Jumps through space

In PCMH, two equally efficient pathways for electron transfer from the flavin N5 to the heme iron were identified in GREENPATH calculations. One path follows the tyrosyl covalent link to FAD at the C8-methyl position, whereby electrons can travel from C8M via the Tyr 384 phenolic ether bond, tunnel through the tyrosine ring atoms and make a through-space jump across the subunit interface to the carbonyl oxygen of Ala 49 in the cytochrome (Figure 16). From there the electrons follow backbone... 

FIGURE 15. Electron transfer pathways in FCB2. The best path for electron transfer from flavin to heme based on GREENPATH calculations. Dashed lines represent paths along hydrogen bonds and dotted lines represent a through-space jump. Path 1 involves a water molecule while path 2 does not. 

FIGURE 17. Electron transfer pathways in FCSD. Through-space jumps are indicated hy dotted lines and paths along hydrogen bonds are indicated by dashed lines. Four paths (ln4) with decreasing electronic coupling are indicated. Fp and Cy indicate residues in the flavo-protein and the cytochrome subunits, respectively. 

In a third pathway, electrons flow from the N1 position of flavin via a hydrogen bond to Gly 305(N), on through backbone to the Tyr 306 side-chain, followed by a jump from the tyrosine hydroxyl to the methyl CMC atom of heme. The path with weakest coupling involves a through-space jump from the flavin 02 to Trp 391, then a jump to Cys 714 SG, which is covalently linked to the heme. 

FIGURE 18. Electron transfer pathways from the 2Fe-2S center to the flavin ring in fumarate reductase. Dotted lines represent through-space jumps. The four best paths (ln4) are indicated, all of which involve an initial transfer of an electron from the 2Fe-2S center to the SG atom of Cys57 which forms a ligand to an iron atom. 

Salt bridges, hydrogen bonds and through-space jumps... 

Figure 16.1 (a) Change of concentration in the interior of a sample where the concentration at the boundary increases with time if the increase is exponential with time, the profiles can be exponential through space, (b) Change of concentration where the concentration at the boundary is jumped to a new value and then kept constant the profiles are of error-function type. 

Example of a tunneling pathway. The donor is coupled to the bonded pathway through bond 1 and the acceptor through bond 10. There are three bonded segments and two through-space jumps (between orbitals 4 and 5 and between orbitals 6 and 7). 

Between Qa and Qbi the dominant pathways were identified in the same way as above (Fig. 2). The interference is highly destructive, since the paths between Qa and His 2i9 gj, mediated by a hydrogen bond and a few strong through space jumps with similar strengths but different phases. The paths between His and Qb have a similar structure. 

Figure 3. Calculated ET pathways from the disulfide to the copper center in Pseudomonas aeruginosa azurin. Calculation was performed by using the methodology of Beratan et al (24). Hydrogen bonds are shown by broken lines and the through-space jump by a thin line. Some distances (in angstroms) are also indicated in the figure.

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