A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template‐Directed Ligation

Abstract

Bistable reaction networks provide living cells with chemically controlled mechanisms for long‐term memory storage. Such networks are also often switchable and can be flipped from one state to the other. We target here a major challenge in systems chemistry research, namely developing synthetic, non‐enzymatic, networks that mimic such a complex function. Therefore, we describe a dynamic network that depending on initial thiodepsipeptide concentrations leads to one of two distinct steady states. This bistable system is readily switched by applying the appropriate stimuli. The relationship between the reaction network topology and its capacity to invoke bistability is then analyzed by control experiments and theory. We suggest that demonstrating bistable behavior using synthetic networks further highlights their possible role in early evolution, and may shine light on potential utility for novel applications, such as chemical memories.

Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

“…As discussed earlier in Section 2.4 , multiple stable steady states are critical for Darwinian evolution in self-reproducing networks [ 16 , 55 ]. This system was then further exploited to experimentally demonstrate bistability in a chemical network due to the higher-order catalysis by a dimer template [ 129 ]. Since there is a difference in the rate of formation of thioester product (T) and its decomposition to substrates (E and N), in the presence of thiols, the reaction starting with only substrates reaches different distributions of E, N, and T (low steady state) compared to when the reaction starts with T + thiol (high steady state) [ 129 ] ( Figure 6 c).…”

“…This system was then further exploited to experimentally demonstrate bistability in a chemical network due to the higher-order catalysis by a dimer template [ 129 ]. Since there is a difference in the rate of formation of thioester product (T) and its decomposition to substrates (E and N), in the presence of thiols, the reaction starting with only substrates reaches different distributions of E, N, and T (low steady state) compared to when the reaction starts with T + thiol (high steady state) [ 129 ] ( Figure 6 c). The bistable behavior is further characterized by keeping the complete reaction system out of equilibrium using a reducing agent TCEP (tris(2-carboxyethyl) phosphine hydrochloride, which reduces disulphides to thiols) as fuel [ 145 ] ( Figure 6 c).…”

“…Peptide-based reproducing systems are also robust against molecular perturbations (chemical changes) as native sequences dominate a reproducer pool even in the presence of mutant sequences [ 146 ]. Furthermore, peptide-based systems are the only ones where bistability has been demonstrated experimentally [ 129 ]; however, since bistability is between two concentrations of the same reaction node, the notion of distinct chemical compositional identity has not yet been established. Another important feature of the self-reproducing peptide system is the ability to control the autocatalytic and spontaneous reactions using environmental control such as the pH and salt concentration [ 138 , 139 ].…”

“…An experimental system should therefore exhibit multiple stable compositions that result from the same food set. While the existence of bistable (two states) compositional identities has been demonstrated using peptide chemistries [ 129 , 145 ], such multi-stability has not yet been demonstrated in other experimental systems.…”

“…( c ) Bistability in the peptide-based autocatalytic system. Here, the reaction starting with a low amount of T and high amount of E, N reaches a different steady state (low steady-state) compared to when it started with higher amount of T and thiol (higher steady-state) [ 129 ] (figure adapted from [ 129 ]). ( d ) Schematic representation of the self-reproducing macrocycle system based on peptide-functionalized dithiol chemistries.…”