairly constant as expected. (B) Probability of second reaction, given that first reaction occurred. As the active zones rotate away from each other, the reaction probability decreases considerably, and the effect of enzyme sphere size becomes more important. Inset shows active zone orientations. (C) Probability of second (overall) reaction. The active zones that face each other demonstrate a more effective pathway. Again, other than the 0° orientation, enzyme size is more important than location of the charge.