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Computer simulations of knotted DNA and proteins

Virnau, P (Johannes Gutenberg-Universitšt Mainz, Germany)
Tuesday 04 September 2012, 13:30-14:10

Seminar Room 1, Newton Institute


When mature bacteriophages such as P2 or P4 are assembled in infected cells, a long linear DNA molecule is loaded into the phage capsid and arranges itself in a toroidal, nematic phase. Intriguingly, experiments show that the DNA is not only highly knotted, but also exhibits a rather uncommon knot spectrum. Observation that DNA molecules in bacteriophage capsids preferentially form torus knots provide a sensitive gauge to evaluate various models of DNA arrangement in phage heads. We demonstrate with computer simulations of a simple bead-spring model that an increasing chain stiffness not only leads to nematic ordering and a (somewhat counter-intuitive) increase of knottedness, it is also the decisive factor in promoting formation of DNA torus knots in phage capsids. In the second part of my presentation I will review recent and not so recent advances in the understanding and modelling of protein knots.

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