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Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution.
Biomolecules, 12(9).
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which toobtain three-dimensional (3D) structures of macromolecular complexes at atomic ornear-atomic resolution. However, de novo building of atomic models fromnear-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, inparticular because poorly resolved side-chain densities hamper sequenceassignment by automatic procedures at a lower resolution. Furthermore,segmentation of EM density maps into individual subunits remains a difficultproblem when the structure of the subunits is not known, or when significantconformational rearrangement occurs between the isolated and associated form ofthe subunits. To tackle these issues, we have developed a graph-based method tothread most of the C-α trace of the protein backbone into the EM density map. TheEM density is described as a weighted graph such that the resulting minimumspanning tree encompasses the high-density regions of the map. A pruningalgorithm cleans the tree and finds the most probable positions of the C-α atoms,by using side-chain density when available, as a collection of C-α tracefragments. By complementing experimental EM maps with contact predictions fromsequence co-evolutionary information, we demonstrate that this approach cancorrectly segment EM maps into individual subunits and assign amino acidsequences to backbone traces to generate atomic models.
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