util.protein: Functions for Proteins (Other Calculations)

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

Functions for Proteins (Other Calculations)

Description

Return chemical formulas of groups in proteins, and calculate heat capacity using an additivity model from the literature.

Usage

  MP90.cp(protein, T)
  group.formulas()

Arguments

protein	proteins specified in any format usable by pinfo
T	numeric, temperature in \degC

Details

group.formulas returns the chemical formulas of each of the 20 common amino acid residues in proteins, as well as the terminal -H and -H (treated as the [H2O] group).

MP90.cp takes protein (name of protein) and T (one or more temperatures in \degC and returns the additive heat capacity (J mol ^{-1}) of the unfolded protein using values of heat capacities of the residues taken from Makhatadze and Privalov, 1990. Those authors provided values of heat capacity at six points between 5 and 125 \degC; this function interpolates (using splinefun) values at other temperatures.

References

Makhatadze, G. I. and Privalov, P. L. (1990) Heat capacity of proteins. 1. Partial molar heat capacity of individual amino acid residues in aqueous solution: Hydration effect J. Mol. Biol. 213, 375–384. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0022-2836(05)80197-4")}

See Also

ionize.aa for an example that compares MP90.cp with heat capacities calculated in CHNOSZ at different temperatures and pHs.

CHNOSZ documentation built on May 29, 2024, 3:30 a.m.