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Metalation calculator: predict metal occupancies in vivo

The metal occupancy of cytosolic metal-binding proteins is predicted from the thermodynamic activities of metals in a cell.

These activities (as standard free-energies,  Δ) have been determined in a bacterial cell (Osman et al. (2019) Nat. Chem. Bio. 15: 241–249).

The calculator is based on Young et al (2021) Nature Communications 1195

The resulting predictions can:

  1. Identify metal-specificity
  2. Infer mis-metalation
  3. Reveal erroneous affinity measurements
  4. Suggest differences between these thermodynamic metal activities and those of the host cell
  5. Indicate where additional mechanisms (such as molecular interactions) must assist metalation

You can access the beta-versions of a metalation calculator here

Notes about kinetics:  (1) Cytosolic available metal is typically bound (and buffered). However, the buffer can become depleted if the rate of demand, for example for an over-expressed recombinant protein, greatly exceeds the rate of metal-import. Metal availability then drops below the steady-state [available metal] (really an activity) value in the calculator. DNA-binding metal sensors, tuned to such changes, have been used to read-out bespoke values enabling speciation of metalation to be predicted (above cited papers and manuscript in preparation); (2) Transfer to/from a nascent protein is likely to follow associative ligand-exchange: This confers rapid on/off rates supporting the accuracy of such calculations; (3) Analogous calculations have been used to estimate the magnitude of ‘kinetic bias’ introduced by metallochaperone-mediated metalation (JACS Au 2023); (4) Ongoing research suggests that relative in vitro binding preferences of proteins that kinetically-trap metals at folding may be used in the calculator (manuscript in preparation). The calculator is a beta-version with testing ongoing (manuscript in preparation). We are keen to have feedback.

For more information and to learn about assumptions and constraints of the calculator contact [email protected]