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

doi:10.1016/j.str.2008.03.005

Structure

Volume 16, Issue 5, 7 May 2008, Pages 673-683

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Summary

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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⁶: These authors contributed equally to this work.

⁷: Present address: Skirball Institute, New York University, New York, NY 10016, USA.

⁸: Present address: Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics and Department of Biology, Columbia University, New York, NY 10032, USA.

Structure

Technical AdvanceFlexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

Summary

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