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Serwer P, Wright ET, Demeler B, et al. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophys Rev. 2017;10(2):583-596doi: 10.1007/s12551-017-0372-5.
Serwer, P., Wright, E. T., Demeler, B., & Jiang, W. (2018). States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophysical reviews, 10(2), 583-596. https://doi.org/10.1007/s12551-017-0372-5
Serwer, Philip, et al. "States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM." Biophysical reviews vol. 10,2 (2018): 583-596. doi: https://doi.org/10.1007/s12551-017-0372-5
Serwer P, Wright ET, Demeler B, Jiang W. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophys Rev. 2018 Apr;10(2):583-596. doi: 10.1007/s12551-017-0372-5. Epub 2017 Dec 14. PMID: 29243090; PMCID: PMC5899731.
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Biophys Rev. 2018 Apr;10(2):583-596. doi: 10.1007/s12551-017-0372-5. Epub 2017 Dec 14.

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

Biophysical reviews

Philip Serwer, Elena T Wright, Borries Demeler, Wen Jiang

Affiliations

  1. Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA. [email protected].
  2. Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
  3. Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.

PMID: 29243090 PMCID: PMC5899731 DOI: 10.1007/s12551-017-0372-5

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 injection; DNA packaging; Nycodenz

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