Theoretical study of the conformation of the H-protein lipoamide arm as a function of its terminal group

The glycine decarboxylase complex consists of four different proteins (the L-, P-, H-, and T-proteins). The H-protein plays a central role in communic ation among the other enzymes, as its lipoamide arm interacts successively with each of the components of the complex. The crystal structures of two s tates of the H-protein have been resolved: the oxidized form, H-ox at 2 Ang strom and the methylamine-loaded form, H-met at 2.2 Angstrom. However, the position of the arm for the reduced form, H-red, is still unknown. We have performed numerical free-energy calculations in order to better understand the differences in the structures and to elucidate the conformation of the arm in H-red. The results of the simulations are in agreement with the crys tallographic results, as the minima of the free energy surface for H-ox and H-met correspond to the crystal structures. For H-red, we observe a single minimum in which the arm is on the surface of the H-protein, close to its position in the H-ox structure. In all of our simulations, the lower, lysin e portion of the arm remains bound to the protein, which substantially redu ces the number of accessible arm configurations. An analysis of the stabili ty of H-met in the cavity shows that electrostatic interactions are crucial for locking the arm in the bottom of the cavity, especially near Glu14. In addition, the analysis shows that there is a water molecule, also observed in the crystallographic structure, that binds to the arm's terminal NH3+ g roup and helps to fix it in the cavity. In conclusion, because of the close agreement of the results of our calculations with the available experiment al evidence, we are able to suggest a structural basis for the observed beh avior. (C) 1999 Wiley-Liss, Inc.