Calculation of Electron Transfer Rates in Proteins
Use the ET Rates Calculator Java Applet to estimate electron tunneling rates:
You need to input three parameters:
Donor-acceptor distance: the edge-to-edge distance of the electron donor and acceptor cofactors. For a simple metal cofactor, the edge includes all metals and all atoms joined by two metals; for a quinone or flavin, this includes any carbonyls and conjugated rings; for porphyrin cofactor, such as heme or chlorophyll, this includes any metal and the conjugated porphyrin macrocycle. If the distance is unknown, try 9 Å for an approximation; this is in the middle of the typical biological productive electron transfer range.
Free energy: put a negative sign for exothermic (downhill) reactions, positive values indicate endothermic (uphill) reactions. If you don't know the free energy of the reaction, try 0 eV for an approximation, i.e. a typical reaction with little driving force.
Reorganization energy: 0.7 eV is a good approximation for intra-protein electron transfer, 1.0 eV is a good approximation for inter-protein electron transfer.
If the structure of the protein is not known, electron transfer rates are calculated based on the following equations:
For exothermic (downhill) reactions (ΔG < 0):
Log10 ket = 13 - 0.6 (R - 3.6) - 3.1 (ΔG +λ)2 /λ
For endothermic (uphill) reactions (ΔG > 0):
The initial constant 13 is the rate at van der Waals contact distance (R = 3.6 Å). The second term describes an approximately exponential fall-off in electron tunneling rate with distance through the insulating barrier. R is the edge-to-edge distance, The third term is the quantized Frank-Condon factor at room temperature. ΔG is free energy and λ is reorganization energy. Both in the unit of eV.