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Structural plasticity of SARS-CoV-2 3CL M^pro active site cavity revealed by room temperature X-ray crystallography

The SARS-CoV-2 3CL main protease (3CL M^pro) is a chymotrypsin-like protease that facilitates the production of non-structural proteins, which are essential for viral replication and is therefore of great interest as a drug target. Here, the authors present the 2.30 Å room temperature crystal structure of ligand-free 3CL M^pro and compare it with the earlier determined low-temperature ligand-free and inhibitor-bound crystal structures.

Daniel W. Kneller
Gwyndalyn Phillips
Andrey Kovalevsky
ResearchOpen Access24 Jun 2020
Nature Communications

Volume: 11, P: 1-6
Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314

The authors highlight the importance of kinetics in GPCR activation. Using solution NMR, they show that the transducer βarrestin1 and the β-arrestin1biased ligand ML314 kinetically tune the conformational ensemble of the neurotensin receptor 1.

Fabian Bumbak
James B. Bower
Joshua J. Ziarek
ResearchOpen Access07 Jun 2023
Nature Communications

Volume: 14, P: 1-14
The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3’-UTR and promoting Rag1 mRNA expression

Regulation of thymocyte development by RNA-binding proteins is not fully characterized. Here the authors show the RBP ARPP21 interacting with the Rag1 3’-UTR to promote Rag1 expression, TCR rearrangement and an increased diversity of the TCR repertoire and that ARPP21 is down regulated by TCR stimulation.

Meng Xu
Taku Ito-Kureha
Vigo Heissmeyer
ResearchOpen Access11 Mar 2024
Nature Communications

Volume: 15, P: 1-20
Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules

Developing inhibitors that target specific protein-protein interactions (PPIs) is challenging. Here, the authors show that target selectivity and PPI blocking can be achieved simultaneously with PPI inhibitors that contain two functional modules, and create a paralog-selective PSD-95 inhibitor as proof-of-concept.

Charlotte Rimbault
Kashyap Maruthi
Matthieu Sainlos
ResearchOpen Access04 Oct 2019
Nature Communications

Volume: 10, P: 1-20
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Determining dynamic ensembles of biomolecules is still challenging. Here the authors present an approach for rapid RNA ensemble determination that combines RNA structure prediction tools and NMR residual dipolar coupling data and use it to determine atomistic ensemble models for a variety of RNAs.

Honglue Shi
Atul Rangadurai
Hashim M. Al-Hashimi
ResearchOpen Access02 Nov 2020
Nature Communications

Volume: 11, P: 1-14
Structural properties of a haemophore facilitate targeted elimination of the pathogen Porphyromonas gingivalis

The pathogenic bacterium Porphyromonas gingivalis causes periodontal disease and depends on porphyrin from host sources. Here the authors show that the P. gingivalis haem uptake system protein A (HusA) mediates the uptake of exogenous porphyrin, present its solution NMR structure and show how HusA can be exploited as a drug target.

Jin-Long Gao
Ann H. Kwan
Neil Hunter
ResearchOpen Access05 Oct 2018
Nature Communications

Volume: 9, P: 1-13
Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

The authors report crystallographic and computational studies that detail how SARS-CoV-2 3CLpro cleaves the host NF-κB Essential Modulator in addition to its canonical viral substrates. The association with the high fitness of SARS-CoV-2 in humans is discussed.

Mikhail A. Hameedi
Erica T. Prates
Daniel Jacobson
ResearchOpen Access08 Sept 2022
Nature Communications

Volume: 13, P: 1-15
Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.

Daniel W. Kneller
Hui Li
Andrey Kovalevsky
ResearchOpen Access27 Apr 2022
Nature Communications

Volume: 13, P: 1-11
Timing of illumination is essential for effective and safe photodynamic therapy: a study in the normal rat oesophagus

J van den Boogert
R van Hillegersberg
H W Tilanus
ResearchOpen Access29 Jan 1999
British Journal of Cancer

Volume: 79, P: 825-830
Characterisation of a cell-free synthesised G-protein coupled receptor

Patrick J. Shilling
Fabian Bumbak
Paul R. Gooley
ResearchOpen Access24 Apr 2017
Scientific Reports

Volume: 7, P: 1-11
Distinct activation modes of the Relaxin Family Peptide Receptor 2 in response to insulin-like peptide 3 and relaxin

Shoni Bruell
Ashish Sethi
Ross A. D. Bathgate
ResearchOpen Access12 Jun 2017
Scientific Reports

Volume: 7, P: 1-12
Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors

Investigation of the autoproccessing mechanism of SARS-CoV-2 main protease precursors reveals an N-terminal intramolecular cleavage event that leads to increased dimer formation and is followed by an intermolecular cleavage step at the C-terminus.

Annie Aniana
Nashaat T. Nashed
John M. Louis
ResearchOpen Access13 Nov 2023
Communications Biology

Volume: 6, P: 1-14
Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain

Structural characterization and catalytic activity of SARS-CoV-2 main protease reveal minimal interface regions enabling dimer formation driven by inhibitor-induced conformational changes of the oxyanion loop.

Nashaat T. Nashed
Daniel W. Kneller
John M. Louis
ResearchOpen Access16 Sept 2022
Communications Biology

Volume: 5, P: 1-14

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Structural plasticity of SARS-CoV-2 3CL M^pro active site cavity revealed by room temperature X-ray crystallography

Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314

The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3’-UTR and promoting Rag1 mRNA expression

Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Structural properties of a haemophore facilitate targeted elimination of the pathogen Porphyromonas gingivalis

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Timing of illumination is essential for effective and safe photodynamic therapy: a study in the normal rat oesophagus

Characterisation of a cell-free synthesised G-protein coupled receptor

Distinct activation modes of the Relaxin Family Peptide Receptor 2 in response to insulin-like peptide 3 and relaxin

Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors

Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain

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