Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Foadi, James; Aller, Pierre; Axford, D.; Owen, Robin L.; Alguel, Yilmaz; Cameron, A. F.; Armour, Wes; Evans, Gary B.

doi:10.1107/s0108767312099679

Cited by 35 publications

(38 citation statements)

References 11 publications

(11 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some of these diffracted anisotropically to ∼1.8 Å resolution (based on a CC 1/2 cut‐off of 0.3) using the microbeam capability of the beamline 23‐ID_C of the APS. The program Blend was used to combine four of the highest resolution datasets (two of which were derived from the same crystal) to yield the merged dataset extending to an overall resolution of approximately 2.0 Å as described in Table . The structure was solved by molecular replacement based on the previously‐determined lower resolution structure (PDB: 4AW6) .…”

Section: Resultsmentioning

confidence: 99%

Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors

et al. 2016

View full text Add to dashboard Cite

The function and localization of proteins and peptides containing C-terminal "CaaX" (Cys-aliphatic-aliphatic-anything) sequence motifs are modulated by post-translational attachment of isoprenyl groups to the cysteine sulfhydryl, followed by proteolytic cleavage of the aaX amino acids. The zinc metalloprotease ZMPSTE24 is one of two enzymes known to catalyze this cleavage. The only identified target of mammalian ZMPSTE24 is prelamin A, the precursor to the nuclear scaffold protein lamin A. ZMPSTE24 also cleaves prelamin A at a second site 15 residues upstream from the CaaX site. Mutations in ZMPSTE24 result in premature-aging diseases and inhibition of ZMPSTE24 activity has been reported to be an off-target effect of HIV protease inhibitors. We report here the expression (in yeast), purification, and crystallization of human ZMPSTE24 allowing determination of the structure to 2.0 Å resolution. Compared to previous lower resolution structures, the enhanced resolution provides: (1) a detailed view of the active site of ZMPSTE24, including water coordinating the catalytic zinc; (2) enhanced visualization of fenestrations providing access from the exterior to the interior cavity of the protein; (3) a view of the C-terminus extending away from the main body of the protein; (4) localization of ordered lipid and detergent molecules at internal and external surfaces and also projecting through fenestrations; (5) identification of water molecules associated with the surface of the internal cavity. We also used a fluorogenic assay of the activity of purified ZMPSTE24 to demonstrate that HIV protease inhibitors directly inhibit the human enzyme in a manner indicative of a competitive mechanism.

show abstract

Section: Resultsmentioning

confidence: 99%

Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Individual data sets were processed using CCP4 58 but these did not contain sufficient anomalous signal to allow structure determination. All five data sets collected using the MXPressE_SAD method were, therefore, combined and scaled using BLEND 59 to 2 Å resolution. The structure was then successfully determined from the copper anomalous signal using SHELX 60 .…”

Section: Methodsmentioning

confidence: 99%

An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion

et al. 2018

View full text Add to dashboard Cite

Thermobia domestica belongs to an ancient group of insects and has a remarkable ability to digest crystalline cellulose without microbial assistance. By investigating the digestive proteome of Thermobia, we have identified over 20 members of an uncharacterized family of lytic polysaccharide monooxygenases (LPMOs). We show that this LPMO family spans across several clades of the Tree of Life, is of ancient origin, and was recruited by early arthropods with possible roles in remodeling endogenous chitin scaffolds during development and metamorphosis. Based on our in-depth characterization of Thermobia’s LPMOs, we propose that diversification of these enzymes toward cellulose digestion might have endowed ancestral insects with an effective biochemical apparatus for biomass degradation, allowing the early colonization of land during the Paleozoic Era. The vital role of LPMOs in modern agricultural pests and disease vectors offers new opportunities to help tackle global challenges in food security and the control of infectious diseases.

show abstract

“…The datasets were indexed and integrated using XDS (Kabsch, 2010). The datasets indexed with the consistent unit cell parameters were subjected to hierarchical cluster analysis based on unit cell similarity using BLEND (Foadi et al, 2013). The clusters of datasets with expected completeness and multiplicity of more than 90% and 2, respectively, were separately merged using XSCALE (Kabsch, 2010) with outlier rejections.…”

Section: Author Contributionsmentioning

confidence: 99%

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

et al. 2018

View full text Add to dashboard Cite

Orexin peptides in the brain regulate physiological functions such as the sleep-wake cycle, and are thus drug targets for the treatment of insomnia. Using serial femtosecond crystallography and multi-crystal data collection with a synchrotron light source, we determined structures of human orexin 2 receptor in complex with the subtype-selective antagonist EMPA (N-ethyl-2-[(6-methoxy-pyridin-3-yl)-(toluene-2-sulfonyl)-amino]-N-pyridin-3-ylmethyl-acetamide) at 2.30-Å and 1.96-Å resolution. In comparison with the non-subtype-selective antagonist suvorexant, EMPA contacted fewer residues through hydrogen bonds at the orthosteric site, explaining the faster dissociation rate. Comparisons among these OXR structures in complex with selective antagonists and previously determined OXR/OXR structures bound to non-selective antagonists revealed that the residue at positions 2.61 and 3.33 were critical for the antagonist selectivity in OXR. The importance of these residues for binding selectivity to OXR was also revealed by molecular dynamics simulation. These results should facilitate the development of antagonists for orexin receptors.

show abstract

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Cited by 35 publications

References 11 publications

Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors

Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors

An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Contact Info

Product

Resources

About