Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead.
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 C5or . 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.
Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.|Department of Physics, Tampere University of Technology, Finland.|COMP, Department of Applied Physics, Aalto University, Finland.
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Ropo
Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.|Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA.
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Blum
Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.
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Baldauf
D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D002118:Calcium / Q000737:chemistry / Q000378:metabolism*; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D007854:Lead / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D011487:Protein Conformation; D013816:Thermodynamics
D000596:Amino Acids; D004151:Dipeptides; D007854:Lead; D002118:Calcium