The protein–membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become important adjuncts for integrating experimental data, developing mechanistic models, and suggesting testable hypotheses regarding viral function. However, the large molecular scales of virus–host interaction also create challenges for detailed molecular simulation. For this reason, continuum membrane models have played a large historical role, although they have become less favored for high-resolution models of protein assemblies and lipid organization. Here, we review recent progress in the field, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations. Based on successes and challenges to date, we suggest a multiresolution strategy that should yield the best mixture of computational efficiency and physical fidelity. This strategy may facilitate further simulations of viral entry by a broader range of viruses, helping illuminate the diversity of viral entry strategies and the essential common elements that can be targeted for antiviral therapies.
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Fuelled by the ‘resolution revolution’, cryo-EM has transformed our molecular understanding of transcriptional regulation in bacteria. As an example, Wood and colleagues (pp. 2695–2710) present the sialic acid gene repressor NanR (PDB-6WFG), where cryo-EM revealed the DNA-binding mode. “E. coli Bacteria” by NIAID is licensed under CC BY 2.0. Cover artwork courtesy of Christopher Horne.
Review Article|
November 16 2021
Computational methods to study enveloped viral entry
Alzbeta Tuerkova;
Alzbeta Tuerkova
1Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
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Peter M. Kasson
1Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
2Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, U.S.A.
Correspondence: Peter M. Kasson (kasson@virginia.edu)
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Publisher: Portland Press Ltd
Received:
September 17 2021
Revision Received:
October 25 2021
Accepted:
October 27 2021
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society
2021
Biochem Soc Trans (2021) 49 (6): 2527–2537.
Article history
Received:
September 17 2021
Revision Received:
October 25 2021
Accepted:
October 27 2021
Citation
Alzbeta Tuerkova, Peter M. Kasson; Computational methods to study enveloped viral entry. Biochem Soc Trans 17 December 2021; 49 (6): 2527–2537. doi: https://doi.org/10.1042/BST20210190
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