Evidence map›Paper›PMID 25288726›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2014

Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4.

Reza Vafabakhsh, Kiran Kondabagil, Emmy E Earnest, Kyung Suk Lee, Zhihong Zhang, Li Dai, Karin A Dahmen, Venigalla B Rao, Taekjip Ha

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed.

  1. Article
  2. The Fantastic Single-Molecule Techniques.Chemical & biomedical imaging · 2026
    Review
  3. Review
  4. Article
  5. Viral Genomic DNA Packaging Machinery.Sub-cellular biochemistry · 2024
    Review
  6. Article
  7. Review
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Energetic cost of building a virus.Proceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  14. Article
  15. Article
  16. Article
  17. Review
  18. Structure and mechanism of the ATPase that powers viral genome packaging.Proceedings of the National Academy of Sciences of the United States of America · 2015
    Article
  19. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Reza VafabakhshDepartment of Physics, University of Illinois at Urbana-Champaign.
Kiran KondabagilDepartment of Biology, The Catholic University of America, Washington, DC 20064.
Emmy E EarnestDepartment of Physics, University of Illinois at Urbana-Champaign.
Kyung Suk LeeDepartment of Physics, University of Illinois at Urbana-Champaign.
Zhihong ZhangDepartment of Biology, The Catholic University of America, Washington, DC 20064.
Li DaiDepartment of Biology, The Catholic University of America, Washington, DC 20064.
Karin A DahmenDepartment of Physics, University of Illinois at Urbana-Champaign.
Venigalla B RaoDepartment of Biology, The Catholic University of America, Washington, DC 20064 rao@cua.edu tjha@illinois.edu.
Taekjip HaDepartment of Physics, University of Illinois at Urbana-Champaign, Howard Hughes Medical Institute, Urbana, IL 61801; and rao@cua.edu tjha@illinois.edu.

Funding

Structural studies of bacteriophage T4 and their potential medical applicationsR01AI081726 · NIAID · PURDUE UNIVERSITY · PI KUHN, RICHARD J., RAO, VENIGALLA B. · 2010 to 2019
$6.2M
Phase T4 Head Assembly and Initiation of InfectionR01AI011676 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI BLACK, LINDSAY W · 1985 to 2013
$4.1M
Single Molecule Study of Helicase MechanismsR01GM065367 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI HA, TAEKJIP · 2002 to 2014
$3.6M
STRUCTURE OF A SMALL SPHERICAL VIRUSR01AI011219 · NIAID · PURDUE UNIVERSITY WEST LAFAYETTE · PI KUHN, RICHARD J. · 1985 to 2020
$2.4M
Structural studies of bacteriophage T4 and their potential medical applicationsR56AI081726 · NIAID · PURDUE UNIVERSITY · PI ROSSMANN, MICHAEL G · 2009 to 2009
$600k
Howard Hughes Medical InstituteNIAID NIH HHS AI081726NIAID NIH HHS R01 AI011219NIAID NIH HHS R01 AI011676NIAID NIH HHS R01 AI081726NIAID NIH HHS R56 AI081726NIGMS NIH HHS GM065367NIGMS NIH HHS R01 GM065367
6 · The paper itself

Abstract

Viral DNA packaging motors are among the most powerful molecular motors known. A variety of structural, biochemical, and single-molecule biophysical approaches have been used to understand their mechanochemistry. However, packaging initiation has been difficult to analyze because of its transient and highly dynamic nature. Here, we developed a single-molecule fluorescence assay that allowed visualization of packaging initiation and reinitiation in real time and quantification of motor assembly and initiation kinetics. We observed that a single bacteriophage T4 packaging machine can package multiple DNA molecules in bursts of activity separated by long pauses, suggesting that it switches between active and quiescent states. Multiple initiation pathways were discovered including, unexpectedly, direct DNA binding to the capsid portal followed by recruitment of motor subunits. Rapid succession of ATP hydrolysis was essential for efficient initiation. These observations have implications for the evolution of icosahedral viruses and regulation of virus assembly.

Indexed as

Virus AssemblyAdenosine TriphosphatasesAdenosine TriphosphateBacteriophage T4CapsidCapsid ProteinsDNA PackagingDNA, ViralGenome, ViralMicroscopy, FluorescenceMolecular Motor ProteinsPhotobleachingProtein ConformationAdenosine TriphosphatasesAdenosine TriphosphateCapsid ProteinsDNA, ViralMolecular Motor Proteinsmolecular motorssingle-molecule fluorescence imagingvirus packaging

Identifiers

PMID25288726
PMCPMC4210281

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.