Abstract
Group contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs energy change (ΔrG'o) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has comparable prediction accuracy compared to existing GC methods and can capture Gibbs energy changes for isomerase and transferase reactions, which exhibit no overall group changes. We also demonstrate dGPredictor's ability to predict the Gibbs energy change for novel reactions and seamless integration within de novo metabolic pathway design tools such as novoStoic for safeguarding against the inclusion of reaction steps with infeasible directionalities. To facilitate easy access to dGPredictor, we developed a graphical user interface to predict the standard Gibbs energy change for reactions at various pH and ionic strengths. The tool allows customized user input of known metabolites as KEGG IDs and novel metabolites as InChI strings (https://github.com/maranasgroup/dGPredictor).
Highlights
Thermodynamic imperatives affect both the direction of metabolic reactions inside the cell and the amount of enzyme needed
The standard Gibbs energy change is commonly used to check for the feasibility of enzyme-catalyzed reactions as thermodynamics plays a crucial role in pathway design for biochemical synthesis
The group contribution methods using expert-defined functional groups have been extensively used for estimating standard Gibbs energy change
Summary
Thermodynamic imperatives affect both the direction of metabolic reactions inside the cell and the amount of enzyme needed. Standard Gibbs energy estimates can be used in conjunction with metabolite concentration values to infer reaction directionalities[3, 4] Such analysis tools have been integrated [3] with genome-scale metabolic models to safeguard against the use of reactions in the wrong direction and eliminate thermodynamically infeasible cycles [3, 5, 6]. The beta-oxidation pathway can be reversed because the overall standard Gibbs energy change in the reverse direction becomes negative when utilizing ferredoxin as the reducing equivalent [7]. This engineered reversed pathway can be used to produce higher-chain linear alcohols and fatty acids with greater energy efficiency [7]. Emerging isotopic labeling experiments such as deuterium-labeled studies [10] can directly quantify ΔrG0o of enzymatic reactions but have so far been limited to central carbon metabolism necessitating the use of predictive computational frameworks
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
