Molecular dynamics-based model refinement and validation for sub-5 Å cryo-electron microscopy maps
- University of Illinois at Urbana Champaign, United States
- University of Illinois at Urbana-Champaign, United States
- University of California, San Francisco, United States
Abstract
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5-Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a convergence radius of ~25Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2Å and 3.4Å resolution. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the respective macromolecules studied, captured employing local root mean square fluctuations. The MDFF tools are made available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.
Data availability
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NIZN[FE4S4] AND NINI[FE4S4] CLUSTERS IN CLOSED AND OPEN ALPHA SUBUNITS OF ACETYL-COA SYNTHASE/CARBON MONOXIDE DEHYDROGENASEPublicly available at the Protien Data Bank (accession no. 1OAO).
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Structure of TRPV1 ion channel determined by single particle electron cryo-microscopyPublicly available at the Protien Data Bank (accession no. 3J5P).
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Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopyPublicly available at the EMDataBank (accesion no. EMD-5778).
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2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitorPublicly available at the Protien Data Bank (accession no. 5A1A).
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2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitorPublicly available at the EMDataBank (accesion no. EMD-2984).
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Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution.Publicly available at the Protien Data Bank (accession no. 5A63).
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Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolutionPublicly available at the EMDataBank (accesion no. EMD-3061).
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Structure of a extracellular domainPublicly available at the Protien Data Bank (accession no. 4UPC).
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Three-dimensional structure of human gamma-secretase at 4.5 angstrom resolutionPublicly available at the EMDataBank (accesion no. EMD-2677).
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Thermoplasma acidophilum 20S proteasomePublicly available at the Protien Data Bank (accession no. 3J9I).
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3D reconstruction of archaeal 20S proteasomePublicly available at the EMDataBank (accesion no. EMD-5623).
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Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopyPublicly available at the Protien Data Bank (accession no. 3J7H).
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Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopyPublicly available at the EMDataBank (accesion no. EMD-5995).
Article and author information
Author details
Reviewing Editor
- Axel T Brunger, Howard Hughes Medical Institute, Stanford University, United States
Version history
- Received: March 16, 2016
- Accepted: July 6, 2016
- Accepted Manuscript published: July 7, 2016 (version 1)
- Accepted Manuscript updated: July 8, 2016 (version 2)
- Version of Record published: August 18, 2016 (version 3)
- Version of Record updated: October 7, 2016 (version 4)
Copyright
© 2016, singharoy et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Molecular dynamics-based model refinement and validation for sub-5 Å cryo-electron microscopy maps
eLife 5:e16105.
https://doi.org/10.7554/eLife.16105
Further reading
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- Structural Biology and Molecular Biophysics
The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension (Jojoa-Cruz et al., 2018). Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e. they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). Here, in an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure of Arabidopsis thaliana (At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization (Murthy et al., 2018). Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.
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- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
The heterochromatin protein 1 (HP1) family is a crucial component of heterochromatin with diverse functions in gene regulation, cell cycle control, and cell differentiation. In humans, there are three paralogs, HP1α, HP1β, and HP1γ, which exhibit remarkable similarities in their domain architecture and sequence properties. Nevertheless, these paralogs display distinct behaviors in liquid-liquid phase separation (LLPS), a process linked to heterochromatin formation. Here, we employ a coarse-grained simulation framework to uncover the sequence features responsible for the observed differences in LLPS. We highlight the significance of the net charge and charge patterning along the sequence in governing paralog LLPS propensities. We also show that both highly conserved folded and less-conserved disordered domains contribute to the observed differences. Furthermore, we explore the potential co-localization of different HP1 paralogs in multicomponent assemblies and the impact of DNA on this process. Importantly, our study reveals that DNA can significantly reshape the stability of a minimal condensate formed by HP1 paralogs due to competitive interactions of HP1α with HP1β and HP1γ versus DNA. In conclusion, our work highlights the physicochemical nature of interactions that govern the distinct phase-separation behaviors of HP1 paralogs and provides a molecular framework for understanding their role in chromatin organization.
