A coarse-grained representation of DNA immersed in an external protein force-field

Cecilia Bores, Oliver Henrich, Chuanying Chen, B. Montgomery Pettitt

Research output: Contribution to journalMeeting abstractpeer-review


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 languageEnglish
Pages (from-to)209a-209a
Number of pages1
JournalBiophysical Journal
Issue number3, Suppl 1
Early online date11 Feb 2022
Publication statusPublished - 11 Feb 2022


  • DNA
  • protein
  • Escherichia coli


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