Figure 2

(A–E) Docking interface between rabbit muscle LDH (PDB:3H3F³⁵) and rabbit muscle GAPDH (PDB:1J0X³⁶). The figures show only the interacting subunits to bring in focus the interaction interface. The figures show docking interactions in the absence of NAD(H). Black CPK models were used to mark the position of NAD(H) binding sites. (A) The docking surfaces between rmGAPDH (left) and rmLDH (right) consist of flexible loops that have highest values for temperature b-factor. The protein surfaces are shown as transparent gray contours to illustrate relative orientations when the two proteins make their first contacts at the start of docking. (B,C) The figures show rmGAPDH-rmLDH complex that was extracted from frame 825 in Supplement Movie 1. (B) the two proteins are shown in the surface mode to highlight large complementary surfaces (7790 Ų) that are not readily apparent from the ribbon models. The surfaces are shown 30% transparent to mark the NAD(H) sites buried under the protein surface. (C) the complex is sliced through the plane that is passing through the NAD(H) binding sites to show a central “channeling” cavity that is surrounded by two NAD(H) binding sites from rmGAPDH and one NAD(H) site from rmLDH. (D,E) The complex is shown in the same orientation as in panels A to C. (D) the complex was sliced through the plane that is passing through the NAD(H) binding sites to show the electric fields that are connecting the sites. (E) The red and blue colors indicate isopotential surfaces around the complex at −0.5 and 0.5 k_B*T/e respectively. The two presentations show that the positive electric fields that can support NAD(H) channeling between the adjacent subunits in rmLDH and rmGAPDH tetramers can merge together to support NAD(H) channeling within the rmLDH-rmGAPDH complex. Thus NAD(H) channeling in the complex is an extension of NAD(H) channeling between the adjacent subunits in rmLDH and rmGAPDH tetramers.