Topological bio-scaling analysis as a universal measure of protein folding
Scaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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The Royal Society
2022-07-01
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| Series: | Royal Society Open Science |
| Subjects: | |
| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsos.220160 |
| _version_ | 1797840300463357952 |
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| author | Sergey Shityakov Ekaterina V. Skorb Michael Nosonovsky |
| author_facet | Sergey Shityakov Ekaterina V. Skorb Michael Nosonovsky |
| author_sort | Sergey Shityakov |
| collection | DOAJ |
| description | Scaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power exponents α = 1 (linear stretched molecule), α = 0.5 (the ideal chain) and α = 0.333 (compact globule) are significant. During folding, the molecule undergoes the transition from the one-dimensional linear to the three-dimensional globular state within a very short time. However, intermediate states with fractional dimensions can be stabilized by modifying the solubility (e.g. by changing the solution temperature). Topological properties, such as dimension, correlate with the interaction energy, and thus by tuning the solubility one can control molecular interaction. We investigate these correlations using the example of a well-studied short model of Trp-cage protein. The radius of gyration is used to estimate the fractal dimension of the chain at different stages of folding. It is expected that the same principle is applicable to much larger molecules and that topological (dimensional) characteristics can provide insights into molecular folding and interactions. |
| first_indexed | 2024-04-09T16:12:43Z |
| format | Article |
| id | doaj.art-c4a4da33854e4475a9434a5c1960d007 |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-04-09T16:12:43Z |
| publishDate | 2022-07-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-c4a4da33854e4475a9434a5c1960d0072023-04-24T09:20:17ZengThe Royal SocietyRoyal Society Open Science2054-57032022-07-019710.1098/rsos.220160Topological bio-scaling analysis as a universal measure of protein foldingSergey Shityakov0Ekaterina V. Skorb1Michael Nosonovsky2Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, RussiaInfochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, RussiaInfochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St Petersburg 191002, RussiaScaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power exponents α = 1 (linear stretched molecule), α = 0.5 (the ideal chain) and α = 0.333 (compact globule) are significant. During folding, the molecule undergoes the transition from the one-dimensional linear to the three-dimensional globular state within a very short time. However, intermediate states with fractional dimensions can be stabilized by modifying the solubility (e.g. by changing the solution temperature). Topological properties, such as dimension, correlate with the interaction energy, and thus by tuning the solubility one can control molecular interaction. We investigate these correlations using the example of a well-studied short model of Trp-cage protein. The radius of gyration is used to estimate the fractal dimension of the chain at different stages of folding. It is expected that the same principle is applicable to much larger molecules and that topological (dimensional) characteristics can provide insights into molecular folding and interactions.https://royalsocietypublishing.org/doi/10.1098/rsos.220160Trp-cagefoldingergodicityscalingfractal dimension |
| spellingShingle | Sergey Shityakov Ekaterina V. Skorb Michael Nosonovsky Topological bio-scaling analysis as a universal measure of protein folding Royal Society Open Science Trp-cage folding ergodicity scaling fractal dimension |
| title | Topological bio-scaling analysis as a universal measure of protein folding |
| title_full | Topological bio-scaling analysis as a universal measure of protein folding |
| title_fullStr | Topological bio-scaling analysis as a universal measure of protein folding |
| title_full_unstemmed | Topological bio-scaling analysis as a universal measure of protein folding |
| title_short | Topological bio-scaling analysis as a universal measure of protein folding |
| title_sort | topological bio scaling analysis as a universal measure of protein folding |
| topic | Trp-cage folding ergodicity scaling fractal dimension |
| url | https://royalsocietypublishing.org/doi/10.1098/rsos.220160 |
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