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Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in the tobacco plant both remote leaf necrosis and the induction of a resistance against subsequent attack by various micro-organisms. The crystal structure of b-cryptogein (CRY), secreted by Phytophthora cryptogea, was previously reported as well as the first structure of a SCP/sterol complex, the ergosterol-complexed, mutated CRY (K13H). In K13H, the ergosterol molecule is encapsulated in a large internal hydrophobic cavity which is not present in CRY. This binding induces a minor conformational change in the protein structure. Molecular dynamics studies were undertaken to precise the structural behaviour of CRY and K13H with respect to the complexation of the ergosterol. Although it is not possible to simulate the entrance of the ergosterol in the protein, we assume that capture and release of the ligand possibly both occur following the same path. Our results show that, in the complex K13H, the ergosterol molecule is pushed towards the residue 13 which play a key role in the necrotic activity of the protein. It is likely that the polarity of residue 13, favouring the binding of the hydroxyl of the ligand, would be involved in the recognition of the sterol and in an optimisation of its orientation. Thus, in a first step, the molecule of ergosterol would be rotated around itself to a position which makes possible, in a second step, its translation to the internal cavity, as a key in a keyhole.

A conformational search by simulated annealing has been performed on two peptides derivated from the tetradecapeptide used to isolate the Xenopus laevis skin maturation RXVRG-endoprotease. The Ala 12 derivative, obtained by substitution in the hydrophobic C terminal fragment and the undecapeptide 4-14, obtained by deletion of an acidic rich tripeptide, were studied. No unique structure has been found for the tetradecapeptide Ala 12. This structural disorganization could explain the loss of activity of the endoprotease towards the substituted peptide. For the undecapeptide, two different models in accordance with the NMR data were found. The conformational differences between these two models are located in the consensus sequence and in each case an hairpin-like conformation is observed. These results could be related to the enhanced cleavage activity of the maturation enzyme. The obtained structures are also compared with those of the original tetradecapeptide.

Simulated annealing techniques were used to explore the conformational space of the potent antithrombotic peptide L.Lys-L.Arg-L.Asp-L.Ser (KRDS) and of two analogs: D.Lys-L.Arg-L.Asp-L.Ser (KDRDS), which is inactive, and L.Lys-L.Arg-L.Glu-L.Glu (KREE), which exhibits a strong biological activity. For each peptide, a set of initial conformations was generated and submitted to simulated annealing, including a heating to 1000 K followed by a cooling to 300 K. 200 resulting conformations of each compound were analyzed and classified according to the network of electrostatic interactions involving charged side chains and charged C- and N-terminal groups. A reduced number of conformational classes was obtained and conformations corresponding to predominant classes were found to be in qualitative agreement with structural parameters deduced from 1H NMR spectra. A comparison between the classes of the active and non active peptide was achieved. Some conformations were found to be specific of active peptides.