Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain
Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor; Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related prot...
| Main Authors: | , , |
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| Format: | Journal Article |
| Published: |
The American Society for Biochemistry and Molecular Biology Inc
2017
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| Online Access: | http://hdl.handle.net/20.500.11937/54450 |
| _version_ | 1848759374258896896 |
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| author | Agostino, M. Öther-Gee Pohl, S. Dharmarajan, Arunasalam |
| author_facet | Agostino, M. Öther-Gee Pohl, S. Dharmarajan, Arunasalam |
| author_sort | Agostino, M. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor; Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related proteins (sFRPs), which also contain a Frizzled-like CRD. The large number of Wnts, Frizzleds and sFRPs, as well as the hydrophobic nature of Wnt, pose challenges to laboratory-based investigations of interactions involving Wnt. Here, utilizing structural knowledge of a representative Wnt-Frizzled CRD interaction, as well as experimentally-determined binding affinities for a selection of Wnt-Frizzled CRD interactions, we generate homology models of Wnt-Frizzled CRD interactions and develop a quantitative structure-activity relationship for predicting their binding affinities. The derived model incorporates a small selection of terms derived from scoring functions used in protein-protein docking, as well as an energetic term considering the contribution made by the lipid of Wnt to the Wnt-Frizzled binding affinity. Validation with an external test set suggests that the model can accurately predict binding affinity for 75% of cases, and that the error associated with the predictions is comparable to the experimental error. The model was applied to predict the binding affinities of the full range of mouse and human Wnt-Frizzled and Wnt-sFRP interactions, indicating trends in Wnt binding affinity for Frizzled and sFRP CRDs. The comprehensive predictions made in this study provide the basis for laboratory-based studies of previously unexplored Wnt-Frizzled and Wnt-sFRP interactions, which in turn, may reveal further Wnt signaling pathways. |
| first_indexed | 2025-11-14T09:58:52Z |
| format | Journal Article |
| id | curtin-20.500.11937-54450 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T09:58:52Z |
| publishDate | 2017 |
| publisher | The American Society for Biochemistry and Molecular Biology Inc |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-544502018-01-04T03:38:38Z Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain Agostino, M. Öther-Gee Pohl, S. Dharmarajan, Arunasalam Wnt signaling pathways are of significant interest in development and oncogenesis. The first step in these pathways typically involves the binding of a Wnt protein to the cysteine-rich domain (CRD) of a Frizzled receptor; Wnt-Frizzled interactions can be antagonized by secreted Frizzled-related proteins (sFRPs), which also contain a Frizzled-like CRD. The large number of Wnts, Frizzleds and sFRPs, as well as the hydrophobic nature of Wnt, pose challenges to laboratory-based investigations of interactions involving Wnt. Here, utilizing structural knowledge of a representative Wnt-Frizzled CRD interaction, as well as experimentally-determined binding affinities for a selection of Wnt-Frizzled CRD interactions, we generate homology models of Wnt-Frizzled CRD interactions and develop a quantitative structure-activity relationship for predicting their binding affinities. The derived model incorporates a small selection of terms derived from scoring functions used in protein-protein docking, as well as an energetic term considering the contribution made by the lipid of Wnt to the Wnt-Frizzled binding affinity. Validation with an external test set suggests that the model can accurately predict binding affinity for 75% of cases, and that the error associated with the predictions is comparable to the experimental error. The model was applied to predict the binding affinities of the full range of mouse and human Wnt-Frizzled and Wnt-sFRP interactions, indicating trends in Wnt binding affinity for Frizzled and sFRP CRDs. The comprehensive predictions made in this study provide the basis for laboratory-based studies of previously unexplored Wnt-Frizzled and Wnt-sFRP interactions, which in turn, may reveal further Wnt signaling pathways. 2017 Journal Article http://hdl.handle.net/20.500.11937/54450 10.1074/jbc.M117.786269 The American Society for Biochemistry and Molecular Biology Inc fulltext |
| spellingShingle | Agostino, M. Öther-Gee Pohl, S. Dharmarajan, Arunasalam Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title | Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title_full | Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title_fullStr | Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title_full_unstemmed | Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title_short | Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domain |
| title_sort | structure-based prediction of wnt binding affinities for frizzled-type cysteine-rich domain |
| url | http://hdl.handle.net/20.500.11937/54450 |