Evidence map›Paper›PMID 33328225›Full record

ArticleScience advances2020

Self-assembly-based posttranslational protein oscillators.

Ofer Kimchi, Carl P Goodrich, Alexis Courbet, Agnese I Curatolo, Nicholas B Woodall, David Baker, Michael P Brenner

Abstract read
In one paragraph

Article in Science advances, 2020. 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. Article
  3. Article
  4. 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

7 authors.

Ofer KimchiHarvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA. okimchi@g.harvard.edu.ORCID 0000-0002-0801-0727
Carl P GoodrichHarvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.ORCID 0000-0002-1307-5074
Alexis CourbetDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0003-0539-7011
Agnese I CuratoloHarvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.ORCID 0000-0001-9649-505X
Nicholas B WoodallDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA.
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0001-7896-6217
Michael P BrennerHarvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.ORCID 0000-0002-5673-7947

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems.

Identifiers

PMID33328225
PMCPMC7744077

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Registered trials

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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.