MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
By Rodrigo Vargas Honorato, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin. 2019
34 citations recorded by the source corpus.
Modeling biomolecular assemblies is an important field in computational structural biology. The inherent complexity of their energy landscape and the computational cost associated with modeling large and complex assemblies are major drawbacks for integrative modeling approaches. The so-called coarse-graining approaches, which reduce the degrees of freedom of the system by grouping several atoms into larger “pseudo-atoms,” have been shown to alleviate some of those limitations, facilitating the identification of the global energy minima assumed to correspond to the native state of the complex, while making the calculations more efficient. Here, we describe and assess the implementation of the MARTINI force field for DNA into HADDOCK, our integrative modeling platform. We combine it with our previous implementation for protein-protein coarse-grained docking, enabling coarse-grained modeling of protein-nucleic acid complexes. The system is modeled using MARTINI topologies and interaction parameters during the rigid body docking and semi-flexible refinement stages of HADDOCK, and the resulting models are then converted back to atomistic resolution by an atom-to-bead distance restraints-guided protocol. We first demonstrate the performance of this protocol using 44 complexes from the protein-DNA docking benchmark, which shows an overall ~6-fold speed increase and maintains similar accuracy as compared to standard atomistic calculations. As a proof of concept, we then model the interaction between the PRC1 and the nucleosome (a former CAPRI target in round 31), using the same information available at the time the target was offered, and compare all-atom and coarse-grained models.
Subfields: Molecular Biology
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In Molecular Biology
- Frank DiMaio
- David Baker
- Ivan V. Anishchenko
- Minkyung Baek
- Ryan McHugh
- Sergey Ovchinnikov
- Yang Zhang
- Tanja Kortemme
Citations in the corpus
- Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA (2023, methodology): “Current approaches for protein–nucleic acid complex structure prediction involve building models of the protein and nucleic acid (NA) components separately and then building up complexes using computational docking calculations 1–3 .”
- The HADDOCK2.4 web server for integrative modeling of biomolecular complexes (2024, unknown): “…of complexes: (i) an antibody–antigen complex by using knowledge of the hypervariable loops and an NMR-based definition of the epitope binding site (Procedure 1) and (ii) a nucleosome complex illustrating the coarse-graining capabilities of the server to model large complexes 34,35 (Procedure 2).”
- Accurate prediction of nucleic acid and protein-nucleic acid complexes using RoseTTAFoldNA (2022, methodology): “Current approaches to protein-nucleic acid complex structure prediction involve building models of the protein and nucleic acid components separately and then building up complexes using computational docking calculations [1–3].”