Chemical-proteomics profiling of reactive cysteines near a hydrophobic pocket
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Lu Hu
LAB HEAD: Xu Wu
PROVIDER: PXD070770 | Pride | 2025-11-20
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 85310.mzXML | Mzxml | |||
| 85312.mzXML | Mzxml | |||
| 90833.mzXML | Mzxml | |||
| 90835.mzXML | Mzxml | |||
| B4_replicate1.mzid | Mzid |
Items per page: 5 1 - 5 of 14 |
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Project description:acylation also called S-palmitoylation is an important reversible protein post-translational modification in organisms. However, its function remains unknown in pathogenic fungi. Here, we found treatment of rice false fungus Ustilaginoidea virens with S-palmitoylation inhibitor 2-BP resulted in a significant decrease in fungal virulence and growth rate. Deletion of the S-acyltransferase proteins from U. virens indicated that two S-acyltransferases UvPfa3 and UvPfa4 were required for fungal virulence. Comprehensive identification of S-palmitoylation sites and proteins in U. virens revealed a total of 4089 S-palmitoylation sites were identified within 2192 proteins and S-palmitoylation proteins were involved in diverse biological processes. Interestingly, S-palmitoylation proteins were significantly enriched in mitogen-activated protein kinase (MAPK) pathway and MAP kinase UvSlt2 was confirmed to be a S-palmitoylation protein which was palmitoylated by UvPfa4. Mutations of S-palmitoylation sites in UvSlt2 resulted in significantly reduced fungal virulence and decreased kinase enzymatic activity and phosphorylation level. Molecular dynamics simulations demonstrated mutation of S-palmitoylation sites in UvSlt2 caused decreased hydrophobic solvent-accessible surface area, and thereby affected binding between the UvSlt2 enzyme and substrates. Taken together, S-palmitoylation promotes U. virens virulence through palmitoylating MAP kinase UvSlt2 by palmitoyltransferase UvPfa4 and enhancing enzymatic activity and phosphorylation level of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrates. Our studies provide a framework for dissecting the biological functions of S-palmitoylation, and reveal an important role for S-palmitoylation in regulating virulence of pathogen.
2024-10-14 | PXD048216 | Pride
Project description:acylation also called S-palmitoylation is an important reversible protein post-translational modification in organisms. However, its function remains unknown in pathogenic fungi. Here, we found treatment of rice false fungus Ustilaginoidea virens with S-palmitoylation inhibitor 2-BP resulted in a significant decrease in fungal virulence and growth rate. Deletion of the S-acyltransferase proteins from U. virens indicated that two S-acyltransferases UvPfa3 and UvPfa4 were required for fungal virulence. Comprehensive identification of S-palmitoylation sites and proteins in U. virens revealed a total of 4089 S-palmitoylation sites were identified within 2192 proteins and S-palmitoylation proteins were involved in diverse biological processes. Interestingly, S-palmitoylation proteins were significantly enriched in mitogen-activated protein kinase (MAPK) pathway and MAP kinase UvSlt2 was confirmed to be a S-palmitoylation protein which was palmitoylated by UvPfa4. Mutations of S-palmitoylation sites in UvSlt2 resulted in significantly reduced fungal virulence and decreased kinase enzymatic activity and phosphorylation level. Molecular dynamics simulations demonstrated mutation of S-palmitoylation sites in UvSlt2 caused decreased hydrophobic solvent-accessible surface area, and thereby affected binding between the UvSlt2 enzyme and substrates. Taken together, S-palmitoylation promotes U. virens virulence through palmitoylating MAP kinase UvSlt2 by palmitoyltransferase UvPfa4 and enhancing enzymatic activity and phosphorylation level of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrates. Our studies provide a framework for dissecting the biological functions of S-palmitoylation, and reveal an important role for S-palmitoylation in regulating virulence of pathogen.
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Project description:The Hippo Pathway is a critical signaling network that regulates organ size and cellular proliferation in metazoans. The transcriptional enhanced associate domain (TEAD) family of transcription factors serve as the receptors for the downstream effectors of the Hippo pathway, YAP and TAZ, to upregulate expression of multiple genes involved in proliferation, cell-fate determination, polarity, and survival1. Recent work revealed that TEAD proteins are palmitoylated at a conserved cysteine with the lipid tail extending into the hydrophobic core of the protein2. Mutagenic and covalent modulation of the palmitoylation site disrupts Hippo signaling2,3; however, an understanding of why TEAD proteins require this seemingly essential modification and the therapeutic implications of modulating TEAD palmitoylation has remained elusive. Here we report the identification and optimization of a potent pan-TEAD small molecule that binds the TEAD lipid pocket (LP), blocks palmitoylation, and dysregulates TEAD activity in multiple cancer cell lines. Cellular and biochemical data interrogating the mechanism of action for our compound reveal TEAD palmitoylation to function as a checkpoint that regulates TEAD homeostasis. We show that bypassing this checkpoint with a small molecule increases TEAD protein levels thereby decreasing the ability of YAP/TAZ to activate downstream target gene transcription in a dominant-negative manner. Our study demonstrates a new role for lipidation in protein signaling and establishes the TEAD LP as a bona fide therapeutic site for modulation of the Hippo Pathway.
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Project description:Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short FG peptides to isolated capsid hexamers have been characterized, how these proteins engage biologically relevant extended HIV-1 capsid lattices is unknown. We have identified that prion-like low complexity regions (LCR) enable avid binding of CPSF6, NUP153 and SEC24C to curved hexameric capsid lattices. Structural studies reveal that LCR-LCR interactions mediate multivalent CPSF6 assembly, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. CPSF6 LCR mediated avid binding to HIV-1 cores is essential for functional virus-host interactions in infected cells. Investigational drug lenacapavir can access unoccupied hydrophobic pockets in the CPSF6-HIV-1 complex and potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results elucidate previously undescribed mechanisms of virus-host interactions and potent inhibition of HIV-1.
2022-08-31 | PXD030332 | Pride
Project description:S-palmitoylation is the covalent attachment of palmitic acid to cysteine residues through a thioester bond. S-palmitoylation is highly abundant in neurons, where it plays a fundamental role in neuronal development. In addition, S-palmitoylation is associated with many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, knowledge of S-palmitoylation in neurodevelopment is limited due to technological challenges in analysing this highly hydrophobic modification of proteins. Here, we use two orthogonal methods, acyl-biotin exchange and lipid metabolic labelling, to identify S-acylated proteins and sites in neuronal cells. We identified 650 S-palmitoylated proteins by both methods, including proteins that are well-known for their role in neuronal differentiation. Importantly, significant changes in the abundance of S-palmitoylated proteins were detected during neuronal differentiation. Overall, the combination of methods described here provides the advantage of cross-validation of the identified S-palmitoylated proteins and should be used further to study S-palmitoylation in the central nervous system to understand physiology and neurodegenerative diseases.
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Project description:Flotillin-1 contributes to invasion and metastasis in triple negative breast cancer (TNBC). Palmitoylation, the process of conjugating palmitoyl-CoA to proteins, plays an essential role in protein stability and trafficking. Flotillin-1 is modified by palmitoylation, however, the role of its palmitoylation in the context of metastasis has not been explored. Using palmitoylation defective flotillin-1 constructs, we have demonstrated that flotillin-1 palmitoylation contributes to its stability and metastatic capabilities in vivo. Further investigation led to the identification of zDHHC5 as the main palmitoyl acyl transferase responsible for palmitoylating flotillin-1, which also contributed to its stability by preventing its poly-ubiquitylation. To assess the ability to target flotillin-1 palmitoylation therapeutically, we designed a competitive peptide, which displayed efficacy in blocking flotillin-1 palmitoylation in vitro without altering palmitoylation of other zDHHC5 substrates, highlighting its specificity. Additionally, multiple TNBC tumor models expressing a doxycycline inducible flotillin-1 palmitoylation inhibiting peptide construct displayed attenuated tumor growth and lung metastasis. The current study has demonstrated the palmitoylation of flotillin-1, a known metastasis inducing protein, to be essential for its protein stability. The demonstrated methods in blocking its palmitoylation through the delivery of a competitive peptide provide proof-of-concept data for further development as a potential targeted therapeutic in TNBC.
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Project description:Mutations in Ppt1, which is a depalmitoylation enzyme result in early onset neurodegeneration, therefore, we hypothesized that the protein content of brain membranes from mutant newborn mice will differ from those derived from wild-type. This unbiased analysis revealed that the majority of the differentially identified proteins are palmitoylated and their upstream pathway analysis point to neurodegenerative diseases. One of the differentially expressed proteins was Rab3IP, which is a direct downstream effector of Rab11 and affects the guanine nucleotide-exchange activity of Rab3IP toward Rab8. Rab3IP, Rab11 and Rab8 are known to be involved in ciliogenesis. Rab3IP distribution in cilia differed between the wild type and the mutant cells. Our analysis showed that these three proteins are palmitoylated. Site-directed mutagenesis of the palmitoylation sites of Rab11 affects its intracellular localization. Most importantly, in MEFs, neuroblasts, neurons and brain preparations, longer cilia were detected in Ppt1-/-. Collectively, our studies suggest that cilia abnormalities need to be considered as part of the pathophysiology of CLN1. Mutations in Ppt1, which is a depalmitoylation enzyme result in early onset neurodegeneration, therefore, we hypothesized that the protein content of brain membranes from mutant newborn mice will differ from those derived from wild-type. This unbiased analysis revealed that the majority of the differentially identified proteins are palmitoylated and their upstream pathway analysis point to neurodegenerative diseases. One of the differentially expressed proteins was Rab3IP, which is a direct downstream effector of Rab11 and affects the guanine nucleotide-exchange activity of Rab3IP toward Rab8. Rab3IP, Rab11 and Rab8 are known to be involved in ciliogenesis. Rab3IP distribution in cilia differed between the wild type and the mutant cells. Our analysis showed that these three proteins are palmitoylated. Site-directed mutagenesis of the palmitoylation sites of Rab11 affects its intracellular localization. Most importantly, in MEFs, neuroblasts, neurons and brain preparations, longer cilia were detected in Ppt1-/-. Collectively, our studies suggest that cilia abnormalities need to be considered as part of the pathophysiology of CLN1. Mutations in Ppt1 result in early onset neurodegeneration, therefore, we hypothesized that the levels of proteins extracted from purified brain membranes of newborn mice will differ. One of the main effects of palmitoylation is changing the hydrophobic index of proteins and thus affecting these proteins interactions with different membranal domains. Assuming that PPT1 substrates are over palmitoylated in Ppt1-/- brains it is possible that its localization to specific membranal domain is different than in the wild-type brains. We isolated Triton X-100 soluble membranes from three wild-type and three Ppt1-/- brains and identified the proteins by PalmPISC. Many of the identified proteins were found to be palmitoylated. A second feature, which was noted is that many of the differential proteins (62 out of 88, 70%) can be detected in the cilia proteome (http://v3.ciliaproteome.org/cgi-bin/index.php). This observation led to test whether ciliary proteins differ between wild-type and Ppt1-/-. Cilia were prepared from newborn dissociated brain cell cultures and analyzed by MS
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