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Quantitative Biology, Biomolecules, q-bio.BM, Physics, Atomic and Molecular Clusters, physics.atm-clus, Physics, Chemical Physics, physics.chem-ph
Abstract:
We derive structural and binding energy trends for twenty amino acids, their
dipeptides, and their interactions with the divalent cations Ca$^{2+}$,
Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data
set consists of 45,892 first-principles predicted conformers with relative
energies up to about 4 eV (about 400kJ/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 C$_5$ or equatorial C$_7$. 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.
Cd$^{2+}$ and Hg$^{2+}$ show the largest binding energies - a potential
correlation with their known high acute toxicities. Ca$^{2+}$ and Pb$^{2+}$
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.
