Integrative structural modelling and visualisation of a cellular organelle
Models of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite of tools to research, curate, construct and visualise the current state of knowledge. The model integrates experimental information from proteomics, structural biology, cryoelectron microscopy...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Cambridge University Press
2022-01-01
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| Series: | QRB Discovery |
| Subjects: | |
| Online Access: | https://www.cambridge.org/core/product/identifier/S2633289222000102/type/journal_article |
| _version_ | 1827994302420090880 |
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| author | Ludovic Autin Brett A. Barbaro Andrew I. Jewett Axel Ekman Shruti Verma Arthur J. Olson David S. Goodsell |
| author_facet | Ludovic Autin Brett A. Barbaro Andrew I. Jewett Axel Ekman Shruti Verma Arthur J. Olson David S. Goodsell |
| author_sort | Ludovic Autin |
| collection | DOAJ |
| description | Models of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite of tools to research, curate, construct and visualise the current state of knowledge. The model integrates experimental information from proteomics, structural biology, cryoelectron microscopy and X-ray tomography, and is used to generate models of mature and immature vesicles. A new method was developed to generate a confidence score that reconciles inconsistencies between three available proteomes using expert annotations of cellular localisation. The models are used to simulate soft X-ray tomograms, allowing quantification of features that are observed in experimental tomograms, and in turn, allowing interpretation of X-ray tomograms at the molecular level. |
| first_indexed | 2024-04-10T04:38:54Z |
| format | Article |
| id | doaj.art-b4a4b94ef2a247e4b65ec7d554c42962 |
| institution | Directory Open Access Journal |
| issn | 2633-2892 |
| language | English |
| last_indexed | 2024-04-10T04:38:54Z |
| publishDate | 2022-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | QRB Discovery |
| spelling | doaj.art-b4a4b94ef2a247e4b65ec7d554c429622023-03-09T12:43:36ZengCambridge University PressQRB Discovery2633-28922022-01-01310.1017/qrd.2022.10Integrative structural modelling and visualisation of a cellular organelleLudovic Autin0https://orcid.org/0000-0002-2197-191XBrett A. Barbaro1https://orcid.org/0000-0003-2156-7877Andrew I. Jewett2https://orcid.org/0000-0001-9861-3048Axel Ekman3https://orcid.org/0000-0002-4210-2617Shruti Verma4https://orcid.org/0000-0002-0929-2973Arthur J. Olson5https://orcid.org/0000-0003-0558-4618David S. Goodsell6https://orcid.org/0000-0002-5932-2130Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USADepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USAModels of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite of tools to research, curate, construct and visualise the current state of knowledge. The model integrates experimental information from proteomics, structural biology, cryoelectron microscopy and X-ray tomography, and is used to generate models of mature and immature vesicles. A new method was developed to generate a confidence score that reconciles inconsistencies between three available proteomes using expert annotations of cellular localisation. The models are used to simulate soft X-ray tomograms, allowing quantification of features that are observed in experimental tomograms, and in turn, allowing interpretation of X-ray tomograms at the molecular level.https://www.cambridge.org/core/product/identifier/S2633289222000102/type/journal_articleInsulin secretory granuleintegrative mesoscale modellingpancreatic beta cellstructural biology |
| spellingShingle | Ludovic Autin Brett A. Barbaro Andrew I. Jewett Axel Ekman Shruti Verma Arthur J. Olson David S. Goodsell Integrative structural modelling and visualisation of a cellular organelle QRB Discovery Insulin secretory granule integrative mesoscale modelling pancreatic beta cell structural biology |
| title | Integrative structural modelling and visualisation of a cellular organelle |
| title_full | Integrative structural modelling and visualisation of a cellular organelle |
| title_fullStr | Integrative structural modelling and visualisation of a cellular organelle |
| title_full_unstemmed | Integrative structural modelling and visualisation of a cellular organelle |
| title_short | Integrative structural modelling and visualisation of a cellular organelle |
| title_sort | integrative structural modelling and visualisation of a cellular organelle |
| topic | Insulin secretory granule integrative mesoscale modelling pancreatic beta cell structural biology |
| url | https://www.cambridge.org/core/product/identifier/S2633289222000102/type/journal_article |
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