Origin of the Dendritic Effect in Multivalent Enzyme-Like Catalysts

Abstract

Functionalization of multivalent structures such as dendrimers and monolayer passivated nanoparticles with catalytically active groups results in very potent catalysts, a phenomenon described as the positive dendritic effect. Here, we describe a series of peptide dendrons and dendrimers of increasing generation functionalized at the periphery with triazacyclononane, a ligand able to form a strong complex with Zn(II). Kinetic studies show that these metallodendrimers very efficiently catalyze the cleavage of the RNA model compound HPNPP, with dendrimer D32 exhibiting a rate acceleration of around 80,000 (kcat/k(uncat)) operating at a concentration of 600 nM. A theoretical model was developed to explain the positive dendritic effect displayed by multivalent catalysts in general. A detailed analysis of the saturation profile and the Michaelis-Menten parameters kcat and KM shows that it is not necessary to ascribe the positive dendritic effect to, for instance, changes in the catalytic site, increased substrate binding constant, or changes in the microenvironment. Rather it appears that the efficient catalytic behavior of multivalent catalysts is mainly determined by two factors: the number of catalytic sites occupied by substrate molecules under saturation conditions, and the efficiency of the multivalent system to generate catalytic sites in which multiple catalytic units act cooperatively on the substrate.

Catalytic Self‐Assembled Monolayers on Au Nanoparticles: The Source of Catalysis of a Transphosphorylation Reaction

“…To have a meaningful discussion of these “averaged” values, one has to know the intrinsic effect originating from the multivalency of the system. Previously we have performed such an analysis on a series of homofunctionalised dendrimers of increasing valency 42. Rather interestingly, we observed that the clustering of catalytic units on a multivalent scaffold gives spontaneously rise to a positive dendritic effect; that is, an increased catalytic efficiency ( k cat / K M ) as a function of the dendrimer valency on the condition that catalysis requires the simultaneous action of two catalytic units.…”

“…In all cases we have shown that catalysis requires the cooperative action of two catalytic units. For systems 3 42 and 4 ,59 we were able to determine the Michaelis–Menten parameters, which are added in Table 2. By themselves these are reasonable catalysts in terms of rate acceleration ( k cat / k uncat ), but their activity becomes insignificant when compared to the NP‐based system.…”

“…The gain of the NP system lies mainly in a strongly increased k cat value (>13 times compared to 3 ) and to a lesser extent on an increased binding affinity (≈4 times compared to 3 ). In a previous study,42 we had already discussed that lysine‐based dendrimers are not optimal scaffolds for surface modifications, because of the asymmetric branching units. Nanoparticles are on the opposite side of the spectrum, inducing an excellent alignment of the catalytic units.…”

Combining Medium Effects and Cofactor Catalysis: Metal‐Coordinated Synzymes Accelerate Phosphate Transfer by 108

“…These catalysts take advantage of the "dendritic effect", which does not necessarily mimic the specific microenvironment characteristic of an enzymatic pocket, but allows the formation of catalytic sites in which multiple catalytic units act A C H T U N G T R E N N U N G cooperatively on the substrate. [35] It is not clear, a priory, which polymer modifications create the right sort of environment, so we again use protocols for the combinatorial modification of PEI. These allow the incorporation of hydrophobic groups (mimicking the "hydrophobic core" of an enzyme) and guanidinium groups in varying proportions (reflecting the natural phosphate anchor arginine that is frequently found in active sites).…”

Detection of Enzyme Activity through Catalytic Signal Amplification with Functionalized Gold Nanoparticles

“…Detailed kinetic studies revealed that catalysis results from the cooperative action of two triazacyclononane·Zn II (TACN·Zn II ) complexes localized on the surface of the monolayer. [21,22] Au-MPC 1, which is fully covered with the TACN·Zn II complex, displays enzymelike saturation behavior with the "overall" values k cat = 6.7 10 À3 s À1 and K M = 0.31 mm at pH 7.5 in H 2 O. [23] This system is intriguing for the following reasons: a) under the experimental conditions, there is practically no background reaction, since k uncat under the same conditions is of the order of 10 À7 s À1 ; b) the reaction can be monitored visibly by measuring the absorbance of the p-nitrophenol product at 400 nm; c) a surprisingly high affinity is observed for the binding of HPNPP to 1.…”