ArticleMolecular & cellular proteomics : MCP2012
Probing the conformation of the ISWI ATPase domain with genetically encoded photoreactive crosslinkers and mass spectrometry.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Remodeling of Individual Nucleosomes in Nucleosome Arrays.Methods in molecular biology (Clifton, N.J.) · 2025Article
- NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo.Nucleic acids research · 2024Article
- A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler.Life science alliance · 2023Article
- A case of convergent evolution: Several viral and bacterial pathogens hijack RSK kinases through a common linear motif.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Function of a strand-separation pin element in the PriA DNA replication restart helicase.The Journal of biological chemistry · 2019Article
- A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions.Molecular microbiology · 2018Article
- Protein Chemical Approaches to Understanding PTEN Lipid Phosphatase Regulation.Methods in enzymology · 2018Article
- Complementary Benzophenone Cross-Linking/Mass Spectrometry Photochemistry.Analytical chemistry · 2017Article
- Article
- An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase.Nucleic acids research · 2016Article
- An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Molecular Features of Phosphatase and Tensin Homolog (PTEN) Regulation by C-terminal Phosphorylation.The Journal of biological chemistry · 2016Article
- Automated structure modeling of large protein assemblies using crosslinks as distance restraints.Nature methods · 2016Article
- A family of photoswitchable NMDA receptors.eLife · 2016Article
- Life span extension by targeting a link between metabolism and histone acetylation in Drosophila.EMBO reports · 2016Article
- DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints.Nucleic acids research · 2015Article
- Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density.Molecular and cellular biology · 2015Article
- Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes.Journal of molecular biology · 2014Article
- Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.Journal of structural biology · 2014Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a strategy for rapidly gaining structural information about a protein from crosslinks formed by genetically encoded unnatural amino acids. We applied it to ISWI, a chromatin remodeling enzyme involved in chromatin assembly, DNA replication and transcription. ISWI is part of the vast Snf2 family of helicase-related proteins, many of which constitute the catalytic cores of chromatin remodeling complexes. Structural information about this family is scarce, hampering our mechanistic understanding of chromatin remodeling. Making use of cells that harbor a special tRNA/aminoacyl-tRNA synthetase pair, several residues within the ATPase domain of ISWI were individually substituted with the UV-reactive unnatural amino acid p-benzoyl-p-phenylalanine. Intramolecular crosslinks could be mapped with amino acid precision by high resolution tandem mass spectrometry and the novel bioinformatic tool "Crossfinder." Most crosslinks were fully consistent with published crystal structures of ISWI-related ATPases. A subset of crosslinks, however, disagreed with the conformations previously captured in crystal structures. We built a structural model using the distance information obtained from the crosslinks and the structure of the closest crystallized relative, Chd1. The model shows the ATPase lobes strongly rotated against each other, a movement postulated earlier to be necessary to achieve a catalytically competent state. The minimal requirements for solubility and protein amounts make our approach ideal for studying structures and conformations of proteins that are not amenable to conventional structural techniques.
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