title: Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control.
abstract: Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics. Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure. An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error. In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms. Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps). In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size. EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains.
authors.affiliation: IMPMC, Sorbonne Universités, CNRS UMR 7590, UPMC Univ Paris 6, MNHN, IRD UMR 206, 75005 Paris, France.
authors.forename: Slavica
authors.identifier: 0000-0001-5112-2743
authors.initials: S
authors.lastname: Jonić
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain.
authors.forename: Carlos Oscar S
authors.identifier: 0000-0002-9473-283X
authors.initials: CO
authors.lastname: Sorzano
mesh_terms: D046911:Macromolecular Substances / Q000737:chemistry / Q000648:ultrastructure*; D008854:Microscopy, Electron; D008958:Models, Molecular; D008962:Models, Theoretical; D016011:Normal Distribution; D011487:Protein Conformation
chemical_list: D046911:Macromolecular Substances