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| 2. |
- Benz, Caroline, et al.
(författare)
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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
- 2022
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Ingår i: Molecular Systems Biology. - : EMBO Press. - 1744-4292 .- 1744-4292. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of similar to 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteomewide discovery of SLiM-based interactions.
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| 3. |
- Jansson, Nils, et al.
(författare)
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Cobalt and REE distribution at the Zinkgruvan Zn-Pb-Ag and Cu deposit, Bergslagen, Sweden
- 2022
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Ingår i: EGU General Assembly 2022. - : Copernicus GmbH.
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Konferensbidrag (refereegranskat)abstract
- The metamorphosed, stratiform, c. 1.9 Ga Zinkgruvan Zn-Pb-Ag deposit is one of Europe’s largest producers of Zn. Since 2010, disseminated Cu mineralization is also mined from dolomite marble in a hydrothermal vent-proximal position in the stratigraphic footwall. Local enrichments of Co and REE exist in the vent-proximal mineralization types, albeit their distribution is poorly known. This contribution provides new data on the distribution of Co and REE within the Zinkgruvan deposit.LA-ICP-MS analysis suggest that lattice-bound cobalt in sphalerite range between 44 ppm and 1372 ppm, with the lowest and highest values occurring in distal and proximal mineralization, respectively. Proximal Co-rich sphalerite is always Fe-rich. Lattice-bound Co also occur in pyrrhotite; ranging from 52 ppm in distal ore to 1608 ppm in proximal ore. There is a concurrent increase in lattice-bound Ni from 3 ppm to 529 ppm. In proximal ore, Co is also hosted by cobalt minerals such as costibite (27.37 wt.% Co), safflorite (16.21 wt.% Co), nickeline (7.54 wt.% Co), cobaltite (32.74 wt.% Co) and cobaltpentlandite (25.49 wt.% Co). Automated quantitative mineralogy suggest that these minerals are highly subordinate to sphalerite (<70.11%) and pyrrhotite (<14.69%), amounting to <2.88% cobalt minerals with safflorite being most common (up to 2.67%). Cobalt deportment calculations suggest that the proportion of whole-rock Co that is lattice-bound to sphalerite and pyrrhotite ranges from 7.80% to 100%, with sphalerite being the main host. Whole-rock As and Ni contents pose a strong control on whether Co occurs lattice-bound or as Co minerals.LA-ICP-MS analysis show that accessory apatite in proximal, marble-hosted Cu mineralization carries a few thousand ppm ∑REE, but locally up to c. 1.6 wt.% ∑REE. The apatite can be subdivided into two types. Type 1 apatite is characterized by dumbbell-shaped chondrite-normalized REE profiles with relative enrichment of in particular Sm-Tb, depletion of Yb-Lu relative to La-Pr, local positive Gd anomalies, and weak positive to negative Eu anomalies. Type 2 apatite is characterized by flat to negatively sloping REE profiles from La to Gd and relative HREE depletion. Additional REE is hosted by monazite. Type 1 apatite was only found as a gangue to Cu mineralization. The Type 1 apatite REE signature is characteristic of hydrothermal apatite, and a direct genetic association with vent-proximal Cu mineralization can be inferred.Comparison with published REE contents in apatite suggest that vent-proximal Zinkgruvan apatite is locally as REE-rich as apatite from Kiruna-type apatite iron oxide deposits, and more REE-rich than apatite in other metamorphosed sediment-hosted sulphide deposits in the world, such as the Gamsberg deposit (RSA).
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| 4. |
- Kassa, Eszter, et al.
(författare)
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
- 2024
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to mass-spectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for a model peptide that successfully pulled down a known interactor using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
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| 5. |
- Kassa, Eszter, et al.
(författare)
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
- 2023
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Ingår i: Analytical Biochemistry. - : Elsevier. - 0003-2697 .- 1096-0309. ; 663
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Tidskriftsartikel (refereegranskat)abstract
- Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to massspectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for model peptides that successfully pulled down known interactors using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
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| 6. |
- Kruse, Thomas, et al.
(författare)
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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
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| 7. |
- Mihalic, Filip, et al.
(författare)
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Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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| 8. |
- Mihalic, Filip, et al.
(författare)
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
- 2022
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Ingår i: Nature Communications. - : Cold Spring Harbor Laboratory. - 2041-1723.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1,712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
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| 9. |
- Mihalič, Filip, et al.
(författare)
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
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