<p>Zhang and Gunner Photosynthesis Research 2013</p><p>SUPPLEMENTARY MATERIALS</p><p>Mathematica equations used to create Figure 2 and 6.</p><p>(RTotal - RX - RY ) × (X Total - RX ) = RX × K X</p><p>(RTotal - RX - RY ) × (YTotal - RY - RXY - RYY ) = RY × KY</p><p>(RX - RXY ) × (YTotal - RY - RXY - RYY ) = RXY × K XY</p><p>(RY - RXY ) × (YTotal - RY - RXY - RYY ) = RYY × KYY (S1)</p><p>RT is the total concentration of RCs (RCT). XT is the added XQ (XQT); YT is YQT. There are four kinds RCs that can be distinguished by their charge recombination kinetics: </p><p>RX and RY: RCs with XQ or YQ at the QA site (XQA or YQA) with empty QB sites. RXY RCs with XQ at the QA site and YQ at the QB site (XQA:YQB), RYY RCs with YQ at the both sites (YQA:YQB). KX, KY are the dissociation constants for XQ and YQ at the QA site. KXY and KYY the Kds for these quinones at the QB site. KXY= KYY here.</p><p>Binding non-native quinones to the QA site. </p><p>Figure s.1. QA activity as a function of quinone concentration. The theoretical lines are the best fit to the data using Eqn. 3. Values for the Kd and maximum amplitude at saturation are given in Tables 1 and 2. (●):AQ; (▼): Me-NQ; ():NQ; (♦) diMe-BQ; (■) triMe-BQ. Titration carried out with 1 µM RCs; 10mM Tris, 0.005% LDAO, pH = 7.8 at T=2982 K.</p><p>1 Zhang and Gunner Photosynthesis Research 2013</p><p>Estimating the energy level of NQB with a low potential diMeAm-NQA.</p><p>The observed rate is a combination of indirect thermal back reaction rate and direct tunneling rate (Kleinfeld et al. 1984, Labahn et al. 1994) obs kBP = kBAP + kBP = akBHP + (1 - a)kBP (s.2)</p><p>+ -  is the fraction of RCs in the P QA state and the recombination rate is kBAP.</p><p>The free energy difference between QAQB- and QA-QB is given by the equilibrium distribution of the two forms of RCs. </p><p>(s.3)</p><p>Thus:</p><p> obs o kBP - kBP - DGAB = kBT ln( obs ) kBP - kBAP (s.4)</p><p>References Kleinfeld D, Okamura MY, Feher G (1984) Electron transfer in reaction centers of Rhodopseudomonas sphaeroides: I.</p><p>+ - - Determination of the charge recombination pathway of D QAQB and free energy and kinetic relations between QA QB</p><p>- and QAQB . Biochim Biophys Acta 766: 126-140. </p><p>+ - Labahn A, Paddock ML, McPherson PH, Okamura MY, Feher G (1994) Direct charge recombination from D QAQB to</p><p>DQAQB in bacterial reaction centers from Rhodobacter sphaeroides. J Phys Chem 98: 3417-3423. </p><p>2</p>