Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control

Figure 2

Normal modes of pseudoatomic structures from EM density maps for simulations of structural flexibility. (a, b) EM density map of a compact conformation of Tomato Bushy Stunt Virus from [57] (a) and a displacement of pseudoatoms along the normal mode describing the swelling motion of the virus capsid that has also been observed experimentally [57, 58] (b). (c, d) EM density map of a DNA polymerase Pol α-B subunit complex of the eukaryotic primosome from [59] (c) and a displacement of pseudoatoms along the normal mode describing the bending-unbending motion that has also been observed experimentally [30, 59] (d). In this figure, very small spheres are used to represent 3D Gaussian functions (referred to as pseudoatoms) and not all spheres are shown in order to avoid their overlapping and allow a nicer visualization of the displacement of pseudoatoms along the particular normal mode.

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