Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons

Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J. Williams, Ryan McGreevy, Jane Richardson, Abhishek Singharoy, Emad Tajkhorshid

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Accurate structure determination from electron density maps at 3–5 Å resolution necessitates a balance between extensive global and local sampling of atomistic models, yet with the stereochemical correctness of backbone and sidechain geometries. Molecular Dynamics Flexible Fitting (MDFF), particularly through a resolution-exchange scheme, ReMDFF, provides a robust way of achieving this balance for hybrid structure determination. Employing two high-resolution density maps, namely that of β-galactosidase at 3.2 Å and TRPV1 at 3.4 Å, we showcase the quality of ReMDFF-generated models, comparing them against ones submitted by independent research groups for the 2015–2016 Cryo-EM Model Challenge. This comparison offers a clear evaluation of ReMDFF's strengths and shortcomings, and those of data-guided real-space refinements in general. ReMDFF results scored highly on the various metric for judging the quality-of-fit and quality-of-model. However, some systematic discrepancies are also noted employing a Molprobity analysis, that are reproducible across multiple competition entries. A space of key refinement parameters is explored within ReMDFF to observe their impact within the final model. Choice of force field parameters and initial model seem to have the most significant impact on ReMDFF model-quality. To this end, very recently developed CHARMM36m force field parameters provide now more refined ReMDFF models than the ones originally submitted to the Cryo-EM challenge. Finally, a set of good-practices is prescribed for the community to benefit from the MDFF developments.

Original languageEnglish (US)
JournalJournal of Structural Biology
DOIs
StateAccepted/In press - Jan 1 2018

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Structural Models
Molecular Dynamics Simulation
Galactosidases
Electrons
Research

Keywords

  • Cryo-EM data challenge
  • Force fields
  • Hybrid modeling
  • Molecular dynamics flexible fitting
  • Resolution-exchange
  • Structure determination

ASJC Scopus subject areas

  • Structural Biology

Cite this

Wang, Y., Shekhar, M., Thifault, D., Williams, C. J., McGreevy, R., Richardson, J., ... Tajkhorshid, E. (Accepted/In press). Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons. Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2018.08.003

Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons. / Wang, Yuhang; Shekhar, Mrinal; Thifault, Darren; Williams, Christopher J.; McGreevy, Ryan; Richardson, Jane; Singharoy, Abhishek; Tajkhorshid, Emad.

In: Journal of Structural Biology, 01.01.2018.

Research output: Contribution to journalArticle

Wang, Yuhang ; Shekhar, Mrinal ; Thifault, Darren ; Williams, Christopher J. ; McGreevy, Ryan ; Richardson, Jane ; Singharoy, Abhishek ; Tajkhorshid, Emad. / Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons. In: Journal of Structural Biology. 2018.
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