X-ray Footprinting Solves Mystery of Metal-Breathing Protein


Results from X-ray footprinting mass spectrometry (XFMS) experiments at Lawrence Berkeley National Laboratory’s (LBNL) Advanced Light Source, mapped out on these three-dimensional structural renderings of a protein, helped researchers identify where the protein binds with a mineral. Red areas indicate possible binding areas. [Reprinted with permission from Fukushima, T., et al. DOI:10.1021/jacs.7b06560. Copyright (2017) American Chemical Society.]

Scientists have discovered the details of an unconventional coupling between a protein from the metal-reducing bacterium Shewanella oneidensis and a mineral that allows the bacterium to breathe when oxygen is unavailable.

The researchers used an X-ray-based technique known as “footprinting” to pinpoint the chemical connections between the bacterial protein and nanoparticles composed of iron and oxygen. Footprinting reveals interactions of proteins in a near-native environment. The technique identified a surprisingly small and weak binding site that had already been mapped, but it also revealed how the site bound to the metal-containing mineral which conventional techniques had been unable to do.

This study is providing ideas on how to redesign these proteins to make better electronic connections and thus more sensitive bioelectronic sensors. It could also lead to new innovations in linking proteins to other materials for bio-based electronic devices, such as sensors that can diagnose disease or detect contaminants. And it could help researchers understand and control the chemical reactions sparked by these protein-material interactions and, eventually, how organisms remodel their environment and make biominerals.

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Instruments and Facilities

X-ray beamline 5.3.1 of the Advanced Light Source (ALS) to perform “footprinting” and mass spectrometry at the Biological Nanostructures Facility at the Molecular Foundry, both at Lawrence Berkeley National Laboratory (LBNL), and the LBNL-led DOE Joint BioEnergy Institute.

Funding Acknowledgements

Work supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory (LBNL), performed at the Molecular Foundry and Advanced Photon Source (APS) at Argonne National Laboratory (ANL) and used resources of the Joint BioEnergy Institute (JBEI), supported by the Office of Basic Energy Sciences (OBES) and Office of Biological and Environmental Research (OBER), U.S. Department of Energy (DOE) Office of Science, under Contract No. DE-AC02-05CH11231. CMA-F support: Office of Naval Research, Award number N000141310551.


Fukushima, T., et al. “The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface.” J. Am. Chem. Soc. 139(36), 12647–12654, (2017). [DOI:10.1021/jacs.7b06560]