Exploring cryo-electron microscopy with molecular dynamics

John W. Vant, Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, Abhishek Singharoy

Research output: Contribution to journalReview articlepeer-review

Abstract

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Original languageEnglish (US)
Pages (from-to)569-581
Number of pages13
JournalBiochemical Society transactions
Volume50
Issue number1
DOIs
StatePublished - Feb 2022

ASJC Scopus subject areas

  • Biochemistry

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