Biochemical reaction networks articles from across Nature Portfolio

Xenopus egg extracts constitute a cell-like system for studying biochemical reactions. Here Chen and co-workers show that extract protein synthesis and degradation are differently affected by cytoplasmic concentration and viscosity.

Developing predictive mechanistic models in biology is challenging. Elektrum uses neural architecture search, kinetic models and transfer learning to discover CRISPR–Cas9 cleavage kinetics, achieving high performance and biophysical interpretability.

Studying metabolism in distinct subcellular compartments typically involves isolating organelles. Here, the authors demonstrate a quantitative approach to infer cytosolic and mitochondrial metabolic activities based on experiments with intact cells, maintaining physiological conditions.

Cardiomyocyte-specific disruption of the circadian clock leads to changes in specific miRNAs, potentially influencing processes such as circadian rhythms, cellular signaling, and metabolism, suggesting a connection between circadian regulation and cardiac function.

Enzymatic pathways control a host of cellular processes, but the complexity of such pathways has made them difficult to predict. Elektrum combines neural architecture search, kinetic models and transfer learning to effectively discover CRISPR–Cas9 cleavage kinetics.

Investigation of multi-omic changes and their effects on regulation of metabolic pathways confirm anaplerotic deficiencies in methylmalonic acidaemia, strengthening the need for future therapies aimed at replenishing intermediates of the tricarboxylic acid cycle.

DNA nanotechnology and synthetic biology both aim to expand the range of dynamic behaviours exhibited by rationally programmed biomolecules. Now, the programmability of synthetic transcriptional circuits has been improved to enable synthesis of dynamic biomolecular circuits with unmatched complexity.

Comprehensive modeling of cellular networks of cells with a minimal genome.

In this issue, a large and multiscale whole-body model of organ-specific regulation and metabolism for type 1 diabetes is developed, providing important details on glucose and insulin dynamics.