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Photo-crosslinking of SurA (p-azido-Phe) to unfolded Omps (OmpA and OmpX)

ABSTRACT: To investigate the structural basis of SurA’s chaperone function, we characterized crosslinks between it and two of its clients, OmpA and OmpX, and used those as distance restraints to build structural models.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Stephen Fried

LAB HEAD: Stephen Fried

PROVIDER: PXD021870 | Pride | 2020-10-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	All_Variants_pAF.fasta	Fasta
	SurApaf105_OmpA_Trypsin_1.raw	Raw
	SurApaf105_OmpA_Trypsin_1.zhrm	Other
	SurApaf105_OmpA_Trypsin_GluC_1.raw	Raw
	SurApaf105_OmpA_Trypsin_GluC_1.zhrm	Other

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1 - 5 of 129

Publications

SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins.

Marx Dagan C DC Plummer Ashlee M AM Faustino Anneliese M AM Devlin Taylor T Roskopf Michaela A MA Leblanc Mathis J MJ Lessen Henry J HJ Amann Barbara T BT Fleming Patrick J PJ Krueger Susan S Fried Stephen D SD Fleming Karen G KG

Proceedings of the National Academy of Sciences of the United States of America 20201022 45

The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network, both due to its genetic interaction with the β-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well-understood. Here, we use a co ...[more]

PMID: 33093201

Similar Datasets

Chemical-crosslinking of SurA with DSBU to unfolded Omps (OmpA and OmpX)

Project description:To investigate the structural basis of SurA’s chaperone function, we characterized crosslinks between it and two of its clients, OmpA and OmpX, and used those as distance restraints to build structural models.

2020-10-29 | PXD021872 | Pride

Identification of SurA inter-domain dynamics and client binding by XL-MS

Project description:We present XL-MS data of apo-SurA and SurA in complex with OmpX to define (1) interdomain interactions in the periplasmic chaperone SurA, and (2) the binding site of OmpX on SurA.

2020-05-22 | PXD016993 | Pride

Inter-domain dynamics in the chaperone SurA and multi-site binding to its unfolded outer membrane protein clients revealed by HDX-MS

Project description:We present HDX-MS data of apo-SurA, SurA in complex with OmpX, OmpF and a peptide with sequence WEYIPNV to define (1) interdomain dynamics in the periplasmic chaperone SurA, and (2) the binding site of OmpX, OmpF and WEYIPNV on SurA.

2020-05-22 | PXD017010 | Pride

XL-MS data of BAM and SurA binding

Project description:We present XL-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM

2022-07-12 | PXD030209 | Pride

HDX-MS data of BAM and SurA binding

Project description:We present HDX-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM and vice versa.

2022-07-12 | PXD030268 | Pride

SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins.

Project description:The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network, both due to its genetic interaction with the β-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well-understood. Here, we use a combination of photo-crosslinking, mass spectrometry, solution scattering, and molecular modeling techniques to elucidate the key structural features that define how SurA solubilizes uOMPs. Our experimental data support a model in which SurA binds uOMPs in a groove formed between the core and P1 domains. This binding event results in a drastic expansion of the rest of the uOMP, which has many biological implications. Using these experimental data as restraints, we adopted an integrative modeling approach to create a sparse ensemble of models of a SurA•uOMP complex. We validated key structural features of the SurA•uOMP ensemble using independent scattering and chemical crosslinking data. Our data suggest that SurA utilizes three distinct binding modes to interact with uOMPs and that more than one SurA can bind a uOMP at a time. This work demonstrates that SurA operates in a distinct fashion compared to other chaperones in the OMP biogenesis network.

| S-EPMC7668074 | biostudies-literature

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

2010-01-20 | GSE14064 | GEO

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells. Strains: E. coli K-12 BW25113 wild type, ompA mutant Medium: LB Cell type: Biofilm cells grown on glasswool and polystyrene surfaces Time: 15 h Temperature: 37C Strains: BW25113 ompA/pCA24N_ompA and ompA/pCA24N Medium: LB Time: 7 h Temperature: 37C Cell type: suspension cells, induced by 0.1 mM IPTG

2010-11-03 | E-GEOD-14064 | biostudies-arrayexpress

FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe

Project description:Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wide information on protein structure and has been applied to a range of biological and biophysical questions. Although LiPMS can be carried out with standard laboratory reagents and mass spectrometers, analyzing the data can be slow and poses unique challenges compared to typical quantitative proteomics workflows. To address this, we leverage the fast, sensitive, and accurate search and label-free quantification algorithms in FragPipe and then process its output in FLiPPR. FLiPPR formalizes a specific data imputation heuristic that carefully uses missing data in LiP-MS experiments to report on the most significant structural changes. Moreover, FLiPPR introduces a new data merging scheme (from ions to cut-sites) and a protein-centric multiple hypothesis correction scheme, collectively enabling processed LiP-MS datasets to be more robust and less redundant. These improvements substantially strengthen statistical trends when previously published data are reanalyzed with the FragPipe/FLiPPR workflow. As a final feature, FLiPPR facilitates the collection of structural metadata to identify correlations between experiments and structural features. We hope that FLiPPR will lower the barrier for more users to adopt LiP-MS, standardize statistical procedures for LiP-MS data analysis, and systematize output to facilitate eventual larger-scale integration of LiP-MS data.

2024-05-24 | PXD047776 | Pride

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctions in haploid and diploid yeast

2012-01-01 | E-GEOD-33986 | biostudies-arrayexpress

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