ArticleGenome research2011
Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 45 citations in OpenAlex.
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- Ferrosome Organelles Spatially Insulate a Redox-Active Ferrous Phosphate Biomineral from Cytosolic ROS Chemistry.bioRxiv : the preprint server for biology · 2026Article
- Elucidating the zinc-binding proteome of Fusarium oxysporum f. sp. lycopersici with particular emphasis on zinc-binding effector proteins.Archives of microbiology · 2023Article
- Assessing the prospect of XAFS experiments of metalloproteins under in vivo conditions at Indus-2 synchrotron facility, India.Journal of synchrotron radiation · 2023Article
- The Inner Shell Spectroscopy beamline at NSLS-II: a facility for in situ and operando X-ray absorption spectroscopy for materials research.Journal of synchrotron radiation · 2022Article
- Millisecond timescale reactions observed via X-ray spectroscopy in a 3D microfabricated fused silica mixer.Journal of synchrotron radiation · 2021Article
- A skipping rope translocation mechanism in a widespread family of DNA repair helicases.Nucleic acids research · 2021Article
- Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.Scientific reports · 2020Article
- Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features.BioMed research international · 2020Article
- A bacterial DNA repair pathway specific to a natural antibiotic.Molecular microbiology · 2019Article
- Characterizing metal-binding sites in proteins with X-ray crystallography.Nature protocols · 2018Article
- Article
- Computational approaches forBioscience reports · 2017Review
- Article
- Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics.International journal of molecular sciences · 2016Review
- Metalloproteomics: challenges and prospective for clinical research applications.Expert review of proteomics · 2014Review
- MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 3 countries.
Funding
Abstract
High-throughput X-ray absorption spectroscopy was used to measure transition metal content based on quantitative detection of X-ray fluorescence signals for 3879 purified proteins from several hundred different protein families generated by the New York SGX Research Center for Structural Genomics. Approximately 9% of the proteins analyzed showed the presence of transition metal atoms (Zn, Cu, Ni, Co, Fe, or Mn) in stoichiometric amounts. The method is highly automated and highly reliable based on comparison of the results to crystal structure data derived from the same protein set. To leverage the experimental metalloprotein annotations, we used a sequence-based de novo prediction method, MetalDetector, to identify Cys and His residues that bind to transition metals for the redundancy reduced subset of 2411 sequences sharing <70% sequence identity and having at least one His or Cys. As the HT-XAS identifies metal type and protein binding, while the bioinformatics analysis identifies metal- binding residues, the results were combined to identify putative metal-binding sites in the proteins and their associated families. We explored the combination of this data with homology models to generate detailed structure models of metal-binding sites for representative proteins. Finally, we used extended X-ray absorption fine structure data from two of the purified Zn metalloproteins to validate predicted metalloprotein binding site structures. This combination of experimental and bioinformatics approaches provides comprehensive active site analysis on the genome scale for metalloproteins as a class, revealing new insights into metalloprotein structure and function.
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