(158h) It Takes Two to Tango! Examples of Experiments/Simulations Combinations to Tackle Cancer Biology

Authors: 
Marson, D., University of Trieste
Pricl, S., University of Trieste
Laurini, E., University of Trieste
Aulic, S., University of Trieste
Mio, A., University of Trieste
Fermeglia, M., University of Trieste

In this work we will present the main
results obtained from two different case studies in which coupled
computational/experimental approaches have been
applied.

The first case focuses on the RAD51 DNA
strand exchange protein, that play a central role in homologous recombination
(HR). Under physiological conditions in which only Mg++ ions are
present while no ATP is required, RAD51 inactive form is tightly
controlled by a double-heptameric doughnut-like assembly. while
its active conformation in the presence of ATP corresponds to nucleoprotein
filament bound to a single-strand DNA (ssDNA) in the proximity of the nucleic
acid damage site. Proofs from TEM imaging obtained in this research have revealed
for the first time that the inactive, double-heptmericheptameric
form of RAD51 can also bind to ssDNA with lower affinity thorough aspecific
electrostatic interactions. By means of all-atoms molecular dynamics
simulations we confirmed the observed binding and obtained detailed description
of the binding interface and its effects on the RAD51 assembly.

The second case study is related to another
coupled experimental-computational liaison in which we studied the
effects of the presence of two DNA intercalant molecules (cisplatin and YOYO-1)
on the mechanical properties of a 66-bases double strand DNA (dsDNA) [figure 1].
It is known that at the molecular level cellular processes can be severely
affected by variations in the pristine conformation of nucleic acids, and we
reasoned that structural effects induced by intercalant molecules could be
measurable. Our calculations of the elastic moduli, obtained via Steered
Molecular Dynamics (SMD) simulations, were coupled with the study of mechanical
resonance oscillation on a DNA bundle suspended on a microfabricated
super-hydrophobic substrate. Experimental results and constant-force computational
experiments supported our initial hypothesis. Accordingly, we demonstrated that
the presence of the intercalant molecules affects the elastic moduli of the
dsDNA in a concentration-dependent way.

 

Figure 1:
Simulated conformational structures of the DNA (top), DNA-YOYO-1 (centre) and
DNA-cisplatin (bottom) under uniaxial stretching deformation. Each top model
corresponds to the initial structure while the second model represents the
final conformation attained at the maximum simulated strain in the elastic
moduli calculation.