Comparison of energy-minimized structures of [PdII(mida)] complexes of peptide sequences used in immobilized metal ion affinity chromatography protein separations

Abstract Molecular mechanics calculations were performed using the mm 2, Spartan, mmff 94 and sybyl programs to examine the stabilities of complexes of the formulation [Pd II (mida)L 3 ] and [Pd II (mida)(hexamer peptide)] (mida 2− = N -methyliminodiacetate) as influenced by steric factors of the three coordination positions other than the point of attachment to the mida 2− ligand. The series of monodentate ligands (L) follows a stability order of lowest energy (most stable) to highest energy (least stable) as follows: (Cl − ) 3 ∼(H − ) 3 2 (NH 3− n Me n ) 3 2 (NH 3 ) 3 ) 3 2 ) 3 2 Me) 3 3 ) 3 (im=imidazole, Me=methyl; n =1 to 3). The calculations show that for monodentate ligand sets, the two cis imidazoles plus amine donors set provides the energetically best donor system rather than an all imidazole or all amine set of donors for typical N-donors that are available from peptides. The same ligand set is used by the peptide anchor of sequence Ser–Pro–His–His–Gly–Gly (SPHHGG), which provides the best protein anchor that can be removed in the pH 5 to pH 7 ‘chromatography window’ from Cu II (ida)-derivatized columns for immobilized metal ion affinity chromatography (IMAC) protein separations. Also, the L 3 series of the present study shows that increasing the substitution around the amine donor enhances the stability through better σ donation in spite of increasing steric interactions. A limited peptide series was also treated by four molecular mechanics procedures. The outcome of the stability order as predicted by the four separate computer methods is more mixed when chelation between the imidazole and amine donors is included in the calculations. The peptides amH 6 , imH 6 , amH 4 G 2 , imH 4 G 2 , GHPHHG, SPHHGG, and G 6 were evaluated. The ligand notation amH 6 and imH 6 , etc., implies the situation with the N-terminal donor as the amine and as the histidyl group respectively. The ligand G 6 was coordinated as the terminal amine and two deprotonated amido donors. In general, the G 6 -type coordination provides a low energy situation comparable to the best donor sets of the side chain type of coordination (SPHHGG, amH 6 , GHPHHG, etc.). The mmff 94, sybyl and Spartan calculations produced the energy-minimization order of (most to least stable): G 6 4 G 2 6 ≲GHPHHG∼SPHHGG≪amH 4 G 2 ∼amH 6 . This follows the same order as the binding stabilities of the coordinated ligands toward elution behavior on Cu II (ida)-derivatized IMAC columns, although the elution order is surely related to the strength of the Pd II ligand bonds as well as steric interactions within the ligand set (the latter measured in the molecular mechanics calculations). The molecular mechanics calculations by Spartan, mmff 94 and sybyl also suggest that chelation of the peptide chain changes the best donor set of the (im) 2 (amine) type that is found for monodentate donors to the (histidyl im) 3 donor set. This may be due to elimination of rotational steric effects that exist for the freely rotating monodentate (im) 3 ligation by forcing less interactive dihedral angles on the coordinating histidines within the special HXHH coordinating run. The energetic choice favoring side chain histidine coordination versus ionized peptido N coordination results in more stable [Pd(mida)(hexamer peptides)] with an average of 23 kcal mol −1 lower energy for the side-chain-coordinated forms using two histidyl donors (e.g. approximately 11.5 kcal mol −1 of side chain donors, or per chelate loop involving the side chain).