We present a multi-scale approach aiming at studying DNA immersed in the external field generated by a protein. Our model captures different levels of detail by coupling oxDNA coarse-grained model with a variable representation of a rigid protein -covering the range from coarse grained to full atomistic. The cross-interactions between the nucleic acids and the protein are defined via a Lennard-Jones potential plus Debye interactions that account for the implicit effect of salt on DNA electrostatics. We have used the nuclease domain of colicin E7 from Escherichia coli as a case study for parameterizing and testing the model. We have also studied the parallel performance of the model in different systems using the LAMMPS molecular dynamics engine. Many DNA-protein complexes whose computational complexity remains challenging may benefit from this approach.
|Number of pages||1|
|Issue number||3, Suppl 1|
|Early online date||11 Feb 2022|
|Publication status||Published - 11 Feb 2022|
- Escherichia coli