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MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing.

Rodrigo V Honorato1,2, Jorge Roel-Touris1, Alexandre M J J Bonvin1

  • 1Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.

Frontiers in Molecular Biosciences
|October 22, 2019
PubMed
Summary
This summary is machine-generated.

Coarse-graining biomolecular assemblies with the MARTINI force field in HADDOCK accelerates protein-nucleic acid complex modeling. This approach enhances computational efficiency by approximately six-fold while maintaining accuracy compared to all-atom methods.

Keywords:
biomolecular complexescoarse-grainingdockingforce fieldnucleic acids

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Area of Science:

  • Computational structural biology
  • Biomolecular modeling
  • Biophysics

Background:

  • Modeling complex biomolecular assemblies presents computational challenges due to high degrees of freedom.
  • Coarse-graining methods reduce complexity by representing groups of atoms as single pseudo-atoms, improving efficiency.
  • Integrative modeling requires efficient methods for large and complex biological systems.

Purpose of the Study:

  • To implement and assess the MARTINI force field for DNA within the HADDOCK platform for coarse-grained protein-nucleic acid modeling.
  • To enable efficient and accurate modeling of protein-DNA complexes using a coarse-grained approach.
  • To evaluate the performance and accuracy of the combined coarse-grained protocol.

Main Methods:

  • Integration of the MARTINI force field for DNA into the HADDOCK integrative modeling platform.
  • Application of coarse-grained docking and refinement stages using MARTINI parameters.
  • Conversion of coarse-grained models back to atomistic resolution using a guided protocol.
  • Validation using a protein-DNA docking benchmark and a case study of PRC1-nucleosome interaction.

Main Results:

  • The protocol achieved an approximate 6-fold speed increase compared to standard all-atom calculations.
  • The accuracy of the coarse-grained models was comparable to all-atom calculations.
  • Successful modeling of protein-DNA complexes, including a proof-of-concept for the PRC1-nucleosome interaction.

Conclusions:

  • The implemented coarse-grained MARTINI force field in HADDOCK significantly enhances the efficiency of protein-nucleic acid complex modeling.
  • This approach offers a viable strategy for tackling large and complex biomolecular assemblies computationally.
  • The method maintains accuracy, making it suitable for integrative structural biology studies.