Minimization programs for potential energy calculations in crystals and isolated molecules and macromolecules

Crystal structure, conformation, and potential energy calculations of the chemotactic peptide N-formyl-L-Met-L-Leu-L-Phe-OMe

The tripeptide N-formyl-L-Met-L-Leu-L-Phe-OMe (FMLP-OMe) crystallizes in the orthorhombic system, space group P 2(1)2(1)2(1), with the following unit-cell parameters: a = 21.727, b = 21.836, c = 5.133 A, Z = 4. The structure has been solved and refined to a final R of 0.068 for 1838 independent reflexions with I greater than 2 omega (I). The peptide backbone is folded at the Leu residue (phi L = -67.7, psi L = -49.1 degrees) without intramolecular hydrogen bonds. Considering each peptide plane, the Leu side-chain is oriented on the same side of that of the Phe residue and on the opposite side of that of the Met residue, respectively. The crystal conformation differs from all the other conformations proposed for FMLP-OMe and the anionic form of N-formyl-L-Met-L-Leu-L-Phe-OH (FMLP) in solution accounts for the amphiphilic character of the peptide, giving rise, through intermolecular hydrogen bonds, to a stacking of molecules which could be maintained in the aggregation states experimentally observed in solvents of low polarity. Intramolecular potential energy calculations have been carried out in order to compare the energies of the various backbone conformers.

Potential energy calculations on phenylalanine rotamers in different boat forms of proline-containing cyclic dipeptides

Previous potential energy calculations have always indicated that the folded conformation is the most stable one for cyclic dipeptides containing benzylic side chains. We have carried out intramolecular van der Waals potential energy calculations on cyclo-(D-Phe-L-Pro), N-(N-phenylacetyl-L-alanyl)-cyclo-(L-Phe-D-Pro) and N-(pyruvoyl)-cyclo-(L-Phe-D-Pro) adopting the geometries found in their crystal structures. The calculations made on these compounds, having the peptide skeleton made of the same aminoacid residues but differing in the degree of buckling of the boat, show that there is a dependence between diketopiperazine ring and phenylalanine side-chain conformations. The folded conformer is preferred as long as it is allowed by the degree of buckling of the boat. When the boat becomes highly buckled, as in the case of the pyruvoyl derivative, the folded rotamer is no longer favoured. This is the first energy calculation to demonstrate that the folded rotamer is not always the most stable one.