What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

Fraser, James S.; Lindorff‐Larsen, Kresten; Bonomi, Massimiliano

doi:10.1021/acs.jcim.0c00123

Cited by 22 publications

(17 citation statements)

References 33 publications

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“…Recent advances in post-processing cryo-EM images also allowed to identify multiple conformational states of the biological complexes (Jin et al, 2019) or even to describe the conformational variability of their single subunits (Bai et al, 2015). These advancements and opportunities introduced by single-particle cryo-EM are paving the way for an explosion of computational methods aimed at processing, refining and interpreting cryo-EM data (Dodd et al, 2020;Fraser et al, 2020;Kim et al, 2020;Palermo et al, 2020).…”

mentioning

confidence: 99%

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

Nierzwicki

Palermo

2021

Front. Mol. Biosci.

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Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function.

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confidence: 99%

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

Nierzwicki

Palermo

2021

Front. Mol. Biosci.

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“…To quantify the effects of different cooling rates on structural ensembles of large biomolecular complexes typically studied by cryo-EM, we used T-quench simulations, i.e., all-atom explicit-solvent MD simulations of a ribosome ⋅ EF-Tu complex with linearly decreasing temperatures at different rates. A similar approach was proposed in a recent viewpoint article 68 . To that aim, we repeated T-quench simulations 41 times for each cooling rate, starting from 41 snapshots of an ensemble at a temperature of 277.15 K (4 °C).…”

Section: Resultsmentioning

confidence: 97%

Effects of cryo-EM cooling on structural ensembles

Bock¹,

Grubmüller²

2022

Nat Commun

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Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.

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“…all-atom explicit-solvent MD simulations of a ribosome complex with linearly decreasing temperatures at different rates. A similar approach was proposed in a recent viewpoint article 63 . To that aim, we repeated T-quench simulations 41 times for each cooling rate, starting from 41 snapshots of an ensemble at 277.15 K (4 • C), the temperature used in the experiment before plunge-freezing 25 .…”

Section: Effects Of Different Cooling Rates On the Ensemblementioning

confidence: 97%

Effects of cryo-EM cooling on structural ensembles

Bock¹,

Grubmüller²

2021

Preprint

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Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed by the cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome resulting in reduction of B-factors in the ensemble imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.

show abstract

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

Cited by 22 publications

References 33 publications

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

Effects of cryo-EM cooling on structural ensembles

Effects of cryo-EM cooling on structural ensembles

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