ArticleBiology open2018
Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
Open access · goldAbstract read
In one paragraph
Article in Biology open, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
1.5field-weighted citation impact, top 17% of its field
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.
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.
Who cites it
16 citing papers in PubMed, 29 citations in OpenAlex.
- Article
- A map of the rubisco biochemical landscape.Nature · 2025Article
- Expert-guided protein language models enable accurate and blazingly fast fitness prediction.Bioinformatics (Oxford, England) · 2024Article
- Deep mutational scanning of EccDbioRxiv : the preprint server for biology · 2024Article
- yEvo: A modular eukaryotic genetics and evolution research experience for high school students.Ecology and evolution · 2024Article
- Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope.PLoS pathogens · 2023Article
- Regulation of ubiquitin and ubiquitin-like modifiers by phosphorylation.The FEBS journal · 2022Review
- Mechanistic basis for ubiquitin modulation of a protein energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural and functional characterization of G protein-coupled receptors with deep mutational scanning.eLife · 2020Article
- Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.ACS chemical biology · 2020Article
- Article
- Variant effect predictions capture some aspects of deep mutational scanning experiments.BMC bioinformatics · 2020Article
- MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.Genome biology · 2019Article
- Estimating dispensable content in the human interactome.Nature communications · 2019Article
- Biophysical and Mechanistic Models for Disease-Causing Protein Variants.Trends in biochemical sciences · 2019Review
- Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation.Nature structural & molecular biology · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
65 authors at 4 institutions in 1 country.
David MavorBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Kyle A BarlowBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Daniel AsarnowBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Yuliya BirmanBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Derek BritainBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Weilin ChenBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Evan M GreenBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Lillian R KennerBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Bruk MensaChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Leanna S MorinishiBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Charlotte A NelsonBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Erin M PossChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Pooja SureshBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Ruilin TianBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Taylor ArharChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Beatrice E AryChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
David P BauerBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Ian D BergmanChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Rachel M BrunettiBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Cynthia M ChioChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Shizhong A DaiChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Miles S DickinsonChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Susanna K ElledgeChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Cole V M HelsellBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Nathan L HendelBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Emily KangChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Nadja KernBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Matvei S KhoroshkinBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Lisa L KirkemoChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Greyson R LewisBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Kevin LouChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Wesley M MarinBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Alison M MaxwellChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Peter F McTigueChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Douglas Myers-TurnbullBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Tamas L NagyBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Andrew M NataleBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Keely OltionChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Sergei PourmalChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Gabriel K RederBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Nicholas J RettkoChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Peter J RohwederChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Daniel M C SchwarzChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Sophia K TanBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Paul V ThomasBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Ryan W TibbleChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Jason P TownBioinformatics Graduate Group, University of California, San Francisco 94158, USA.
Mary K TsaiChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Fatima S UgurChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Douglas R WassarmanChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Alexander M WolffBiophysics Graduate Group, University of California, San Francisco 94158, USA.
Taia S WuChemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
Derek BogdanoffDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Jennifer LiDepartment of Chemistry Undergraduate Program, University of California, Davis 95616, USA.
Kurt S ThornDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Shane O'ConchúirDepartment of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA.
Danielle L SwaneyDepartment of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA.
Eric D ChowDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Hiten D MadhaniDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Sy ReddingDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Daniel N BolonDepartment of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA.
Tanja KortemmeDepartment of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA.
Joseph L DeRisiDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
Martin KampmannDepartment of Biochemistry and Biophysics, University of California, San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.
James S FraserDepartment of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.ORCID http://orcid.org/0000-0002-5080-2859
University of California, San Francisco · USQB3 · USUniversity of California, Davis · USUniversity of Massachusetts Chan Medical School · US
Funding
Rapid production of SARS-CoV-2 molecular clones using CRISPR-based yeast recombineeringR01AI100272 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MADHANI, HITEN D · 2012 to 2025
$11.3MProject 3: Autophagy dysfunction and neuronal activity in FTDU54NS100717 · NINDS · WEILL MEDICAL COLL OF CORNELL UNIV · PI GAN, LI · 2016 to 2020
$10.8MSTRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1MRESEARCH TRAINING IN CHEMISTRY AND CHEMICAL BIOLOGYT32GM064337 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CRAIK, CHARLES SCOTT · 2002 to 2021
$7.8MMechanisms of Gene SilencingR01GM071801 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Hiten D Madhani · 2005 to 2026
$7.1MBMI Bioinformatics Training GrantsT32GM067547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2003 to 2022
$6.6MMicrobial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5MIntegrative Program in Complex Biological System (ipCBS)T32EB009383 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MARSHALL, WALLACE, WEINER, ORION D · 2009 to 2022
$3.2MRelating protein interaction networks to physiology by systematic mutant analysesR01GM112844 · NIGMS · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI BOLON, DANIEL N · 2015 to 2023
$2.7MRewiring of the human protein homeostasis network in normal and disease contextsDP2GM119139 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KAMPMANN, MARTIN · 2015 to 2015
$2.3MComputational design of protein-based small-molecule biosensorsR01GM110089 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 2015 to 2022
$2.3MDiscovery of Protein Network FunctionR01GM117189 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 2016 to 2019
$2.2MNCI NIH HHS K99 CA181494NCI NIH HHS R00 CA181494NIAID NIH HHS R01 AI100272NIAID NIH HHS R01 AI120464NIAID NIH HHS R56 AI126726NIAID NIH HHS T32 AI060537NIBIB NIH HHS T32 EB009383NIGMS NIH HHS DP2 GM119139NIGMS NIH HHS R01 GM071801NIGMS NIH HHS R01 GM110089NIGMS NIH HHS R01 GM112844NIGMS NIH HHS R01 GM117189NIGMS NIH HHS T32 GM008284NIGMS NIH HHS T32 GM064337NIGMS NIH HHS T32 GM067547NIH HHS DP5 OD009180NINDS NIH HHS U54 NS100717
Abstract
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl
Indexed as
Deep mutational scanningEvolutionUbiquitin
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
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.