PXD027071

PXD027071 is an original dataset announced via ProteomeXchange.

Title	Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid
Description	Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI’s evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. We use mass spectrometry to identify cut sites outside of the gastrobody.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:24:32.958.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niels Wicke
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	6550 iFunnel Q-TOF LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-02 08:24:30	ID requested
1	2021-08-12 21:45:48	announced
⏵ 2	2024-10-22 05:24:37	announced	2024-10-22: Updated project metadata.

10.1038/s42003-021-02487-2;

Wicke N, Bedford MR, Howarth M, Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid. Commun Biol, 4(1):960(2021) [pubmed]

submitter keyword: SBTI, protease, gastrobody

Mark Howarth
contact affiliation	Department of Biochemistry, University of Oxford
contact email	mark.howarth@bioch.ox.ac.uk
lab head
Niels Wicke
contact affiliation	Department of Biochemistry, University of Oxford
contact email	niels.wicke@stcatz.ox.ac.uk
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/2021/08/PXD027071

PRIDE project URI

• PRIDE
  1. PXD027071
     1. Label: PRIDE project
     2. Name: Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid