Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Statistical crystallography reveals an allosteric network in SARS-CoV-2 Mpro

ABSTRACT: To interpret and transmit biological signals, proteins use correlated motions. Experimental determination of these dynamics and the structural distributions they generate remains a key challenge. Here, using 1146 crystal structures of the main protease (Mpro) from SARS-CoV-2, we were able to infer a model of the enzyme’s structural fluctuations. Mpro is regulated by concentration, becoming enzymatically active after forming a homodimer. To understand the structural changes that enable dimerization to activate catalysis, we employed our model, predicting which regions of the dimerization domain are structurally correlated with the active site. Mutations at these positions, expected to disrupt catalysis, resulted in a dramatic reduction in activity in one case, a mild effect in the second, and none in the third. Additional crystallography and biophysical experiments provide a mechanistic explanation for these results. Our work suggests that a statistical crystallography, in which numerous crystallographic datasets are analyzed, can reveal the structural fluctuations of protein native states and help uncover their biological function.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

SUBMITTER: Kira Schamoni-Kast

LAB HEAD: Charlotte Uetrecht

PROVIDER: PXD076496 | Pride | 2026-04-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Kd_conc_dependence_WT_N214A_scans.zip	Other
	Mpro_Kd_10_20uM_raw_data.zip	Other
	Mpro_Kd_2uM_raw_data.zip	Other
	Mpro_Kd_scans_all_data.zip	Other
	Mpro_mutant_peak_list.xlsx	Xlsx

Items per page:

1 - 5 of 6

Similar Datasets

The kinetics of nsp7-11 polyprotein processing and impact on complexation with nsp16 among human coronaviruses

Project description:In coronavirus (CoV) infection, polyproteins (pp1a/pp1ab) are processed into non-structural proteins (nsps), which largely form the replication/transcription complex (RTC). The polyprotein processing and complex formation is critical and offers potential therapeutic targets. However, the interplay of polyprotein processing and RTC-assembly remains poorly understood. Here, we studied two key aspects: The order of polyprotein processing by viral main protease Mpro and its influence on complex formation with the methyltransferase nsp16. Moreover, we established an approach to determine rate constants k from cleavage sites in structured CoV polyprotein based on native mass spectrometry (MS). The high sensitivity and precision of our method allowed quantification of multi-reaction kinetics of nsp7-11 processing from four human pathogenic CoV species. The experimentally determined rate constants are put into perspective with a comprehensive analysis of primary sequences and structural models, revealing distinct cleavage mechanisms for each site based on their local structural environments. Our systematic approach provides a blueprint for kinetic analysis of complex multi-cleavage reactions.

2025-07-08 | PXD049009 | Pride

Transcription profiling by array of mouse promyelocyte granulocytes with activated MYC-ER protein

Project description:The mouse promyelocyte (MPRO) granulocyte cell model expressing the MYC-ER fusion protein encoding transgene was used as a system to perform gene expression profiling in a granulocytic cell setting of low endogenous MYC expression (differentiated MYC-ER MPROs, D4) where we then activated the MYC-ER protein for 24 h with 4-OHT (D5T) as compared to a EtOH vehicle treated control (D5E).

2011-06-01 | E-MEXP-2794 | biostudies-arrayexpress

Transcription profiling by array of mouse promylocyte cell line induced to differentiate over four days

Project description:The Mouse Promylocyte (MPRO) cell line was induced to differentiate over four days during which time MYC expression decreases. MYC is required for rDNA transcription; by looking at global gene expression under these conditions, our aim was to correlate the expression of Pol I related/specific genes with that of MYC as well as contrast to those genes specific to Pol II and III transcription.

2011-06-01 | E-MEXP-2786 | biostudies-arrayexpress

Global murine neutrophil response to highly and less virulent influenza A (H3N2) virus infections at 3 and 9 h post-infection

Project description:Array analysis of total RNA obtained from MPRO neutrophils collected at 3 and 9 h post-infection with highly and less virulent influenza A (H3N2) viruses. Viruses (designated as LVI, HVI and MPI) were derived from influenza strain virus A/Aichi/2/68 (Aichi68). LVI is Aichi68 propagated in eggs, HVI is mouse adapted Aichi68, and MPI is HVI propagated in MDCK. Infection: lung homogenate (mock), LVI, HVI and MPI; time of sample collection: 3 and 9 h post-infection; two biological replicates for each group.

2014-03-19 | E-GEOD-55995 | biostudies-arrayexpress

Characterization of MPro substrate specificity by HTPS

Project description:Characterization of MPro substrate specificity by HTPS using temporal resolution (5min, 30min, 4hrs, 24hrs)

2025-07-02 | PXD044733 | Pride

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro (HDX-MS pulse labeling)

Project description:SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic, entailing enormous disruption worldwide. Its ~30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein, and the data suggest that the nsp7-10/11 structure in complex with Mpro strongly resembles the unbound polyprotein. Our array of techniques supports the notion that interplay between polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we leveraged assays of limited proteolysis by Mpro of nsp7-11 using a series of inhibitors/binders to characterize Mpro inhibition using a polyprotein substrate.

2022-12-19 | PXD033702 | Pride

Transcription profiling of mouse macrophages infected with Leishmania amazogensis amastigotes

Project description:L. amazonensis (LV79 strain, ref.: MPRO/BR/1972/M1841) amastigotes were added or not to BALB/c mouse bone marrow-derived macrophage cultures at a multiplicity of 4 per macrophage. Parasite-harboring macrophages (samples I1 and I2) and parasite-free ones (samples (UI1 and UI2) were cultured at 34M-0C for 24h before RNA extraction and hybridization onto Affymetrix GeneChips Mouse430_2.

2009-01-01 | E-MEXP-1595 | biostudies-arrayexpress

AR dimerization surface mutants and wt in PC3 cells

Project description:Mutations of the androgen receptor (AR) associated with prostate cancer and androgen insensitivity syndrome may profoundly influence its structure, protein interaction network and binding to chromatin, resulting in altered transcription signatures and drug responses. Current structural information fails to explain the effect of pathological mutations on AR structure-function relationship. Here we have thoroughly studied the effects of selected mutations that span the complete dimer interface of AR ligand-binding domain (AR-LBD) using X-ray crystallography in combination with in vitro, in silico, and cell-based assays. We show that these variants alter AR-dependent transcription and responses to anti-androgens by inducing a previously undescribed allosteric switch in the AR-LBD that increases exposure of residue Arg761 and ultimately leads to its enhanced methylation. We also corroborate the relevance of residues Arg761 and Tyr764 for AR dimerization and function. Together, our results reveal allosteric coupling of AR dimerization and post-translational modifications as a disease mechanism with implications for precision medicine.

2023-03-01 | GSE210393 | GEO

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro (XL-MS)

2022-12-19 | PXD033748 | Pride

Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15

Project description:The catalytic domain of PARP15 dimerizes, forming the same dimer interface in solution that had already been captured by X-ray crystallography of the domain. Furthermore, we show that the formation of dimers is a prerequisite for catalytic activity and that monomeric mutant variants of the domain were catalytically inactive. Our findings suggest a regulatory mechanism by which dimerization is linked to either target engagement or placement of a catalytic residue, rather than NAD+ co-substrate binding, and by which the two protomers of the dimer operate independent of one another.

2025-09-29 | PXD067296 | Pride