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. Author manuscript; available in PMC: 2013 Sep 1.
Published in final edited form as: Arch Biochem Biophys. 2012 May 26;525(1):82–91. doi: 10.1016/j.abb.2012.05.012

Figure 4. Selected snapshots for alternative charge redistribution pathways in the Tyr-(Ala4)-Cys peptide.

Figure 4

The figure shows the three paths for ET as predicted with the pathways algorithm and taken from the explicit water MD simulation (see Methods for details). The peptide is shown as bold sticks. (A) Through-bond path, (B) through-space jump and (C) through two consecutive jumps involving a bridging water molecule. The predicted ET paths are shown in orange arrows. Surrounding waters were omitted for clarity. The relative contribution of each pathway (A, B or C) to intramolecular electron transfer in the shown studied peptides for one, two and four alanine spacers, are indicated in the text. The percent contribution for each path type in each peptide was computed by visually inspecting and counting the corresponding path type in one hundred snapshots.