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PXD038492 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLC-MSMS of Hela cell extracts on pull down with de novo modular peptide binding proteins
Descriptionwe describe a general approach for de novo design of proteins made out of repeating units that bind peptides with repeating sequences such that there is a one to one correspondence between repeat units on the protein and peptide. We develop a rapid docking plus geometric hashing method to identify protein backbones and protein-peptide rigid body arrangements that are compatible with bidentate hydrogen bonds between side chains on the protein and the backbone of the peptide; the remainder of the protein sequence is then designed using Rosetta to incorporate additional interactions with the peptide and drive folding to the desired structure. We use this approach to design, from scratch, alpha helical repeat proteins that bind six different tripeptide repeat sequences--PLP, LRP, PEW, IYP, PRM and PKW-- in near polyproline 2 helical conformations.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterTomos Morgan
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-12-01 03:47:40ID requested
12023-03-17 05:42:28announced
22023-04-24 02:07:53announced2023-04-24: Updated project metadata.
32023-11-14 08:45:02announced2023-11-14: Updated project metadata.
Publication List
Wu K, Bai H, Chang YT, Redler R, McNally KE, Sheffler W, Brunette TJ, Hicks DR, Morgan TE, Stevens TJ, Broerman A, Goreshnik I, DeWitt M, Chow CM, Shen Y, Stewart L, Derivery E, Silva DA, Bhabha G, Ekiert DC, Baker D, De novo design of modular peptide-binding proteins by superhelical matching. Nature, 616(7957):581-589(2023) [pubmed]
Keyword List
submitter keyword: Hela, gelbands,LC-MSMS
Contact List
Emmanuel Derivery
contact affiliationMedical Research Council - Laboratory of molecular biology
contact emailderivery@mrc-lmb.cam.ac.uk
lab head
Tomos Morgan
contact affiliationMRC-LMB
contact emailtmorgan@mrc-lmb.cam.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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