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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 
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 
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 
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. 
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 
ProteomicsDiscovery and Characterization of a Novel Carbohydrate-Active Enzyme from the Anaerobic Fungus Piromyces finnis
Dwelling in the gut of herbivores, anaerobic gut fungi (AGF) have evolved several strategies to efficiently degrade unpretreated biomass. Their genomes encode a diverse array of carbohydrate-active enzymes (CAZymes), yet exceedingly few of these enzymes have been validated. Here, we developed a pred...
ORGANISM(S): Escherichia coli 
2025-07-31 | PXD061558 | Pride
Cazymes Jbei Proteomics High-throughput screen Heterologous expression 
ProteomicsEdible mycelium bioengineered for enhanced nutritional value and sensory appeal using a new synthetic biology toolkit
Genetic engineering of filamentous fungi has promise for accelerating the transition to a more sustainable food system and enhancing the nutritional value, sensory appeal, and scalability of microbial foods. However, genetic tools and demonstrated use cases for bioengineered food production by edibl...
ORGANISM(S): Aspergillus oryzae 
2024-03-22 | PXD043152 | Pride
Bioengineering Nutrition Synthetic biology Edible mycelium 
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