Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots

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Foilsithe in:	Biophysical Journal vol. 87, no. 5 (Nov 2004), p. 2968-2975
Príomhchruthaitheoir:	Flammini, Alessandro
Rannpháirtithe:	Maritan, Amos, Stasiak, Andrzej
Foilsithe / Cruthaithe:	Biophysical Society
Ábhair:	Bacteriophage T4 > genetics Computer Simulation DNA, Viral > chemistry Models, Chemical Models, Molecular Models, Statistical Nucleic Acid Conformation Knots Cells DNA polymerase Enzymes Molecules Physical properties Deoxyribonucleic acid > DNA Polymers
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Achoimre:	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
Foinse:	Science Database