Representing catalytic mechanisms with rule composition

TL;DR

This paper introduces a graph transformation-based method to represent and analyze multi-step catalytic mechanisms through composite rules and overlay graphs, enabling automated reasoning about enzyme reactions.

Contribution

It presents a novel approach for representing reaction mechanisms with composite rules and overlay graphs, extending existing formalisms for automated chemical reasoning.

Findings

Constructed overlay graphs for enzyme reactions in the Mechanism and Catalytic Site Atlas.

Demonstrated the use of composite rules to explore reaction mechanisms in the Rhea database.

Provided a framework for coarse-graining and analyzing catalytic mechanisms computationally.

Abstract

Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a rule for modifying a molecular graph and a mechanism is a sequence of such rules. To generate a compact representation of a multi-step reaction, we compose the rules of individual steps into a composite rule, providing a rigorous and fully automated approach to coarse-graining. While the composite rule retains the graphical conditions necessary for the execution of a mechanism, it also records information about transient changes not visible by comparing educts and products. By projecting the rule onto a single "overlay graph", we generalize Fujita's idea of an Imaginary Transition Structure from elementary reactions to composite reactions. The utility of the overlay graph construct is exemplified in the context of enzyme-catalyzed reactions. In a first application, we exploit mechanistic information in the Mechanism and Catalytic Site Atlas to construct overlay graphs of hydrolase reactions listed in the database. These graphs point at a spectrum of catalytic entanglement of enzyme and substrate, de-emphasizing the notion of a singular catalyst in favor of a collection of catalytic sites that can be distributed across enzyme and substrate. In a second application, we deploy composite rules to search the Rhea database for reactions of known or unknown mechanism that are, in principle, compatible with the mechanisms implied by the composite rules. We believe this work adds to the utility of graph-transformation formalisms in representing and reasoning about chemistry in an automated yet insightful fashion.