CHAIN-SPHERE MODELS FOR COMPLEXES OF BIOLOGICAL INTEREST - MONTE-CARLO SIMULATION AND HYDRODYNAMIC PROPERTIES

Many complexes of biological interest, like nucleosomes or nu bodies and DNA-protein complexes, can be modelled like a structure composed by a sphere joined to a rigid rod or to a flexible chain of identical beads. In this work we present a theoretical study using these models for the evaluation of some reduced conformational and hydrodynamic properties: end-to-end distance, radius of gyration and translational friction coefficient. Two kinds of models were employed: a sphere joined to one of the two ends of a rod or chain and a sphere joined to the halfpoint of a rod or chain, i.e. the models show one or two arms, respectively. Several cases were studied, varying the number of chain beads N = 10,20,30,...60 (with radius sigma less-than-or-equal-to 1/2 and bond length b = 1) and the radius of the sphere R = 1,2,4,8 (in units of b). For the flexible models the position of the chain beads have been obtained randomly from Monte Carlo simulations. For these models we have made also a statistical treatment in order to obtain averaged values of the conformational and hydrodynamic properties. Finally, we conducted a comparison of our theoretical results with the experimental data for nucleosomes. The overall agreement is good and gives confidence in the applicability of our results to similar macromolecular complexes.