Figure 3
rmLDH and rmGAPDH share complementary surface shape and electric potentials at the interaction sites. The figure shows rmGAPDH:rmLDH complex just as in Fig. 2B–E, except that the two proteins were taken apart to expose the binding contacts62. rmLDH and rmGAPDH have large complementary surfaces (7790 Å2) and the strongest interactions are focused on two hot spots. In the first spot (740 Å2), the most protruded section of NADH binding domain on Q subunit in GAPDH (a.a. 57–74) is wedged between the active site loop (a.a. 98–104) and the active site helix (a.a. 226–245) in D subunit on LDH. The strongest interactions at this site are the three ionic bonds between Glu 76 on GAPDH and ARG 111 on LDH. In the second interaction spot (1210 Å2), the catalytic domain on subunit C in LDH binds to the cleft between the catalytic and NADH binding domain on P subunit in GAPDH (a.a. 99–105, a.a. 122–126, a.a. 209–229). Driven by the thermodynamic wobbling between the interacting proteins this interaction site can have as many as 9 binding interactions. The strongest interactions at this site are the three ionic bonds between Arg 176 on GAPDH and Glu 103 on LDH.
