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Metalation calculators

Conditional calculators for E. coli JM109 (DE3) grown aerobically, exposed to hydrogen peroxide and grown anaerobically were first reported in Foster et al. (2022) Metallomics 14(9), mfac058. This manuscript also contains tutorial information on the uses and constraints of metalation calculators. A spreadsheet version of the original idealised Salmonella calculator was first released in Young et al. (2021) Nature Communications 12, 1195. Iterative refinements, for example to estimates of the intracellular metal availabilities or for additional conditions and cell types, will be catalogued here. The hyper-aerated E. coli calculator was added on 4th August 2022, used vigorously aerated small volume cultures grown in baffled flasks, with notably reduced iron availability, and the underlying data for these hyper-aerated cells has been made available in BioRxiv.

To predict the metalation state of a protein or other biomolecule, fill in values in the table for as many determined metal affinities (and availabilities if known) as possible. Where affinities are unknown, use the toggle buttons to exclude that metal.

Oval Picture of Flasks

Idealised Salmonella

(Default Settings for Metal Availability)

Metal Affinity (M) Metal affinities of molecule (M) (dissociation constants, KD) ∆G (kJ mol-1) ∆G for complexation with the molecule (kJ mol-1) Metal Availability (M) Buffered available metal concentration (M) Available ∆G (kJ mol-1) Buffered available free energy of metal (kJ mol-1) Occupancy Molecule occupancy with metal under these availabilities
Total Metalation

The calculator is based on Nature Communications 12 1195- (2021). Supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council. Background considerations and underlying assumptions

To predict the metalation state of a protein or other biomolecule, fill in values in the table for as many determined metal affinities (and availabilities if known) as possible. Where affinities are unknown, use the toggle buttons to exclude that metal.

Oval Picture of Flasks

Idealised Salmonella

(Default Settings for Metal Availability)

Metal Affinity (M) Metal affinities of molecule (M) (dissociation constants, KD) ∆G (kJ mol-1) ∆G for complexation with the molecule (kJ mol-1) Metal Availability (M) Buffered available metal concentration (M) Available ∆G (kJ mol-1) Buffered available free energy of metal (kJ mol-1) Occupancy Molecule occupancy with metal under these availabilities
Total Metalation

The calculator is based on Nature Communications 12 1195- (2021). Supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council. Background considerations and underlying assumptions

To predict the metalation state of a protein or other biomolecule, fill in values in the table for as many determined metal affinities (and availabilities if known) as possible. Where affinities are unknown, use the toggle buttons to exclude that metal.

Oval Picture of Flasks

Idealised Salmonella

(Default Settings for Metal Availability)

Metal Affinity (M) Metal affinities of molecule (M) (dissociation constants, KD) ∆G (kJ mol-1) ∆G for complexation with the molecule (kJ mol-1) Metal Availability (M) Buffered available metal concentration (M) Available ∆G (kJ mol-1) Buffered available free energy of metal (kJ mol-1) Occupancy Molecule occupancy with metal under these availabilities
Total Metalation

The calculator is based on Nature Communications 12 1195- (2021). Supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council. Background considerations and underlying assumptions

To predict the metalation state of a protein or other biomolecule, fill in values in the table for as many determined metal affinities (and availabilities if known) as possible. Where affinities are unknown, use the toggle buttons to exclude that metal.

Oval Picture of Flasks

Idealised Salmonella

(Default Settings for Metal Availability)

Metal Affinity (M) Metal affinities of molecule (M) (dissociation constants, KD) ∆G (kJ mol-1) ∆G for complexation with the molecule (kJ mol-1) Metal Availability (M) Buffered available metal concentration (M) Available ∆G (kJ mol-1) Buffered available free energy of metal (kJ mol-1) Occupancy Molecule occupancy with metal under these availabilities
Total Metalation

The calculator is based on Nature Communications 12 1195- (2021). Supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council. Background considerations and underlying assumptions

To predict the metalation state of a protein or other biomolecule, fill in values in the table for as many determined metal affinities (and availabilities if known) as possible. Where affinities are unknown, use the toggle buttons to exclude that metal.

Oval Picture of Flasks

Idealised Salmonella

(Default Settings for Metal Availability)

Metal Affinity (M) Metal affinities of molecule (M) (dissociation constants, KD) ∆G (kJ mol-1) ∆G for complexation with the molecule (kJ mol-1) Metal Availability (M) Buffered available metal concentration (M) Available ∆G (kJ mol-1) Buffered available free energy of metal (kJ mol-1) Occupancy Molecule occupancy with metal under these availabilities
Total Metalation

The calculator is based on Nature Communications 12 1195- (2021). Supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council. Background considerations and underlying assumptions

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