Networks and systems biology articles from across Nature Portfolio

Vast majority of cellular activities are carried out by protein complexes that assembled dynamically in response to cellular needs and environmental cues. Here, the authors present Slim-TPCA, an effective and readily deployable strategy to unravel the functional roles of protein complexes en masse across various cellular processes.

Asymmetric glucose tracers reveal the simultaneous use and unique benefits of parallel glycolytic pathways. Cells possessing both textbook glycolysis and Entner–Doudoroff glycolysis have a selective advantage in dynamic environments.

Epichaperomics allow the study of protein-protein interactions and their alterations, but probes have been limited to capturing HSP90 epichaperomes. Here, the authors introduce and validate a toolset of HSP70 epichaperome ligands, and use them in epichaperomics to identify a mechanism with which cancer cells can enhance the fitness of mitotic protein networks.

ESCRT-III is involved in the endolysosomal system and disturbed in neurodegenerative diseases. Here the authors show that disruption of an interaction between ESCRT-III member CHMP2B and α-synuclein by a peptide inhibitor mitigates neurodegeneration in Parkinson’s disease models.

Heavy water metabolic labeling followed by liquid chromatography coupled mass spectrometry (LC-MS) is a powerful approach to characterize in vivo protein turnover rates, however, peptide co-elution causes overlap of their isotope profiles in LC-MS and affects the proteome coverage. Here, the authors develop an approach to increase the proteome coverage for in vivo protein turnover by using partial isotope profiles from two mass isotopomers.

Molecular chaperones establish essential protein-protein interaction networks. Modified versions of these assemblies are generally enriched in certain maladies. A study published in Nature Communications used epichaperomics to identify unique changes occurring in chaperone-formed protein networks during mitosis in cancer cells.

Identifying new proteoforms — structural variants of proteins — is frequently challenging, particularly on the proteome-wide scale. A new study leverages their differential thermal stabilities to identify proteoform functional groups by deep thermal proteome profiling.

We developed a computational method to reveal the drug-induced single-cell transcriptomic landscape. This algorithm enabled us to impute unknown drug-induced single-cell gene expression profiles using tensor imputation, predict cell type-specific drug efficacy, detect cell-type-specific marker genes, and identify the trajectories of regulated biological pathways while considering intercellular heterogeneity.

Characterization of cell death kinetics identifies new on- and off-target small-molecule modulators of ferroptosis and reveals a role of amino acid metabolism in regulating ferroptosis sensitivity.

DNA-based dynamic networks show adaptation to external stimuli toward the generation of the fittest constituent. This selection principle has now been implemented to control the catalytic efficiency of an enzymatic reaction.

Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, the author discusses how recent developments in nonequilibrium thermodynamics provide new insight on how CRNs process energy and perform sophisticated tasks, and describes open challenges in the field.