scholarly journals Cryo-EM structure of the NLRP3 decamer bound to the cytokine release inhibitory drug CRID3

2021 ◽  
Author(s):  
Inga V. Hochheiser ◽  
Michael Pilsl ◽  
Gregor Hagelueken ◽  
Jonas Moecking ◽  
Michael Marleaux ◽  
...  
Keyword(s):  
Small Molecules ◽  
Nucleotide Binding Domain ◽  
Native Form ◽  
Spherical Structure ◽  
Cryo Electron Microscopy ◽  
Rational Drug ◽  
Inhibitory Drug ◽  
Drug Optimization ◽  
Apical Axis

NLRP3 is an intracellular sensor protein whose activation by a broad spectrum of exogenous and endogenous stimuli leads to inflammasome formation and pyroptosis. The mechanisms leading to NLRP3 activation and the way how antagonistic small molecules function remain poorly understood. Here we report the cryo-electron microscopy structures of full-length NLRP3 in its native form and complexed with the inhibitor CRID3 (also named MCC950). Inactive, ADP-bound NLRP3 is a decamer composed of homodimers of intertwined LRR domains that assemble back-to-back as pentamers with the NACHT domain located at the apical axis of this spherical structure. Molecular contacts between the concave sites of two opposing LRRs are mediated by an acidic loop extending from an LRR transition segment. Binding of CRID3 significantly stabilizes the NACHT and LRR domains relative to each other, allowing structural resolution of 3.9-4.2 Ang. CRID3 binds into a cleft, connecting four subdomains of the NACHT with the transition LRR. Its central sulfonylurea group interacts with the Walker A motif of the NLRP3 nucleotide-binding domain and is sandwiched between two arginines from opposing sites, explaining the specificity of NLRP3 for this chemical entity. With the determination of the binding site of this lead therapeutic, specific targeting of NLRP3 for the treatment of autoinflammatory and autoimmune diseases and rational drug optimization are within reach.

Enhanced information from biological materials through technological improvements in cryo-electron microscopy

1992 ◽  
Vol 50 (1) ◽  
pp. 788-789
Author(s):  
Marc J.C. de Jong ◽  
Wim M. Busing ◽  
Max T. Otten
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Biological Materials ◽  
Electron Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
The Many ◽  
Technological Improvements ◽  
Beam Damage

Biological materials damage rapidly in the electron beam, limiting the amount of information that can be obtained in the transmission electron microscope. The discovery that observation at cryo temperatures strongly reduces beam damage (in addition to making it unnecessaiy to use chemical fixatives, dehydration agents and stains, which introduce artefacts) has given an important step forward to preserving the ‘live’ situation and makes it possible to study the relation between function, chemical composition and morphology.Among the many cryo-applications, the most challenging is perhaps the determination of the atomic structure. Henderson and co-workers were able to determine the structure of the purple membrane by electron crystallography, providing an understanding of the membrane's working as a proton pump. As far as understood at present, the main stumbling block in achieving high resolution appears to be a random movement of atoms or molecules in the specimen within a fraction of a second after exposure to the electron beam, which destroys the highest-resolution detail sought.

scholarly journals Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy

2021 ◽  
Author(s):  
Z. Faidon Brotzakis ◽  
Thomas Lohr ◽  
Michele Vendruscolo
Keyword(s):  
Infectious Disease ◽  
Electron Microscopy ◽  
Severe Acute Respiratory Syndrome ◽  
Intermediate State ◽  
Therapeutic Interventions ◽  
Cryo Electron Microscopy ◽  
Welfare Systems

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a highly infectious disease that is severely affecting our society and welfare systems. In order to develop therapeutic interventions against this...

scholarly journals Accurate geometrical restraints for Watson–Crick base pairs

2019 ◽  
Vol 75 (2) ◽  
pp. 235-245 ◽  
Author(s):  
Miroslaw Gilski ◽  
Jianbo Zhao ◽  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Douglas H. Turner ◽  
...  
Keyword(s):  
Structural Information ◽  
Data Bank ◽  
Base Pairs ◽  
Acta Cryst ◽  
Ultrahigh Resolution ◽  
Cryo Electron Microscopy ◽  
Structural Database ◽  
Different Sources ◽  
Best Parameters

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

ELECTROCHEMICAL DNA SENSOR TECHNOLOGY FOR MONITORING OF DRUG–DNA INTERACTIONS

NANO ◽  
2008 ◽  
Vol 03 (04) ◽  
pp. 229-232 ◽  
Author(s):  
A. ERDEM ◽  
H. KARADENIZ ◽  
A. CALISKAN ◽  
A. VASEASHTA
Keyword(s):  
Drug Delivery ◽  
Small Molecules ◽  
Anticancer Drugs ◽  
Point Of Care ◽  
Sensor Technology ◽  
Electrochemical Biosensors ◽  
Dna Sensor ◽  
Dna Interactions ◽  
Electrochemical Dna Sensor

The objective of this investigation is to understand the nature and dynamics of binding small molecules to bio-macromolecules using electrochemical methods. The investigation pertaining to the design of site- and conformation-specific reagents provides a rationale for new studies of drug delivery design. Some anticancer drugs and DNA interactions have been undertaken by using a variety of techniques. Determination of interaction between DNA and DNA-targeted molecules would be valuable in the design of molecule-specific electrochemical biosensors for applications in diagnostics, development of drugs for chemotherapy, and as a biotechnological tool for DNA-based point-of-care diagnosis.

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