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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

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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

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