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A united residue force‐field for calcium–protein interactions
Author(s) -
Khalili Mey,
Saunders Jeffrey A.,
Liwo Adam,
Ołdziej Stanislaw,
Scheraga Harold A.
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.04878904
Subject(s) - dihedral angle , chemistry , ab initio , multipole expansion , crystallography , residue (chemistry) , interaction energy , computational chemistry , docking (animal) , side chain , stereochemistry , physics , hydrogen bond , quantum mechanics , molecule , medicine , nursing , organic chemistry , polymer , biochemistry
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 χ and the dihedral angles λ for the rotation of peptide groups about the C α •••C α 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 2+ ‐Asn, Ca 2+ ‐Gln, and Ca 2+ ‐peptide group interactions) at different distances and orientations were calculated. For each pair, the restricted free energy (RFE) surfaces were calculated by numerical integration over the degrees of freedom lost when switching from the all‐atom model to the united‐residue model. Finally, the analytical expressions for each pair were fitted to the RFE surfaces. This force‐field was able to distinguish the EF‐hand motif from all potential binding sites in the crystal structures of bovine α‐lactalbumin, whiting parvalbumin, calbindin D9K, and apo‐calbindin D9K.