Flexible fitting to cryo-electron microscopy maps with coarse-grained elastic network models


Tekpinar M.

MOLECULAR SIMULATION, vol.44, no.8, pp.688-696, 2018 (Journal Indexed in SCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 44 Issue: 8
  • Publication Date: 2018
  • Doi Number: 10.1080/08927022.2018.1431835
  • Title of Journal : MOLECULAR SIMULATION
  • Page Numbers: pp.688-696

Abstract

Cryo-electron microscopy has become an important tool for protein structure determination in recent decades. Since proteins may exist in multiple conformational states, combining high resolution X-ray or NMR structures with cryo-electron microscopy maps is a useful approach to obtain proteins in different functional states. Flexible fitting methods used in cryo-electron microscopy aim to obtain an unknown protein conformation from a high resolution structure and a cryo-electron microscopy map. Since all-atom flexible fitting is computationally expensive, many efficient flexible fitting algorithms that utilize coarse-grained elastic network models have been proposed. In this study, we investigated performance of three coarse-grained elastic network model-based flexible fitting methods (EMFF, iModFit, NMFF) using 25 protein pairs at four resolutions. This study shows that the application of coarse-grained elastic network models to flexible fitting of cryo-electron microscopy maps can provide fast and fruitful models of various conformational states of proteins.