Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome
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 cel...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2022-01-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.202110584 |
| _version_ | 1827014868669038592 |
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| author | Caroline Benz Muhammad Ali Izabella Krystkowiak Leandro Simonetti Ahmed Sayadi Filip Mihalic Johanna Kliche Eva Andersson Per Jemth Norman E Davey Ylva Ivarsson |
| author_facet | Caroline Benz Muhammad Ali Izabella Krystkowiak Leandro Simonetti Ahmed Sayadi Filip Mihalic Johanna Kliche Eva Andersson Per Jemth Norman E Davey Ylva Ivarsson |
| author_sort | Caroline Benz |
| collection | DOAJ |
| description | 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 ~ 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 proteome‐wide discovery of SLiM‐based interactions. |
| first_indexed | 2024-03-07T17:58:14Z |
| format | Article |
| id | doaj.art-f6abadd527bf44d9a60e048c7d8b617c |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2025-02-18T14:14:47Z |
| publishDate | 2022-01-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-f6abadd527bf44d9a60e048c7d8b617c2024-10-28T09:18:53ZengSpringer NatureMolecular Systems Biology1744-42922022-01-0118112710.15252/msb.202110584Proteome‐scale mapping of binding sites in the unstructured regions of the human proteomeCaroline Benz0Muhammad Ali1Izabella Krystkowiak2Leandro Simonetti3Ahmed Sayadi4Filip Mihalic5Johanna Kliche6Eva Andersson7Per Jemth8Norman E Davey9Ylva Ivarsson10Department of Chemistry ‐ BMC, Uppsala UniversityDepartment of Chemistry ‐ BMC, Uppsala UniversityDivision of Cancer Biology, The Institute of Cancer ResearchDepartment of Chemistry ‐ BMC, Uppsala UniversityDepartment of Chemistry ‐ BMC, Uppsala UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityDepartment of Chemistry ‐ BMC, Uppsala UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityDepartment of Medical Biochemistry and Microbiology, Uppsala UniversityDivision of Cancer Biology, The Institute of Cancer ResearchDepartment of Chemistry ‐ BMC, Uppsala UniversityAbstract 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 ~ 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 proteome‐wide discovery of SLiM‐based interactions.https://doi.org/10.15252/msb.202110584intrinsically disordered regionspeptidesphage displayprotein–protein interactionsshort linear motifs |
| spellingShingle | Caroline Benz Muhammad Ali Izabella Krystkowiak Leandro Simonetti Ahmed Sayadi Filip Mihalic Johanna Kliche Eva Andersson Per Jemth Norman E Davey Ylva Ivarsson Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome Molecular Systems Biology intrinsically disordered regions peptides phage display protein–protein interactions short linear motifs |
| title | Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome |
| title_full | Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome |
| title_fullStr | Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome |
| title_full_unstemmed | Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome |
| title_short | Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome |
| title_sort | proteome scale mapping of binding sites in the unstructured regions of the human proteome |
| topic | intrinsically disordered regions peptides phage display protein–protein interactions short linear motifs |
| url | https://doi.org/10.15252/msb.202110584 |
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