NSLS-II MX beamlines FMX for micro-crystallography &amp; AMX for highly automated MX

Fuchs, Martin; Sweet, Robert M.; Berman, L. E.; Bhogadi, Dileep; Hendrickson, Wayne A.; Chubar, Oleg; Yang, Lin; McSweeney, Seán; Schneider, Dieter K.

doi:10.1107/s2053273314082667

Cited by 4 publications

(5 citation statements)

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“…Crystals were harvested and frozen directly from hanging drops. Diffraction data was collected at NSLSII AMX beamline [113]. Data reduction was performed using DIALS [114].…”

Section: Crystallization and Structure Determinationmentioning

confidence: 99%

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

et al. 2023

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HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

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“…Crystals were harvested and frozen directly from hanging drops. Diffraction data was collected at NSLSII AMX beamline [113]. Data reduction was performed using DIALS [114].…”

Section: Crystallization and Structure Determinationmentioning

confidence: 99%

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

et al. 2023

View full text Add to dashboard Cite

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“…Crystallographic details are shown in Table 2. The images were processed and scaled at the 17-ID-1 (AMX) beamline of the National Synchrotron Light Source II at Brookhaven (28). The integrated data were scaled in CPP4i2 (29, 30), using AIMLESS (31).…”

Section: Methodsmentioning

confidence: 99%

“…(AMX) beamline of the National Synchrotron Light Source II at Brookhaven (28). The integrated data were scaled in CPP4i2 (29,30), using AIMLESS (31).…”

Section: X-ray Crystallography Proceduresmentioning

confidence: 99%

Distant sequence regions of JBP1 contribute to J-DNA binding

Vries

Ammerlaan

Heidebrecht

et al. 2023

Preprint

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Base-J (β-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxylase domain (THD) and a J-DNA binding domain (JDBD). How the THD synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for Molecular Dynamics (MD) simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. A high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

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“…Crystallographic details are shown in Table 2 . The images were processed and scaled at the 17-ID-1 (AMX) beamline of the National Synchrotron Light Source II at Brookhaven ( 36 ). The integrated data were scaled in CPP4i2 ( 37 , 38 ) using AIMLESS ( 39 ).…”

Section: Methodsmentioning

confidence: 99%

Distant sequence regions of JBP1 contribute to J-DNA binding

et al. 2023

View full text Add to dashboard Cite

Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

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NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX

Cited by 4 publications

References 0 publications

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

Distant sequence regions of JBP1 contribute to J-DNA binding

Distant sequence regions of JBP1 contribute to J-DNA binding

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