The protein folding rate and the geometry and topology of the native state
Abstract Proteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in applied knot theory allow to characteriz...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-04-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-09924-0 |
| _version_ | 1818480594931154944 |
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| author | Jason Wang Eleni Panagiotou |
| author_facet | Jason Wang Eleni Panagiotou |
| author_sort | Jason Wang |
| collection | DOAJ |
| description | Abstract Proteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in applied knot theory allow to characterize the topological characteristics of proteins (knotted or not). By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein’s native state. |
| first_indexed | 2024-12-10T11:25:32Z |
| format | Article |
| id | doaj.art-4f133a98c4b34b3183ef4c1ef6e1b7b0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-10T11:25:32Z |
| publishDate | 2022-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-4f133a98c4b34b3183ef4c1ef6e1b7b02022-12-22T01:50:45ZengNature PortfolioScientific Reports2045-23222022-04-0112111110.1038/s41598-022-09924-0The protein folding rate and the geometry and topology of the native stateJason Wang0Eleni Panagiotou1Department of Physics, University of PennsylvaniaDepartment of Mathematics and SimCenter, University of Tennessee at ChattanoogaAbstract Proteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in applied knot theory allow to characterize the topological characteristics of proteins (knotted or not). By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein’s native state.https://doi.org/10.1038/s41598-022-09924-0 |
| spellingShingle | Jason Wang Eleni Panagiotou The protein folding rate and the geometry and topology of the native state Scientific Reports |
| title | The protein folding rate and the geometry and topology of the native state |
| title_full | The protein folding rate and the geometry and topology of the native state |
| title_fullStr | The protein folding rate and the geometry and topology of the native state |
| title_full_unstemmed | The protein folding rate and the geometry and topology of the native state |
| title_short | The protein folding rate and the geometry and topology of the native state |
| title_sort | protein folding rate and the geometry and topology of the native state |
| url | https://doi.org/10.1038/s41598-022-09924-0 |
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