PXD058768

PXD058768 is an original dataset announced via ProteomeXchange.

Title	Integrating Protein Language Models and Automatic Biofoundry for Enhanced Protein Evolution
Description	Traditional protein engineering methods, such as directed evolution, while effective, are often slow and labor-intensive. Advances in machine learning and automated biofoundry present new opportunities for optimizing these processes. This study devises a protein language model-enabled automatic evolution platform, a closed-loop system for automated protein engineering within the Design-Build-Test-Learn cycle. The protein language model ESM-2 makes zero-shot prediction of 96 variants to initiate the cycle. The biofoundry constructs and evaluates these variants, and feeds the results back to a multi-layer perceptron to train a fitness predictor, which then makes prediction of second round of 96 variants with improved fitness. With the tRNA synthetase as a model enzyme, four-rounds of evolution carried out within 10 days lead to mutants with enzyme activity improved by up to 2.4-fold. Our system significantly enhances the speed and accuracy of protein evolution, driving faster advancements in protein engineering for industrial applications.
HostingRepository	PRIDE
AnnounceDate	2024-12-25
AnnouncementXML	Submission_2024-12-24_22:08:16.189.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Haoran Yu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	6520A Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-11 04:29:41	ID requested
⏵ 1	2024-12-24 22:08:16	announced

Dataset with its publication pending

submitter keyword: Protein Language Models,Protein Engineering, Directed Evolution, Automatic Biofoundry

Haoran Yu
contact affiliation	Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
contact email	yuhaoran@zju.edu.cn
lab head
Haoran Yu
contact affiliation	Zhejiang University
contact email	yuhaoran@zju.edu.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/12/PXD058768

PRIDE project URI

• PRIDE
  1. PXD058768
     1. Label: PRIDE project
     2. Name: Integrating Protein Language Models and Automatic Biofoundry for Enhanced Protein Evolution