Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead

Abstract

We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+. The underlying data set consists of more than 45,000 first-principles predicted conformers with relative energies up to ~4 eV (~400 kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C5 or . Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ions with amino acids and dipeptides. Cd2+ and Hg2+ show the largest binding energies–a potential correlation with their known high acute toxicities. Ca2+ and Pb2+ reveal almost identical binding energies across the entire series of amino acids and dipeptides. This observation validates past indications that ion-mimicry of calcium and lead should play an important role in a toxicological context.

Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations

“…Neutral Glu is rather flexible, resulting in 385 isomers predicted within DE B 75 kJ mol À1 . [47][48][49] Five of these were detected by microwave spectroscopy in a cold molecular beam, all with an intramolecular NHÁ Á ÁOC or NÁ Á ÁHO H-bond between the a-carboxyl (a-COOH) and amino (NH 2 ) groups. 50 Protonation of the amino group (NH 2 -NH 3 + ) leads to conformational locking of GluH + by formation of strong cooperative HOCOÁ Á ÁHNH + Á Á ÁOCOH ionic H-bonds.…”

The conformational space of a flexible amino acid at metallic surfaces

“…The sampling of the structure space of the amino acid in two protonation states on metallic surfaces was performed by starting from a previously published dataset comprising stationary points of isolated amino acids and dipeptides. [21,44] For Arg, 1206 structures were present in the database. In order to reduce the number of possibilities, but keeping a representative share of the structures, we considered the 300 lowest energy conformers, the 27 highest energy conformers, and 125 conformers uniformly spanning the energy range in between.…”

“…Not only the global minimum is of interest, but also the relative positioning of other local minima with respect to the structural degrees of freedom are relevant because they can reveal different basins and structures of interest under different conditions. [21][22][23][24][25] In order to handle such high-dimensional data, we make use of recent advances in machine-learning methods that can help to visualize conformational preferences of adsorbed molecules. [26][27][28][29][30][31] In the following, we discuss the impact of the protonation state and the presence or absence of the surface on the accessible conformational space of arginine.…”

Potential Antioxidant Activity of Calcium and Selected Oxidative Stress Markers in Lead- and Cadmium-Exposed Workers

“…Less than 1% is found in extracellular serum calcium [ 20 ]. In contrast to Pb and Cd, Ca is essential for living organisms due to its important role in a multitude of functions, from cell signaling to bone growth [ 21 ]. Serum calcium does not fluctuate with changes in dietary intake.…”