Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
Genome-scale metabolic models (GEMs) are computational representations that enable
mathematical exploration of metabolic behaviors within cellular and environmental …
mathematical exploration of metabolic behaviors within cellular and environmental …
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Enzyme turnover numbers (k cat) are key to understanding cellular metabolism, proteome
allocation and physiological diversity, but experimentally measured k cat data are sparse …
allocation and physiological diversity, but experimentally measured k cat data are sparse …
A bird's-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations
Enzymes catalyze a vast range of reactions. Their catalytic performances, mechanisms,
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration
of the relation between genotype and phenotype. Streamlined integration of enzyme …
of the relation between genotype and phenotype. Streamlined integration of enzyme …
GotEnzymes: an extensive database of enzyme parameter predictions
Enzyme parameters are essential for quantitatively understanding, modelling, and
engineering cells. However, experimental measurements cover only a small fraction of …
engineering cells. However, experimental measurements cover only a small fraction of …
[图书][B] Molecular biology
DP Clark, NJ Pazdernik - 2012 - books.google.com
Molecular Biology, Second Edition, examines the basic concepts of molecular biology while
incorporating primary literature from today's leading researchers. This updated edition …
incorporating primary literature from today's leading researchers. This updated edition …
Highly active rubiscos discovered by systematic interrogation of natural sequence diversity
CO 2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation
properties of plant rubiscos have led to efforts that made it the most kinetically characterized …
properties of plant rubiscos have led to efforts that made it the most kinetically characterized …
Growth of cyanobacteria is constrained by the abundance of light and carbon assimilation proteins
Cyanobacteria must balance separate demands for energy generation, carbon assimilation,
and biomass synthesis. We used shotgun proteomics to investigate proteome allocation …
and biomass synthesis. We used shotgun proteomics to investigate proteome allocation …
Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism
S Donati, M Kuntz, V Pahl, N Farke, D Beuter, T Glatter… - Cell Systems, 2021 - cell.com
Enzymes maintain metabolism, and their concentration affects cellular fitness: high enzyme
levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR …
levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR …
Allosteric feedback inhibition enables robust amino acid biosynthesis in E. coli by enforcing enzyme overabundance
Microbes must ensure robust amino acid metabolism in the face of external and internal
perturbations. This robustness is thought to emerge from regulatory interactions in metabolic …
perturbations. This robustness is thought to emerge from regulatory interactions in metabolic …