PXD065336

PXD065336 is an original dataset announced via ProteomeXchange.

Title	Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids
Description	The pyrrolysyl-tRNA synthetase (PylRS) is widely used to incorporate noncanonical amino acids (ncAAs) into proteins. However, most of ncAA-containing protein yields remain low due to the limited activity of PylRS variants. Here, we apply machine learning (ML) to engineer the tRNA-binding domain of PylRS. The FFT-PLSR model is first applied to explore pairwise combinations of 12 single mutations, generating a variant Com1-IFRS with an 11-fold increase in stop codon suppression efficiency. Deep learning models ESM-1v, Mutcompute, and ProRefiner then identify new mutation sites. Applying FFT-PLSR on these sites yields a variant Com2-IFRS showing a 30.8-fold increase in stop codon suppression efficiency. Transplanting these mutations into 7 other PylRS-derived synthetases improved ncAA-containing protein yield by up to 1149.7-fold. Molecular dynamics simulations are used to explore the molecular change caused by the mutations. This paper presents improved PylRS variants and a machine learning framework for optimizing the enzyme activity.
HostingRepository	PRIDE
AnnounceDate	2025-07-25
AnnouncementXML	Submission_2025-07-25_04:22:03.335.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	2025-06-23 07:22:06	ID requested
⏵ 1	2025-07-25 04:22:04	announced

Zhang Q, Jiang L, Niu Y, Li Y, Chen W, Cheng J, Ding H, Chen B, Liu K, Cao J, Wang J, Ye S, Yang L, Wu J, Xu G, Lin J, Yu H, Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids. Nat Commun, 16(1):6648(2025) [pubmed]

10.1038/s41467-025-61952-2;

submitter keyword: LC-MS,sfGFP,Noncanonical amino acids

Haoran Yu
contact affiliation	Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China (lab head)
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/2025/07/PXD065336

PRIDE project URI

• PRIDE
  1. PXD065336
     1. Label: PRIDE project
     2. Name: Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids