Can bio-inspired information processing steps be realized as synthetic biochemical processes?

TL;DR

This paper explores designing simplified bio-inspired biochemical processes, like feed-forward loops and memory, using enzymatic cascades to understand and harness biological information processing.

Contribution

It proposes a framework for creating synthetic biochemical systems that mimic natural information processing motifs using enzymatic cascades, enabling experimental investigation.

Findings

Design of biochemical feed-forward loops demonstrated

Enzymatic cascades can implement associative memory

Response dynamics to external inputs characterized

Abstract

We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have been identified as the most common information processing motifs in many natural pathways in cellular functioning, and memory-involving processes, specifically, associative memory. Such systems should not be designed to literally mimic nature. Rather, we can be guided by nature's mechanisms for experimenting with new information/signal processing steps which are based on coupled biochemical reactions, but are vastly simpler than natural processes, and which will provide tools for the long-term goal of understanding and harnessing nature's information processing paradigm. Our biochemical processes of choice are enzymatic cascades because of their compatibility with physiological processes in vivo and with electronics (e.g., electrodes) in vitro allowing for networking and interfacing of enzyme-catalyzed processes with other chemical and biochemical reactions. In addition to designing and realizing feed-forward loops and other processes, one has to develop approaches to probe their response to external control of the time-dependence of the input(s), by measuring the resulting time-dependence of the output. The goal will be to demonstrate the expected features, for example, the delayed response and stabilizing effect of the feed-forward loops.