Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM - PubMed (original) (raw)
Comparative Study
. 2004 Sep;147(3):315-26.
doi: 10.1016/j.jsb.2004.03.002.
Affiliations
- PMID: 15450300
- DOI: 10.1016/j.jsb.2004.03.002
Comparative Study
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
Florence Tama et al. J Struct Biol. 2004 Sep.
Abstract
A new method for the flexible fitting of high-resolution structures into low-resolution maps of macromolecular complexes from electron microscopy has been recently described in applications to simulated electron density maps. This method uses a linear combination of low-frequency normal modes in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. Gradient-following techniques in the coordinate space of collective normal modes are used to optimize the overall correlation coefficient between computed and measured electron densities. With this approach, multi-scale flexible fitting can be performed using all-atoms or Calpha atoms. In this paper, illustrative studies of normal mode based flexible fitting to experimental cryo-EM maps are presented for three different systems. Large, functionally relevant conformational changes for elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus are elucidated as the result of the application of NMFF from high-resolution structures to cryo-electron microscopy maps.
Copyright 2004 Elsevier Inc.
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