Directionality is an inherent property of biochemical networks
Feng Yang, Feng Qi, Daniel A. Beard
Abstract
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well established. This work introduces a systematic approach to compute reaction directions, which are constrained by mass balance and thermodynamics, for genome-scale networks. In addition, it is shown that the nonconvex solution space constrained by physicochemical constraints can be approximated by a set of linearized subspaces in which mass and thermodynamic balance are guaranteed. The developed methodology can be used to ab initio predict reaction directions of genome-scale networks based solely on the network stoichoimetry.
Create a lesson
Related papers
Local energetic coupling enhances the expressivity of chemical computation
Marco Tuccio, Jason W. Rocks, Joshua E. Goldford
Are You Learning Biological Signal or Shortcuts? Auditing and Mitigating Bias in Protein-Protein Interaction Datasets
Judith Bernett, Anton Spannagl, Joel Ås et al.
Thermodynamic and Statistical Signatures of Modality Changes in Concentration Distributions Driven by Stochastic Switching Between Two Activity States
Aindrila Deb, Pintu Patra
Orchestra: Corroboration-Based Regulatory Candidate Discovery via Composed Bioinformatics MCP Agents
Jose A. Bird
Systematic pathway comparison on the powerset of rule-based biochemical systems
Anne-Susann Abel, Sissel Banke, Erika M. Herrera Machado et al.
Uncovering Cellular Resolution in scRNAseq via Unbiased Cell and Gene Network Analysis
Olga lanzetta, Luisa Cutillo, Bailey Andrew et al.