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Structure. 2014 Mar 4;22(3):496-506. doi: 10.1016/j.str.2014.01.004. Epub 2014 Feb 6.

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.

Author information

1
IMPMC, Sorbonne Universités-CNRS UMR 7590, UPMC Paris 6, MNHN, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France.
2
Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain.
3
Departamento de Informática, Universidad de Almería, Almería 04120, Spain.
4
Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain.
5
RIKEN, Advanced Institute for Computational Sciences, Kobe, Hyogo 650-0047, Japan.
6
IMPMC, Sorbonne Universités-CNRS UMR 7590, UPMC Paris 6, MNHN, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France. Electronic address: slavica.jonic@impmc.upmc.fr.

Abstract

This article presents a method to study large-scale conformational changes by combining electron microscopy (EM) single-particle image analysis and normal mode analysis (NMA). It is referred to as HEMNMA, which stands for hybrid electron microscopy normal mode analysis. NMA of a reference structure (atomic-resolution structure or EM volume) is used to predict possible motions that are then confronted with EM images within an automatic iterative elastic 3D-to-2D alignment procedure to identify actual motions in the imaged samples. HEMNMA can be used to extensively analyze the conformational changes and may be used in combination with classic discrete procedures. The identified conformations allow modeling of deformation pathways compatible with the experimental data. HEMNMA was tested with synthetic and experimental data sets of E. coli 70S ribosome, DNA polymerase Pol α and B subunit complex of the eukaryotic primosome, and tomato bushy stunt virus.

PMID:
24508340
DOI:
10.1016/j.str.2014.01.004
[Indexed for MEDLINE]
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