BARDIAUX, Benjamin; PELLARIN, Riccardo; RAPISARDA, Chiara; NILGES, Michael

doi:10.1101/2020.01.03.893669

RAPISARDA, Chiara
Microbiologie Fondamentale et Pathogénicité [MFP]

Langue

Document de travail - Pré-publication

Résumé en anglais

Electron cryo-microscopy (cryo-EM) has emerged as a powerful method to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, in particular since poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when no three-dimensional structures of these subunits exist, or when significant conformational changes occur between the isolated and complexed form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C- α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C- α atoms, using side-chain density when available, as a collection of C- α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that our approach can correctly segment EM maps into individual subunits and assign amino acids sequence to backbone traces to generate full-atom models.< Réduire

URI

https://oskar-bordeaux.fr/handle/20.500.12278/182398

DOI

http://dx.doi.org/10.1101/2020.01.03.893669

Unités de recherche

MFP (Laboratoire Microbiologie Fondamentale et Pathogénicité) - UMR 5234

Voir/Ouvrir

Métadonnées

Partager cette publication !

Licence d’utilisation du document

Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution

Langue

Résumé en anglais

URI

DOI

Unités de recherche