inst/tinytest/test-ionize.aa_pK.R

In CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry

# Load default settings for CHNOSZ
reset()

info <- "pK values as a function of temperature are consistent with literature values"
# pK at 0, 100, 200, 300 degrees C digitized from Fig. 4 of Dick et al., 2006
DLH06.pK <- list(`[Cys-]` = c(8.82, 7.44, 7.14, 7.90),
                 `[Asp-]` = c(4.06, 3.80, 4.17, 5.30), 
                 `[Glu-]` = c(4.36, 4.39, 5.11, 6.68), 
                 `[His+]` = c(6.44, 4.91, 3.92, 3.17),
                 `[Lys+]` = c(10.92,8.02, 6.27, 4.75),
                 `[Arg+]` = c(13.38,10.02,8.11, 6.56),
                 `[Tyr-]` = c(9.68, 8.02, 7.59, 8.33),
                 `[AABB+]`= c(2.34, 2.36, 2.62, 2.81),
                 `[AABB-]`= c(10.16,7.85, 6.51, 6.28))
this.pK <- ionize.aa(T = c(0, 100, 200, 300), ret.val = "pK")
# Ionization of [Cys] and [His] is off more than the others
expect_equal(this.pK[, 1], DLH06.pK$`[Cys-]`, tolerance = 1e-1, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 2], DLH06.pK$`[Asp-]`, tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 3], DLH06.pK$`[Glu-]`, tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 4], DLH06.pK$`[His+]`, tolerance = 1e-1, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 5], DLH06.pK$`[Lys+]`, tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 6], DLH06.pK$`[Arg+]`, tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 7], DLH06.pK$`[Tyr-]`, tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 8], DLH06.pK$`[AABB+]`,tolerance = 1e-2, check.attributes = FALSE, info = info)
expect_equal(this.pK[, 9], DLH06.pK$`[AABB-]`,tolerance = 1e-2, check.attributes = FALSE, info = info)

info <- "there is one pK value for each ionizable group at each temperature"
pH <- seq(0, 14, 2)
T <- seq(0, 150, 15)
val <- expand.grid(pH = pH, T = T)
Z <- ionize.aa(pH = val$pH, T = val$T, ret.val = "pK")
expect_equal(length(unique(Z)), 99, info = info)

# Reference

# Dick, J. M., LaRowe, D. E. and Helgeson, H. C. (2006) 
#   Temperature, pressure, and electrochemical constraints on protein speciation: 
#   Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. 
#   Biogeosciences 3, 311--336. https://doi.org/10.5194/bg-3-311-2006