Computational biophysics meets cryo-EM revolution in the search for the functional dynamics of biomolecular systems

Mauricio G.S. Costa, Mert Gur, James M. Krieger, Ivet Bahar*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

4 Citations (Scopus)

Abstract

There is a variety of experimental and computational techniques available to explore protein dynamics, each presenting advantages and limitations. One promising experimental technique that is driving the development of computational methods is cryo-electron microscopy (cryo-EM). Cryo-EM provides molecular-level structural data and first estimates of conformational landscape from single particle analysis but cannot track real-time protein dynamics and may contain uncertainties in atomic positions especially at highly dynamic regions. Molecular simulations offer atomic-level insights into protein dynamics; however, their computing time requirements limit the conformational sampling accuracy, and it is often hard, to assess by full-atomic simulations the cooperative movements of biological interest for large assemblies such as those resolved by cryo-EM. Coarse-grained (CG) simulations permit us to explore such systems, but at the costs of lower resolution and potentially incomplete sampling of conformational space. On the other hand, analytical methods may circumvent sampling limitations. In particular, elastic network models-based normal mode analyses (ENM-NMA) provide unique solutions for the complete mode spectra near equilibrium states, even for systems of megadaltons, and may thus deliver information on mechanisms of motions relevant to biological function. Yet, they lack atomic resolution as well as temporal information for non-equilibrium systems. Given the complementary nature of these methods, the integration of molecular simulations and ENM-NMA into hybrid methodologies has gained traction. This review presents the current state-of-the-art in structure-based computations and how they are helping us gain a deeper understanding of biological mechanisms, with emphasis on the development of hybrid methods accompanying the advances in cryo-EM. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics.

Original languageEnglish
Article numbere1689
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Volume14
Issue number1
DOIs
Publication statusPublished - 1 Jan 2024

Bibliographical note

Publisher Copyright:
© 2023 The Authors. WIREs Computational Molecular Science published by Wiley Periodicals LLC.

Funding

Funding from the CAPES/COFECUB project (#873/2017) is acknowledged by MC. Funding from NIH award R01GM139297 is gratefully acknowledged by IB. Funding from the European Union H2020‐MSCA‐IF‐2020 fellowship grant EnLaCES/101024130 is acknowledged by JMK. Funding from the CAPES/COFECUB project (#873/2017) is acknowledged by MC. Funding from NIH award R01GM139297 is gratefully acknowledged by IB. Funding from the European Union H2020-MSCA-IF-2020 fellowship grant EnLaCES/101024130 is acknowledged by JMK.

FundersFunder number
European Union H2020-MSCA-IF-2020
European Union H2020‐MSCA‐IF‐2020EnLaCES/101024130
National Institutes of HealthR01GM139297

    Keywords

    • conformational ensembles and landscape
    • cryo-electron microscopy
    • elastic network models and normal mode analysis
    • hybrid methods
    • molecular modeling and simulations

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