Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily
SRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein–protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298...
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MDPI AG
2024-01-01
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| author | Neda S. Kazemein Jasemi Mehrnaz Mehrabipour Eva Magdalena Estirado Luc Brunsveld Radovan Dvorsky Mohammad R. Ahmadian |
| author_facet | Neda S. Kazemein Jasemi Mehrnaz Mehrabipour Eva Magdalena Estirado Luc Brunsveld Radovan Dvorsky Mohammad R. Ahmadian |
| author_sort | Neda S. Kazemein Jasemi |
| collection | DOAJ |
| description | SRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein–protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298 SH3 domains in 221 human proteins. Multiple sequence alignment of human SH3 domains is useful for phylogenetic analysis and determination of their selectivity towards PRM-containing peptides (PRPs). However, a more precise functional classification of SH3 domains is achieved by constructing a phylogenetic tree only from PRM-binding residues and using existing SH3 domain–PRP structures and biochemical data to determine the specificity within each of the 10 families for particular PRPs. In addition, the C-terminal proline-rich domain of the RAS activator SOS1 covers 13 of the 14 recognized proline-rich consensus sequence motifs, encompassing differential PRP pattern selectivity among all SH3 families. To evaluate the binding capabilities and affinities, we conducted fluorescence dot blot and polarization experiments using 25 representative SH3 domains and various PRPs derived from SOS1. Our analysis has identified 45 interacting pairs, with binding affinities ranging from 0.2 to 125 micromolar, out of 300 tested and potential new SH3 domain-SOS1 interactions. Furthermore, it establishes a framework to bridge the gap between SH3 and PRP interactions and provides predictive insights into the potential interactions of SH3 domains with PRMs based on sequence specifications. This novel framework has the potential to enhance the understanding of protein networks mediated by SH3 domain–PRM interactions and be utilized as a general approach for other domain–peptide interactions. |
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| spelling | doaj.art-c7001b3fff9d4e5b9493001e5111db302024-01-29T13:50:40ZengMDPI AGCells2073-44092024-01-0113219510.3390/cells13020195Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain SuperfamilyNeda S. Kazemein Jasemi0Mehrnaz Mehrabipour1Eva Magdalena Estirado2Luc Brunsveld3Radovan Dvorsky4Mohammad R. Ahmadian5Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, GermanyInstitute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, GermanyLaboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The NetherlandsLaboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The NetherlandsInstitute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, GermanyInstitute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, GermanySRC homology 3 (SH3) domains are critical interaction modules that orchestrate the assembly of protein complexes involved in diverse biological processes. They facilitate transient protein–protein interactions by selectively interacting with proline-rich motifs (PRMs). A database search revealed 298 SH3 domains in 221 human proteins. Multiple sequence alignment of human SH3 domains is useful for phylogenetic analysis and determination of their selectivity towards PRM-containing peptides (PRPs). However, a more precise functional classification of SH3 domains is achieved by constructing a phylogenetic tree only from PRM-binding residues and using existing SH3 domain–PRP structures and biochemical data to determine the specificity within each of the 10 families for particular PRPs. In addition, the C-terminal proline-rich domain of the RAS activator SOS1 covers 13 of the 14 recognized proline-rich consensus sequence motifs, encompassing differential PRP pattern selectivity among all SH3 families. To evaluate the binding capabilities and affinities, we conducted fluorescence dot blot and polarization experiments using 25 representative SH3 domains and various PRPs derived from SOS1. Our analysis has identified 45 interacting pairs, with binding affinities ranging from 0.2 to 125 micromolar, out of 300 tested and potential new SH3 domain-SOS1 interactions. Furthermore, it establishes a framework to bridge the gap between SH3 and PRP interactions and provides predictive insights into the potential interactions of SH3 domains with PRMs based on sequence specifications. This novel framework has the potential to enhance the understanding of protein networks mediated by SH3 domain–PRM interactions and be utilized as a general approach for other domain–peptide interactions.https://www.mdpi.com/2073-4409/13/2/195ARHGAP12GRB2NCK1proline-rich motifsprotein–protein interactionSH3 domain |
| spellingShingle | Neda S. Kazemein Jasemi Mehrnaz Mehrabipour Eva Magdalena Estirado Luc Brunsveld Radovan Dvorsky Mohammad R. Ahmadian Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily Cells ARHGAP12 GRB2 NCK1 proline-rich motifs protein–protein interaction SH3 domain |
| title | Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily |
| title_full | Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily |
| title_fullStr | Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily |
| title_full_unstemmed | Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily |
| title_short | Functional Classification and Interaction Selectivity Landscape of the Human SH3 Domain Superfamily |
| title_sort | functional classification and interaction selectivity landscape of the human sh3 domain superfamily |
| topic | ARHGAP12 GRB2 NCK1 proline-rich motifs protein–protein interaction SH3 domain |
| url | https://www.mdpi.com/2073-4409/13/2/195 |
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