SCF-MO study of the preferred conformation of a symmetric malonamide derivative: N,N' -dimethyl malonamide

Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database

Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.

Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence

The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.

Tautomers and conformers of malonamide, NH2-C(O)-CH2-C(O)-NH2: vibrational analysis, NMR spectra and ab initio calculations

The conformational and tautomeric compositions of malonamide, NH2-C(O)-CH2-C(O)-NH2 were determined by vibrational spectroscopy and theoretical calculations (HF/6-31G*, B3PW91/6-31G*). Solid state Fourier transform infrared and Raman spectra were analysed. They reveal the existence of a diketo tautomer. Theoretical calculations predict a diketo structure belonging to the C1 symmetry group. No enol form is present in the molecule in the solid. 13C-NMR studies show only signals of a diketo tautomer.

Effects of the phi[NHCO] retromodification on dehydroalanine dipeptide

The potential energy surface of the phi [NHCO] delta Ala dipeptide has been computed using ab initio quantum mechanical calculations at different theoretical levels. Three degenerate minima were found and characterized. The most favoured conformation is stabilized by an intramolecular hydrogen bonding interaction. The other two minima correspond to helical and malonamide-like conformations, being 4.6 kcal/mol and 6.9 kcal/mol less stable than the lowest energy conformation, respectively. Influence of solvent effects on the relative stabilities of the different conformations have been accounted using SCRF calculations. Two implicit solvent models have been considered: water and CCl4. The results indicate that in the both cases the conformation with an intramolecular hydrogen bonding interaction retains its lowest energy.

A quantum-mechanical study of the chain-length dependent stability of the extended and 3(10)-helix conformations in dehydroalanine oligopeptides

A quantum-chemical study of the chain-length dependent stability of the extended, 2-ribbon and 3(10)-helix conformations in dehydroalanine (delta Ala) oligopeptides has been performed by using both semiempirical AM1 and ab initio 4-31G methodologies. The validity of both methods in the study of the conformational properties of delta Ala oligopeptides was tested first on the dipeptide. The results of this test showed that 4-31G and AM1 calculations are in good agreement with 6-31G* calculations and experimental data. In order to monitor the conformational conversions, delta Ala oligopeptides comprising two to six residues were constructed. Molecular geometries were fully optimized using AM1, and the final conformations were verified to be minima by analysis of the corresponding second-derivative matrices. Conformational studies revealed that the 3(10)-helix is stabilized with respect to the 2(7)-ribbon when the number of residues is three or four, at the AM1 and ab initio 4-31G level respectively, while the extended form is the most stable in all the calculations performed. On the other hand, if a linear behaviour is assumed for longer chains, our calculations show a trend that would predict a conversion from extended form to 3(10)-helix in oligopeptides with around six (ab initio 4-31G) or eight (AM1) delta Ala residues. In order to explain these conformational changes, the cooperative effects for the different conformers were investigated. Large cooperative energy effects were found for the 3(10)-helix conformation.