Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK

Roel-Touris, Jorge and Don, Charleen G. and Vargas Honorato, Rodrigo and Rodrigues, João P. G. L. M. and Bonvin, Alexandre M. J. J.. (2019) Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK. Journal of chemical theory and computation, 15 (11). pp. 6358-6367.

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Official URL: https://edoc.unibas.ch/72047/

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Predicting the 3D structure of protein interactions remains a challenge in the field of computational structural biology. This is in part due to difficulties in sampling the complex energy landscape of multiple interacting flexible polypeptide chains. Coarse-graining approaches, which reduce the number of degrees of freedom of the system, help address this limitation by smoothing the energy landscape, allowing an easier identification of the global energy minimum. They also accelerate the calculations, allowing to model larger assemblies. Here, we present the implementation of the MARTINI coarse-grained force field for proteins into HADDOCK, our integrative modelling platform. Docking and refinement are performed at the coarse-grained level and the resulting models are then converted back to atomistic resolution through a distance restraints-guided morphing procedure. Our protocol, tested on the largest complexes of the protein docking benchmark 5, shows an overall ~7-fold speed increase compared to standard all-atom calculations, while maintaining a similar accuracy and yielding substantially more near-native solutions. To showcase the potential of our method, we performed simultaneous 7 body docking to model the 1:6 KaiC-KaiB complex, integrating mutagenesis and hydrogen/deuterium exchange data from mass spectrometry with symmetry restraints, and validated the resulting models against a recently published cryo-EM structure.
Faculties and Departments:05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Pharmazie > Computational Pharmacy (Lill)
UniBasel Contributors:Don, Charleen G.
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Chemical Society
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:19 Aug 2020 06:41
Deposited On:18 Aug 2020 12:44

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