8B7V

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

8B7V の概要

• エントリーDOI: 10.2210/pdb8b7v/pdb
• EMDBエントリー: 15903
• 分子名称: Maltoporin (1 entity in total)
• 機能のキーワード: maltoporin, density fit, automated refinement, cryo-em, membrane protein
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 142277.36

構造登録者

Yvonnesdotter, L.,Rovsnik, U.,Blau, C.,Lycksell, M.,Howard, R.J.,Lindahl, E. (登録日: 2022-10-03, 公開日: 2023-06-21, 最終更新日: 2024-11-13)

主引用文献

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

実験手法

ELECTRON MICROSCOPY (3 Å)