Abstract
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.
Original language | English |
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Pages (from-to) | 209a-209a |
Number of pages | 1 |
Journal | Biophysical Journal |
Volume | 121 |
Issue number | 3, Suppl 1 |
Early online date | 11 Feb 2022 |
DOIs | |
Publication status | Published - 11 Feb 2022 |
Keywords
- DNA
- protein
- Escherichia coli