title: Variability of Protein Structure Models from Electron Microscopy.
abstract: An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Lyman
authors.initials: L
authors.lastname: Monroe
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan.
authors.forename: Genki
authors.initials: G
authors.lastname: Terashi
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA. Electronic address: dkihara@purdue.edu.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020285:Cryoelectron Microscopy / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure
chemical_list: D011506:Proteins
keywords: EMDB; computational modelling; cryo-EM; electron microscopy; model refinement; protein structure modelling; protein tertiary structure; structure biology; structure optimization