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Biophysical Reviews

, Volume 10, Issue 2, pp 583–596 | Cite as

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM

  • Philip Serwer
  • Elena T. Wright
  • Borries Demeler
  • Wen Jiang
Review

Abstract

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

Keywords

Bacteriophage assembly Capsid flexibility DNA packaging DNA injection Nycodenz 

Notes

Compliance with ethical standards

Funding

This study was funded by NIH (R01-GM120600 to BD and R01-AI072035 to WJ) and the Welch Foundation (AQ-764 to PS).

Conflict of interest

Philip Serwer declares that he has no conflict of interest. Elena T. Wright declares that she has no conflict of interest. Borries Demeler declares that he has no conflict of interest. Wen Jiang declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

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Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Biochemistry and Structural BiologyThe University of Texas Health Science CenterSan AntonioUSA
  2. 2.Markey Center for Structural Biology, Department of Biological SciencesPurdue UniversityWest LafayetteUSA

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