Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

Overview

Journal Structure

Publisher Cell Press

Specialties Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Date 2008 May 9

PMID 18462672

Citations 543

Authors

Leonardo G Trabuco

Elizabeth Villa

Kakoli Mitra

Joachim Frank

Klaus Schulten

Affiliations

Soon will be listed here.

Abstract

A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM.

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