Homology modeling and molecular dynamics simulations of lymphotactin

We have modeled the structure of human lymphotactin (hLpnt), by homology mo deling and molecular dynamics simulations. This chemokine is unique in havi ng a single disulfide bond and a long C-terminal tail. Because other struct ural classes of chemokines have two pairs of Cys residues, compared to one in Lpnt, and because it: has been shown that both disulfide bonds are requi red for stability and function, the question arises how the Lpnt maintains its structural integrity. The initial structure of hLpnt was constructed by homology modeling. The first 63 residues in the monomer of hLpnt were mode led using the structure of the human CC chemokine, RANTES, whose sequence a ppeared most similar. The structure of the long C-terminal tail, missing in RANTES, was taken from the human muscle fatty-acid binding protein. In a P rotein Data Bank search, this protein was found to contain a sequence that was most homologous to the long tail. Consequently, the modeled hLpnt C-ter minal tail consisted of both alpha -helical anti beta -motifs. The complete model of the hLpnt monomer consisted of two alpha -helices located above t he five-stranded beta -sheet. Molecular dynamics simulations of the solvate d initial model have indicated that the stability of the predicted fold is related to the geometry of Pro78. The five-stranded beta -sheet appeared to be preserved only when Pro78 was modeled in the cis conformation. Simulati ons were also performed both for the C-terminal truncated forms of the hLpn t that contained one or two (CC chemokine-like) disulfide bands, and for th e chicken Lpnt (cLpnt). Our MD simulations indicated that the turn region ( T30-G34) in hLpnt is important for the interactions with the receptor, and that the long C-terminal region stabilizes both the turn (T30-G34) and the five-stranded beta -sheet. The major conclusion from our theoretical studie s is that the lack of one disulfide bond and the extension of the C-terminu s in hLptn are mutually complementary. It is very likely that removal of tw o Cys residues sufficiently destabilizes the structure of a chemokine molec ule, particularly the core beta -sheet, to abolish its biological function. However, this situation is rectified by the long C-terminal segment. The r ole of this long region is most likely to stabilize the first beta -turn re gion and alpha -helix H1, explaining how this chemokine can function with a single disulfide bond.