8B7V

Automated simulation-based refinement of maltoporin into a cryo-EM density

Summary for 8B7V

• Entry DOI: 10.2210/pdb8b7v/pdb
• EMDB information: 15903
• Descriptor: Maltoporin (1 entity in total)
• Functional Keywords: maltoporin, density fit, automated refinement, cryo-em, membrane protein
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 142277.36

Authors

Yvonnesdotter, L.,Rovsnik, U.,Blau, C.,Lycksell, M.,Howard, R.J.,Lindahl, E. (deposition date: 2022-10-03, release date: 2023-06-21, Last modification date: 2024-11-13)

Primary citation

Yvonnesdotter, L.,Rovsnik, U.,Blau, C.,Lycksell, M.,Howard, R.J.,Lindahl, E.
Automated simulation-based membrane protein refinement into cryo-EM data.
Biophys.J., 122:2773-2781, 2023

PubMed Abstract: The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins-a category that constitutes a disproportionate share of drug targets. We present a protocol for using density-guided molecular dynamics simulations to automatically refine atomistic models into membrane protein cryo-EM maps. Using adaptive force density-guided simulations as implemented in the GROMACS molecular dynamics package, we show how automated model refinement of a membrane protein is achieved without the need to manually tune the fitting force ad hoc. We also present selection criteria to choose the best-fit model that balances stereochemistry and goodness of fit. The proposed protocol was used to refine models into a new cryo-EM density of the membrane protein maltoporin, either in a lipid bilayer or detergent micelle, and we found that results do not substantially differ from fitting in solution. Fitted structures satisfied classical model-quality metrics and improved the quality and the model-to-map correlation of the x-ray starting structure. Additionally, the density-guided fitting in combination with generalized orientation-dependent all-atom potential was used to correct the pixel-size estimation of the experimental cryo-EM density map. This work demonstrates the applicability of a straightforward automated approach to fitting membrane protein cryo-EM densities. Such computational approaches promise to facilitate rapid refinement of proteins under different conditions or with various ligands present, including targets in the highly relevant superfamily of membrane proteins.

PubMed: 37277992
DOI: 10.1016/j.bpj.2023.05.033

Experimental method

ELECTRON MICROSCOPY (3 Å)