Dataset Information

Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross‐Linking, MS/MS, and NMR

ABSTRACT: The endogenous cellular prion protein (PrPC) can misfold into the scrapie isoform (PrPSc) and cause fatal infectious diseases. Despite significant research on the prion protein, both its normal function and whether alterations to that function play a critical role in prion diseases remain unknown. The protein consists of a predominantly alpha-helical C-terminal domain and an unstructured N-terminal domain that can coordinate Cu2+. Previous studies using NMR and EPR have revealed a tertiary association between the N-terminal domain and the C-terminal domain that we have hypothesized to be critical to the protein’s normal function. Here we investigated and quantified the inter-domain interactions within three different prion variants (wild type recombinant mouse PrPC, mutant delta central region (ΔCR), and disease mutant (E199K) after chemical cross-linking with a newly designed MS-cleavable reagent 1-(4-((2,5-Dioxopyrrolidin-1-yl)oxy)-4-oxobutyl)-4-(2-(3-methyl-3H-diazirin-3-yl)ethyl)-1,4-diazabicyclo[2.2.2] octane-1,4-diium (APDC4), followed by nHPLC(RP) and tandem MS analysis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Catherine Costello

LAB HEAD: Catherine E. Costello

PROVIDER: PXD012427 | Pride | 2020-06-16

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	09262017_E199K_0xCu_Chymot_APDC4_15V.mzML.xlinks.csv	Mzml
	09262017_E199K_0xCu_Chymot_APDC4_15V.raw	Raw
	09262017_WT_0xCu_Chymot_APDC4_15V.mzML.xlinks.csv	Mzml
	09262017_WT_0xCu_Chymot_APDC4_15V.raw	Raw
	09262017_deltaCR_0xCu_Chymot_APDC4_15V.mzML.xlinks.csv	Mzml

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Publications

Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR.

McDonald Alex J AJ Leon Deborah R DR Markham Kathleen A KA Wu Bei B Heckendorf Christian F CF Schilling Kevin K Showalter Hollis D HD Andrews Philip C PC McComb Mark E ME Pushie M Jake MJ Costello Catherine E CE Millhauser Glenn L GL Harris David A DA

Structure (London, England : 1993) 20190404 6

The cellular isoform of the prion protein (PrPC) serves as precursor to the infectious isoform (PrPSc), and as a cell-surface receptor, which binds misfolded protein oligomers as well as physiological ligands such as Cu2+ ions. PrPC consists of two domains: a flexible N-terminal domain and a structured C-terminal domain. Both the physiological and pathological functions of PrP depend on intramolecular interactions between these two domains, but the spe ...[more]

PMID: 30956132

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Project description:Mycobacterium polyketide synthase 13 (Pks13) is a protein complex comprised of a closely symmetric parallel dimer of chains, each encoding several enzymatic and transport functions. This module carries out the condensation of two different very long chain fatty acids to produce mycolic acids that are essential components of the mycobacterial cell wall. Here, we use cryo-EM, XL-MS, and integrative modeling to determine the structure and domain trajectories of the dimeric multi-enzyme Pks13 purified endogenously from mycobacteria under normal growth conditions. Structures of the multi-domain assembly revealed by cryogenic electron microscopy (cryoEM) define the ketosynthase (KS), linker, and acyltransferase (AT) domains, each at atomic resolution (1.8Å), with bound substrates defined at 2.4Å and 2.9Å resolution. Image classification reveals two distinct structures with alternate locations of the N-terminal acyl carrier protein (termed ACP1a, ACP1b) seen at 3.6Å and 4.6Å resolution respectively. These two structures suggest plausible intermediate states, related by a ~60Å movement of ACP1, on the pathway for substrate delivery from the fatty acyl-ACP ligase (FadD32) to the ketosynthase domain. The linking sequence between ACP1 and the KS includes an 11 amino acid sequence with 6 negatively charged side chains that lies in different positively charged grooves on the KS in ACP1a versus ACP1b structures. This charge complementarity between the extended chain and the grooves suggests some stabilization of these two distinct orientations. Other domains are visible at lower resolution and indicate flexibility relative to the KS-AT core. The chemical structures of three bound endogenous long chain fatty acid substrates with their proximal regions defined in the structures were determined by electrospray ionization mass spectrometry. The domain proximities were probed by chemical cross-linking and identified by mass spectrometry (XL-MS). These were incorporated into integrative structure modeling to define multiple domain configurations that transport the very long fatty acid chains throughout the multistep Pks13 mediated synthetic pathway.

Dataset Information

Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross‐Linking, MS/MS, and NMR

Dataset's files

Publications

Altered Domain Structure of the Prion Protein Caused by Cu<sup>2+</sup> Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR.

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