A united residue force-field for calcium-protein interactions

Protein Science : a Publication of the Protein Society
Mey KhaliliHarold A Scheraga

Abstract

United-residue potentials are derived for interactions of the calcium cation with polypeptide chains in energy-based prediction of protein structure with a united-residue (UNRES) force-field. Specific potentials were derived for the interaction of the calcium cation with the Asp, Glu, Asn, and Gln side chains and the peptide group. The analytical expressions for the interaction energies for each of these amino acids were obtained by averaging the electrostatic interaction energy, expressed by a multipole series over the dihedral angles not considered in the united-residue model, that is, the side-chain dihedral angles chi and the dihedral angles lambda for the rotation of peptide groups about the C(alpha)...C(alpha) virtual-bond axes. For the side-chains that do not interact favorably with calcium, simple excluded-volume potentials were introduced. The parameters of the potentials were obtained from ab initio quantum mechanical calculations of model systems at the Restricted Hartree-Fock (RHF) level with the 6-31G(d,p) basis set. The energy surfaces of pairs consisting of Ca(2+)-acetate, Ca(2+)-propionate, Ca(2+)-acetamide, Ca(2+)-propionamide, and Ca(2+)-N-methylacetamide systems (modeling the Ca(2+)-Asp(-), Ca(2+)-Glu(-), Ca(...Continue Reading

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Citations

Apr 20, 2005·Current Opinion in Structural Biology·Valentina Tozzini
Jan 4, 2017·Chemical Reviews·Pengfei Li, Kenneth M Merz
Nov 26, 2009·European Biophysics Journal : EBJ·Ricky C K Cheng, Boris S Zhorov
Mar 12, 2013·Applied Microbiology and Biotechnology·Yue-Xiao ShenXia Huang
Jul 21, 2020·Journal of Chemical Information and Modeling·Florencia KleinSergio Pantano
Jun 29, 2017·Journal of Chemical Information and Modeling·Zheng Gong, Huai Sun
Jun 14, 2019·The Journal of Physical Chemistry. B·Adam K SieradzanMariusz Makowski
Oct 15, 2019·Journal of Agricultural and Food Chemistry·Pengbo CuiNa Sun

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