Elucidating the Structural Impacts of Protein InDels
The effects of amino acid insertions and deletions (InDels) remain a rather under-explored area of structural biology. These variations oftentimes are the cause of numerous disease phenotypes. In spite of this, research to study InDels and their structural significance remains limited, primarily due...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/10/1435 |
| _version_ | 1797474958828371968 |
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| author | Muneeba Jilani Alistair Turcan Nurit Haspel Filip Jagodzinski |
| author_facet | Muneeba Jilani Alistair Turcan Nurit Haspel Filip Jagodzinski |
| author_sort | Muneeba Jilani |
| collection | DOAJ |
| description | The effects of amino acid insertions and deletions (InDels) remain a rather under-explored area of structural biology. These variations oftentimes are the cause of numerous disease phenotypes. In spite of this, research to study InDels and their structural significance remains limited, primarily due to a lack of experimental information and computational methods. In this work, we fill this gap by modeling InDels computationally; we investigate the rigidity differences between the wildtype and a mutant variant with one or more InDels. Further, we compare how structural effects due to InDels differ from the effects of amino acid substitutions, which are another type of amino acid mutation. We finish by performing a correlation analysis between our rigidity-based metrics and wet lab data for their ability to infer the effects of InDels on protein fitness. |
| first_indexed | 2024-03-09T20:37:21Z |
| format | Article |
| id | doaj.art-cef264d1675744409594eda8f2c2a673 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T20:37:21Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-cef264d1675744409594eda8f2c2a6732023-11-23T23:08:37ZengMDPI AGBiomolecules2218-273X2022-10-011210143510.3390/biom12101435Elucidating the Structural Impacts of Protein InDelsMuneeba Jilani0Alistair Turcan1Nurit Haspel2Filip Jagodzinski3Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USAThe effects of amino acid insertions and deletions (InDels) remain a rather under-explored area of structural biology. These variations oftentimes are the cause of numerous disease phenotypes. In spite of this, research to study InDels and their structural significance remains limited, primarily due to a lack of experimental information and computational methods. In this work, we fill this gap by modeling InDels computationally; we investigate the rigidity differences between the wildtype and a mutant variant with one or more InDels. Further, we compare how structural effects due to InDels differ from the effects of amino acid substitutions, which are another type of amino acid mutation. We finish by performing a correlation analysis between our rigidity-based metrics and wet lab data for their ability to infer the effects of InDels on protein fitness.https://www.mdpi.com/2218-273X/12/10/1435computational structural biologyprotein InDel mutationsgraph-theoryrigidity |
| spellingShingle | Muneeba Jilani Alistair Turcan Nurit Haspel Filip Jagodzinski Elucidating the Structural Impacts of Protein InDels Biomolecules computational structural biology protein InDel mutations graph-theory rigidity |
| title | Elucidating the Structural Impacts of Protein InDels |
| title_full | Elucidating the Structural Impacts of Protein InDels |
| title_fullStr | Elucidating the Structural Impacts of Protein InDels |
| title_full_unstemmed | Elucidating the Structural Impacts of Protein InDels |
| title_short | Elucidating the Structural Impacts of Protein InDels |
| title_sort | elucidating the structural impacts of protein indels |
| topic | computational structural biology protein InDel mutations graph-theory rigidity |
| url | https://www.mdpi.com/2218-273X/12/10/1435 |
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