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ProteomicsAllosteric priming of E. coli CheY by the flagellar motor protein FliM
We detail simulations and solution measurements to better understand the differences between the native and D13K-Y106W CheY crystal structures. We resolved the complex conformational landscapes by MD simulations with mutual information measures to determine the coupling between protein fragments. Pr...
ORGANISM(S): Escherichia coli BL21(DE3) 
2020-09-21 | PXD020434 | Pride
Xfms Chey Flim Atomistic simulation Flagellar 
ProteomicsA rapid methods development workflow for high-throughput quantitative proteomic applications
we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays
ORGANISM(S): Escherichia coli 
2019-06-27 | PXD011212 | Pride
Workflow Proteomics High-throughput 
ProteomicsModular bottom-up proteomic sample preparation for high-throughput applications
A collection of digital automated proteomic sample preparation protocols detail three optimized step-by-step methods to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protoco...
ORGANISM(S): Rhodotorula toruloides Pseudomonas putida 
2022-02-14 | PXD029122 | Pride
High-throughput Proteomic sample preparation Automation 
ProteomicsMethyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids
Methyl ketone production by P. putida with A. thaliana and switchgrass hydrolysates obtained by dilute acid pretreatment led to the identification of plant-derived amino acids, rather than mono-aromatics, as key stimulative components of these hydrolysates. Shotgun proteomics indicated that the amin...
ORGANISM(S): Pseudomonas putida KT2440 
2019-06-27 | PXD012013 | Pride
Lignin-related aromatics  methyl ketones  biomass hydrolysates  protein  amino acids. 
ProteomicsVerazine Biosynthesis from Simple Sugars in Engineered Saccharomyces cerevisiae
Steroidal alkaloids are FDA-approved drugs (e.g., Zytiga) and promising drug candidates/leads (e.g., cyclopamine); yet many of the ≥ 697 known steroidal alkaloid natural products remain underutilized as drugs because it can be challenging to scale their biosynthesis in their producing organisms. Cyc...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-03-08 | PXD053024 | Pride
Verazine  steroidal alkaloid  natural product  microbial biosynthesis  metabolic engineering  synthetic biology 
ProteomicsMulti-Functional Enzymes and Metabolic Cross-Feeding Constrain Implementation of Genome Scale Metabolic Model Based Designs
Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approa...
ORGANISM(S): Pseudomonas putida KT2440 
2025-03-08 | PXD050285 | Pride
Omics Gsmm Strain engineering 
ProteomicsAdaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4
Rhamnolipids (RL) are well-studied biosurfactants naturally produced by pathogenic strains of P. aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however CH4 provides an intriguing alternative as a substrate for RL pro...
ORGANISM(S): Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z) 
2022-09-19 | PXD029605 | Pride
Methylotuvimicrobium alcaliphilum Adaptive laboratory evolution Rhamnolipids Ch4 
ProteomicsSystematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida
Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO2 has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an...
ORGANISM(S): Pseudomonas putida KT2440 
2025-03-08 | PXD050908 | Pride
Crispr interference (crispri) Pseudomonas Natural products Proteomics Mycosporine-like amino acid (maa) Genome-scale model 
ProteomicsCoupling biomanufacturing to decarbonization through hydrogen and formate-driven metabolism
Biomanufacturing processes are often constrained by cellular energy requirements that are tightly coupled to carbon metabolism in sugar-based fermentation systems. To address this limitation, we engineered Escherichia coli to use hydrogen gas (H2) and formate (HCOO-) as alternative energy sources, e...
ORGANISM(S): Escherichia coli Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha) 
2026-10-15 | PXD061595 | Pride
Nadh Renewable energy Arpa-e Formic acid Metabolic flux analysis Industrial microbiology Gas fermentation Hydrogen gas Bioenergetics 
ProteomicsPredictive genome-wide CRISPRi-guided gene downregulation for enhanced bioproduction
CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, conventional approaches for identifying target genes for CRISPRi-mediated downregulation have largely relied on heuristic methods and trial and error, which are labor-intens...
ORGANISM(S): Pseudomonas putida KT2440 
2026-10-15 | PXD062697 | Pride
Fluxretap Isoprenol Crispri Genome-scale modeling Jbei 
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