Evidence map›Paper›PMID 25443668›Full record

ArticleVirology2014

Designing a nine cysteine-less DNA packaging motor from bacteriophage T4 reveals new insights into ATPase structure and function.

Kiran Kondabagil, Li Dai, Reza Vafabakhsh, Taekjip Ha, Bonnie Draper, Venigalla B Rao

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Virology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Review
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

6 authors.

Kiran KondabagilDepartment of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC, USA.
Li DaiDepartment of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC, USA.
Reza VafabakhshDepartment of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Taekjip HaDepartment of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Howard Hughes Medical Institute, Urbana, IL, USA.
Bonnie DraperDepartment of Biology, St. Andrews University, NC, USA.
Venigalla B RaoDepartment of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC, USA. Electronic address: rao@cua.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
NIAID 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

The packaging motor of bacteriophage T4 translocates DNA into the capsid at a rate of up to 2000 bp/s. Such a high rate would require coordination of motor movements at millisecond timescale. Designing a cysteine-less gp17 is essential to generate fluorescently labeled motors and measure distance changes between motor domains by FRET analyses. Here, by using sequence alignments, structural modeling, combinatorial mutagenesis, and recombinational rescue, we replaced all nine cysteines of gp17 and introduced single cysteines at defined positions. These mutant motors retained in vitro DNA packaging activity. Single mutant motors translocated DNA molecules in real time as imaged by total internal reflection fluorescence microscopy. We discovered, unexpectedly, that a hydrophobic or nonpolar amino acid next to Walker B motif is essential for motor function, probably for efficient generation of OH(-) nucleophile. The ATPase Walker B motif, thus, may be redefined as "β-strand (4-6 hydrophobic-rich amino acids)-DE-hydrophobic/nonpolar amino acid".

Indexed as

Adenosine TriphosphatasesBacteriophage T4Cloning, MolecularDNA PackagingDNA, ViralEscherichia coliGene Expression RegulationGene LibraryMutationProtein ConformationAdenosine TriphosphatasesDNA, ViralATPaseBacteriophage T4DNA packagingMolecular motorVirus assemblyWalker B motif

Identifiers

PMID25443668
PMCPMC4438746

What OpenQuestion holds

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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.