Year: 2021
Type: article
Abstract: While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool to, for example, illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically, when large (bio-)chemical networks are considered where reactions are stereospecific, rigorous techniques are inevitable. We present an approach using the right Cayley graph of a monoid to track atoms concurrently through sequences of reactions and predict their potential location in product molecules. This can not only be used to systematically build hypothesis or reject reaction mechanisms (we will use the ANRORC mechanism “Addition of the Nucleophile, Ring Opening, and Ring Closure” as an example) but also to infer naturally occurring subsystems of (bio-)chemical systems. Our results include the analysis of the carbon traces within the tricarboxylic acid cycle and infer subsystems based on projections of the right Cayley graph onto a set of relevant atoms.
Source: Journal of Computational Biology
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
Funders: Novo Nordisk, Novo Nordisk Fonden
Awards: G1032663478, G6894179864
OpenAlex ID: W3167302837