Probing the conformational heterogeneity of complex I by combination of cryo-electron microscopy, crystallography and normal mode analysis

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.

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Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol

Journal of Structural Biology ◽

10.1016/j.jsb.2014.09.005 ◽

2014 ◽

Vol 188 (2) ◽

pp. 134-141 ◽

Cited By ~ 14

Author(s):

Carlos Oscar S. Sorzano ◽

José Miguel de la Rosa-Trevín ◽

Florence Tama ◽

Slavica Jonić

Keyword(s):

Electron Microscopy ◽

Normal Mode ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Graphical Interface

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Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Protein Science ◽

10.1002/pro.3772 ◽

2019 ◽

Vol 29 (1) ◽

pp. 223-236 ◽

Cited By ~ 2

Author(s):

Mohamad Harastani ◽

Carlos Oscar S. Sorzano ◽

Slavica Jonić

Keyword(s):

Electron Microscopy ◽

Normal Mode ◽

Normal Mode Analysis ◽

Mode Analysis

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RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

International Journal of Modern Physics B ◽

10.1142/s021797920100886x ◽

2001 ◽

Vol 15 (28n30) ◽

pp. 3865-3868 ◽

Cited By ~ 2

Author(s):

H. MIYAOKA ◽

T. KUZE ◽

H. SANO ◽

H. MORI ◽

G. MIZUTANI ◽

...

Keyword(s):

Force Constant ◽

Raman Spectra ◽

Normal Mode ◽

Raman Band ◽

Normal Mode Analysis ◽

Force Constants ◽

Mode Analysis ◽

Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

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