Modular Design of Small Enzymatic Reaction Networks Based on Reversible and Cleavable Inhibitors

Abstract

Systems chemistry aims to mimic the functional behavior of living systems by constructing chemical reaction networks with well-defined dynamic properties.E nzymes can play ak ey role in such networks,b ut there is currently no general and scalable route to the design and construction of enzymatic reaction networks.H ere,w ei ntroduce reversible, cleavable peptide inhibitors that can link proteolytic enzymatic activity into simple network motifs.Asaproof-of-principle,we show auto-activation topologies producing sigmoidal responses in enzymatic activity,e xplore cross-talk in minimal systems,d esign as imple enzymatic cascade,a nd introduce non-inhibiting phosphorylated peptides that can be activated using aphosphatase.

Autocatalysis: Kinetics, Mechanisms and Design

“…The third approach is the catalytic destruction of an inhibitor for the catalyst (Figure 42c). The group of Huck has recently introduced this strategy for constructing positive feedback in the systems based on proteases [183] . They designed oligopeptide inhibitors for trypsin, chymotrypsin, and elastase.…”

“…The group of Huck has recently introduced this strategy for constructing positive feedback in the systems based on proteases. [183] They designed oligopeptide inhibitors for trypsin, chymotrypsin, and elastase. Each oligopeptide contained an amide bond that can be recognized and cleaved by the corresponding protease.…”

Chemical and thermal stabilization of CotA laccase via a novel one-step expression and immobilization in muNS-Mi nanospheres

“…Once produced, the purification technique of these MS and NS is certainly straightforward, consisting in the use of cell lysis and centrifugation cycles bypassing the use of purification columns and other expensive methods, making this platform inexpensive and fewer time consuming. Also, we have previously demonstrated that several proteins can be simultaneously integrated into the same MS or NS, making them suitable for the easy creation of micro/nano reactors that integrate different immobilized enzymes for connected funneled multi-step transformations 34 , 35 . The stabilization observed can be particularly useful when performing complex reactions that require the use of different enzymatic activities requiring different co-factors that may not be fully compatible with all the participating enzymes.…”

Interdependent Dynamic Nitroaldol and Boronic Ester Reactions for Complex Dynamers of Different Topologies

“…[16,[19][20][21][22][23][24][25][26][27][28][29][30][31] Systems based on dynamic covalent bonds can furthermore be applied to chemical oscillation, and lead to complex behavior, switching modes, or out-of-equilibrium regimes. [32][33][34][35][36][37][38][39][40] Moreover, the unique chemistries of reversible chemical bonds enable transfer, inhibition, or emergence of systemic properties, typically based on multiple dynamic processes operating in conjunction. [41][42][43][44] In this regard, dynamic covalent polymers (dynamers) are gaining a lot of attention due to their many features, such as self-assembly/self-organization, adaptive/responsive functions, and emergent properties.…”