Ard Louis

Abstract:

We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of such complexes naturally takes the system into a region of interaction space where (i) the evolutionarily newer interactions are weaker, (ii) subcomplexes involving the stronger interactions are observed to be thermodynamically stable on destabilization of the protein-protein interactions, and (iii) the self-assembly dynamics are hierarchical with these same subcomplexes acting as kinetic intermediates.

Abstract:

We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, viruslike capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the capsid and then acts as a ratchet. Polymers with more complex knots eject more slowly and, for large knots, the knot type, and not the flexibility of the polymer, determines the rate of ejection. We discuss the relation of our results to the ejection of DNA from viral capsids and conjecture that this process has the biological advantage of unknotting the DNA before it enters a cell.

Abstract:

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately and allows strand displacement to occur.