Effect of calcium (II) and magnesium (II) ions on the 18-23 γ-carboxyglutamic acid containing cyclic peptide loop of bovine prothrombin An AMBER molecular mechanics study

The effect of calcium (II) and magnesium (II) ions on the conformation of the 18–23 cyclic peptide loop of bovine prothrombin are investigated by the molecular mechanics program AMBER (Assisted Model Building with Energy Refinement). The work is an extension of an earlier paper (Eastman et al, Int. J. Peptide Protein Res. 27, 1986, 530–553) that employed the program ECEPP (Empirical Conformational Energy Program for Peptides). In the absence of either metal ion, or in the presence of either one Ca(II) or one Mg(II) ion, the lowest‐energy forms found by AMBER have the Gla21‐Pro22 peptide bond in a trans conformation. In the presence of two Ca(II) or Mg(II) ions, the loop form of lowest energy is decidedly cis. The coordination about the Ca(II) and Mg(II) ions is different in both the single and double metal cases. In addition, the peptide chains that emerge from the loop are oriented parallel to each other in the lowest‐energy complex with two Ca(II) ions, but are not parallel in the lowest‐energy complex with two Mg(II) ions.