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ProteomicsProteomics of PHIKZ-infected PAO1 cells after ASO KD of chmA, nvRNAP, picA
Proteomics of PHIKZ-infected cells after ASO-based knockdown. We show specific knockdown of targeted proteins with limited off-targets.
ORGANISM(S): Pseudomonas aeruginosa PAO1H2O Bacteria 
2025-07-23 | PXD062538 | Pride
Pseudomonas Phage 
ProteomicsLight-controlled affinity purification of protein complexes
Methods to affinity purify proteins are widely used in protein research. One important application is to identify interacting proteins of an affinity-purified protein of interest (POI) by mass spectrometry. Here, we developed an optogenetics-derived and light-controlled affinity purification method ...
ORGANISM(S): Homo sapiens (Human) 
2019-03-18 | PXD012156 | Pride
Affinity purification Mass spectrometry Optogenetics Protein-protein interaction Phytochrome Zap70 
ProteomicsThe assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination
The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer’s disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathog...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2023-12-13 | PXD042905 | Pride
Keywords: oxidative phosphorylation (oxphos) Mitochondrial complex i assembly complex (mcia) Fatty acid oxidation (fao) Amyloid-β Ecsit phosphorylation Cryo-em 
ProteomicsDeamidation drives molecular aging of the SARS-CoV-2 spike receptor-binding motif
The spike is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the hACE2 receptor, a critical infection step, and is the preferential target for spike-neutralizing antibodies. Post-translational modifications of the spike receptor-b...
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2022-02-17 | PXD027873 | Pride
Sars-cov-2 Molecular aging Rbd Deamidation 
ProteomicsThe structural mechanism of MCIA complex assembly links mitochondrial redox pathways
The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer’s disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathog...
ORGANISM(S): Escherichia coli 
2023-12-13 | PXD042858 | Pride
Oxidative phosphorylation (oxphos) Mitochondrial complex i assembly complex (mcia) Fatty acid oxidation (fao) Amyloid-β Ecsit phosphorylation Cryo-em 
ProteomicsDeamidation drives molecular aging of the SARS-CoV-2 spike receptor-binding motif
The spike is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the hACE2 receptor, a critical infection step, and is the preferential target for spike-neutralizing antibodies. Post-translational modifications of the spike receptor-b...
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2022-02-15 | PXD028071 | Pride
Sars-cov-2 Molecular aging Rbd Deamidation 
ProteomicsTargeting the paralog encoded protein for degradation accounts for the opposite roles of NRBP1 and NRBP2 in regulating LINE1 retrotransposition
The activation of Long Interspersed Nuclear Element 1 (LINE1/L1) retrotransposons not only leads to genome instability, a factor associated with the development of human diseases, but also plays crucial biological roles in fostering genetic diversity and neuronal functions. Therefore, investigating ...
ORGANISM(S): Homo sapiens (Human) 
2025-06-07 | PXD051452 | Pride
Line1 Retrotransposon Nrbp2 Nrbp1 
ModelsDallePezze2016 - Activation of AMPK and mTOR by amino acids
DallePezze2016 - Activation of AMPK and mTOR by amino acids (Model 3) This model is as described in the Supplementary Software 3 of the reference publication: SBML model similar to Model S2, but including a more complex p70-S6K module. This model is described in the article: A...
2024-09-02 | BIOMD0000000640 | BioModels
ModelsDallePezze2016 - Activation of AMPK and mTOR by amino acids (Model 2)
DallePezze2016 - Activation of AMPK and mTOR by amino acids (Model 2) This model is as described in the Supplementary Software 2 of the reference publication:  SBML model including four amino acids input in the network (simple p70-S6K module). This model is described in the article:...
2017-05-18 | MODEL1705030001 | BioModels
ModelsDallePezze2016 - Activation of AMPK and mTOR by amino acids (Model 1)
DallePezze2016 - Activation of AMPK and mTOR by amino acids (Model 1) This model is as described in Supplementary Software 2 of the reference publication: SBML model including only the canonical amino acid input on mTORC1. This model is described in the article: A systems study reveals ...
2017-05-18 | MODEL1705030000 | BioModels
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