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Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

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.

journal_name

J Struct Biol

journal_title

Journal of structural biology

authors

Tama F,Miyashita O,Brooks CL 3rd

doi

10.1016/j.jsb.2004.03.002

keywords:

subject

Has Abstract

pub_date

2004-09-01 00:00:00

pages

315-26

issue

3

eissn

1047-8477

issn

1095-8657

pii

S1047847704000590

journal_volume

147

pub_type

杂志文章

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