Evidence map›Paper›PMID 38659952›Full record

ArticlebioRxiv : the preprint server for biology2024

Protein codes promote selective subcellular compartmentalization.

Henry R Kilgore, Itamar Chinn, Peter G Mikhael, Ilan Mitnikov, Catherine Van Dongen, Guy Zylberberg, Lena Afeyan, Salman Banani, Susana Wilson-Hawken, Tong Ihn Lee and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Henry R KilgoreWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.ORCID 0000-0003-4851-9656
Itamar ChinnComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Peter G MikhaelComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Ilan MitnikovComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Catherine Van DongenWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Guy ZylberbergComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Lena AfeyanWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Salman BananiWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Susana Wilson-HawkenWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Tong Ihn LeeWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Regina BarzilayComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Richard A YoungWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.

Funding

Targeting Genomic Instability and Evolution in MyelomaP01CA155258 · NCI · DANA-FARBER CANCER INST · PI Jill Corre · 2011 to 2026
$32.5M
Transcriptional regulation in mammalian cellsR35GM144283 · NIGMS · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI RICHARD YOUNG · 2022 to 2026
$4.0M
NCI NIH HHS P01 CA155258NIGMS NIH HHS R35 GM144283
6 · The paper itself

Abstract

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.

Identifiers

PMID38659952
PMCPMC11042338

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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.