PXD038492-1

PXD038492 is an original dataset announced via ProteomeXchange.

Title	LC-MSMS of Hela cell extracts on pull down with de novo modular peptide binding proteins
Description	we 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.
HostingRepository	PRIDE
AnnounceDate	2023-03-17
AnnouncementXML	Submission_2023-03-17_05:42:28.415.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD038492
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	TomosMorgan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-01 03:47:40	ID requested
⏵ 1	2023-03-17 05:42:28	announced
2	2023-04-24 02:07:53	announced	2023-04-24: Updated project metadata.
3	2023-11-14 08:45:02	announced	2023-11-14: Updated project metadata.

10.6019/PXD038492;

submitter keyword: Hela, gelbands,LC-MSMS

EmmanuelDerivery
contact affiliation	Medical Research Council - Laboratory of molecular biology
contact email	derivery@mrc-lmb.cam.ac.uk
lab head
TomosMorgan
contact affiliation	MRC-LMB
contact email	tmorgan@mrc-lmb.cam.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/2023/03/PXD038492

PRIDE project URI

• PRIDE
  1. PXD038492
     1. Label: PRIDE project
     2. Name: LC-MSMS of Hela cell extracts on pull down with de novo modular peptide binding proteins