Proteomics

Dataset Information

0

Kinetic Analysis of DNA Dependent Protein Kinase Catalytic Subunit

ABSTRACT: We investigated the dynamics of protein kinase DNA dependent protein kinase catalytic subunit (DNA-PKcs) through hydrogen deuterium exchange mass spectrometry. Over 1100 peptides could be monitored throughout the kinetics experiment, showing the utility of our nanospray HX-MS configuration for ultra-large proteins such as DNA-PKcs. To match the structurally unassigned helices to sequence from the large disordered regions of DNA-PKcs (a.a 2577-2773), we used integrative modelling. Two sequence assignments were possible. The cluster of models with the helix assignment towards the N-terminal side was favored by reduced kinetics of exchange as measured by HX-MS.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Morgan Hepburn  

LAB HEAD: David C. Schriemer

PROVIDER: PXD016595 | Pride | 2019-12-10

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
DNAPKcs2.5pmol-Label400.5-Thaw-rNep0.3ug-3min-10C-Load0.5pmol-1.wiff Wiff
DNAPKcs2.5pmol-Label400.5-Thaw-rNep0.3ug-3min-10C-Load0.5pmol-1.wiff.scan Wiff
DNAPKcs2.5pmol-Label400.5-Thaw-rNep0.3ug-3min-10C-Load0.5pmol-2.wiff Wiff
DNAPKcs2.5pmol-Label400.5-Thaw-rNep0.3ug-3min-10C-Load0.5pmol-2.wiff.scan Wiff
DNAPKcs2.5pmol-Label400.5-Thaw-rNep0.3ug-3min-10C-Load0.5pmol-3.wiff Wiff
Items per page:
1 - 5 of 57
altmetric image

Publications

SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange.

Saltzberg Daniel J DJ   Hepburn Morgan M   Pilla Kala Bharath KB   Schriemer David C DC   Lees-Miller Susan P SP   Blundell Tom L TL   Sali Andrej A  

Progress in biophysics and molecular biology 20190927

X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone mo  ...[more]

PMID: 31570166

Publication: 1/2

Similar Datasets

Proteomics Integrative Structural Model of DNA-PK Synapsis
2021-01-20 | PXD017931 | Pride
Proteomics Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
2023-09-08 | PXD045012 | Pride
Proteomics tRNA binding to KEOPS human protein complex
2020-12-11 | PXD018007 | Pride
Proteomics Integrative Threading of the DNA-PKcs Disordered Region with Crosslinking Restraints
2019-12-10 | PXD016639 | Pride
Transcriptomics Transcriptome analysis to decipher molecular mechanism in radiation-induced lung fibrosis in DNA-PKcs knockout mouse model
2023-11-09 | E-MTAB-6419 | biostudies-arrayexpress
Proteomics Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family
2020-07-02 | PXD019367 | Pride
Other Phosphorylation at the S2056 1 cluster of DNA-PKcs is dispensable for lymphocyte development and class switch recombination in mice.
2019-04-17 | GSE129895 | GEO
Other Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination
2018-07-26 | GSE117628 | GEO
Proteomics Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides
2023-10-24 | PXD041582 | Pride
Transcriptomics Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion Positive Prostate Cancer
2011-05-18 | E-GEOD-27723 | biostudies-arrayexpress