Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots
Salvato in:
| Pubblicato in: | Biophysical Journal vol. 87, no. 5 (Nov 2004), p. 2968-2975 |
|---|---|
| Autore principale: | |
| Altri autori: | , |
| Pubblicazione: |
Biophysical Society
|
| Soggetti: | |
| Accesso online: | Citation/Abstract Full Text + Graphics Full Text - PDF |
| Tags: |
Nessun Tag, puoi essere il primo ad aggiungerne!!
|
| Abstract: | The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases. [PUBLICATION ABSTRACT] The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases. |
|---|---|
| ISSN: | 0006-3495 1542-0086 |
| Fonte: | Science Database |